KEYS TO UNLOCKING THE BIOFILM PHENOTYPE
OF A VIRULENT ENVIRONMENTAL ISOLATE
OF SALMONELLA
by
Stewart James Clark
A dissertation submitted in partial fulfillment
of the requirements for the degree
of
Doctor of Philosophy
in
Microbiology
MONTANA STATE UNIVERSITY
Bozeman, Montana
August 2008
©COPYRIGHT
by
Stewart James Clark
2008
All Rights Reserved
ii
APPROVAL
of a dissertation submitted by
Stewart James Clark
This dissertation has been read by each member of the dissertation committee and
has been found to be satisfactory regarding content, English usage, format, citation,
bibliographic style, and consistency, and is ready for submission to the Division of
Graduate Education.
Dr. Anne K. Camper
Approved for the Department of Microbiology
Dr. Mike Franklin
Approved for the Division of Graduate Education
Dr. Carl A. Fox
iii
STATEMENT OF PERMISSION TO USE
In presenting this dissertation in partial fulfillment of the requirements for a
doctoral degree at Montana State University, I agree that the Library shall make it
available to borrowers under rules of the Library. I further agree that copying of this
dissertation is allowable only for scholarly purposes, consistent with “fair use” as
prescribed in the U.S. Copyright Law. Requests for extensive copying or reproduction of
this dissertation should be referred to ProQuest Information and Learning, 300 North
Zeeb Road, Ann Arbor, Michigan 48106, to whom I have granted “the exclusive right to
reproduce and distribute my dissertation in and from microform along with the nonexclusive right to reproduce and distribute my abstract in any format in whole or in part.”
Stewart James Clark
August 2008
iv
ACKNOWLEDGMENTS
The author of this dissertation would like to acknowledge those friends and family
both in Bozeman and in South Africa who have played a particularly important support
role over the tenure of this degree.The microarrays used in this research were obtained
through NIAID’s Pathogen Functional Genomics Resource Center, managed and funded
by Division of Microbiology and Infectious Diseases, NIAID, NIH, DHHS and operated
by the J. Craig Venter Institute. This research has been supported by a grant (DAAD 1903-1-0198) from the Army Research Office. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the authors and do not
necessarily reflect the views of the Army Research Office. And finally, this work is for
you, my King.
v
TABLE OF CONTENTS
1. INTRODUCTION ........................................................................................................... 1
2. LITERATURE REVIEW ................................................................................................ 3
Salmonella Background ................................................................................................... 3
Nomenclature ............................................................................................................ 3
History of Salmonella Missouri – an Epidemiology.................................................. 6
Other Examples of Occurrence and Abundance in Water ......................................... 8
Survival in Water and Preferred Environments .........................................................10
Susceptibility to Disinfection .....................................................................................13
The Three C’s of Salmonella Biofilms:
Curli, Cellulose and Cyclic-di-GMP................................................................................16
The Hfq Regulon........................................................................................................22
Iron Utilization Genes ................................................................................................24
1,2-Propanediol Utilization ..............................................................................................26
Pathogenicity
............................................................................................................32
Type III Secretion Systems ........................................................................................34
Salmonella Pathogenicity Island 1 .............................................................................35
Salmonella Pathogenicity Island 2 .............................................................................38
3. A TRANSCRIPTIONAL STUDY OF AN ENVIRONMENTAL SALMONELLA
ENTERICA ISOLATE BIOFILM ....................................................................................41
Introduction
............................................................................................................41
Materials and Methods .....................................................................................................44
Strains and Growth ....................................................................................................44
Biomass Harvesting ...................................................................................................46
RNA Purification .......................................................................................................47
DNA Microarray Transcriptional Profiling ...............................................................48
Data Analysis ............................................................................................................52
Results and Discussion ....................................................................................................55
Bacterial Characterization ..........................................................................................55
RNA Purification .......................................................................................................59
Data Analysis ............................................................................................................60
Conclusions
............................................................................................................71
4. A TRANSCRIPTIONAL COMPARISON OF SALMONELLA
TYPHIMURIUM LT2 AND AN ENVIRONMENTAL ISOLATE
OF SALMONELLA ENTERICA .......................................................................................80
Introduction
............................................................................................................80
Materials and Methods .....................................................................................................81
Strains and Growth ....................................................................................................81
vi
TABLE OF CONTENTS - CONTINUED
Biomass Harvesting ...................................................................................................
RNA Purification .......................................................................................................
DNA Microarray Transcriptional Profiling ...............................................................
Data Analysis ............................................................................................................
Results and Discussion ....................................................................................................
Conclusions
............................................................................................................
83
84
85
89
92
99
5. CONCLUSIONS ............................................................................................................104
Future Work
............................................................................................................106
REFERENCES
............................................................................................................109
APPENDICES
............................................................................................................126
APPENDIX A: Significant Genes Data Set for Chapter 3 ..............................................127
APPENDIX B: Dataset for Figure 12 ..............................................................................136
APPENDIX C: Dataset for Figure 13 ..............................................................................138
APPENDIX D: Dataset for Figure 15 ..............................................................................140
APPENDIX E: Significant MO Genes Data for Chapter 4 ............................................142
APPENDIX F: Significant LT2 Genes Data for Chapter 4 ............................................150
vii
LIST OF TABLES
Table
Page
1.
Salmonella enterica subspecies and numerical designations..................................... 4
2.
Space flight stimulon genes in Salmonella belonging to the
Hfq regulon or involved with iron utilization or biofilm formation ..........................23
3.
Regions of 10 or more genes recently acquired by
Salmonella enterica serotype Typhimurium LT2 ......................................................34
4.
Top six sequences producing significant alignments (NCBI-BLAST)
to a 702 bp sequence obtained by PCR amplifying a portion of the
16S rDNA gene of Salmonella Missouri ...................................................................57
5.
The Institute for Genomic Research functional categories for the
entire annotated genome and uniquely expressed genes of the observed
transcriptomes for the planktonic and biofilm phenotypes ........................................96
viii
LIST OF FIGURES
Figure
Page
1.
Schematic overview of the role of CsgD in biofilm formation .................................18
2.
Scheme illustrating the role of different genes in the pathways
leading to the synthesis of polysaccharides involved in the
biofilm phenotype ......................................................................................................19
3.
Regulatory concept of cyclic-di-GMP metabolism and signaling
on the population level ...............................................................................................21
4.
The struggle for iron: bacteria vs. host ......................................................................25
5.
Anaerobic rhamnose catabolism in Salmonella .........................................................27
6.
Model of cobalamin-dependent utilization of rhamnose
by intracellularly replicating Salmonella to recruit additional
carbon, nitrogen and energy sources ..........................................................................29
7.
Invasion of Salmonella into the host epithelium as the initial
stage of establishing infection (BioCarta, CA). .........................................................36
8.
NCBI-BLAST phylogenetic tree using the neighbor-joining
algorithm indicating relatedness of Salmonella Missouri
(indicated by query ID lcl|13935) to other prokaryotic organisms
based on a 702 bp sequence obtained by PCR amplifying a
portion of the 16S rDNA gene ...................................................................................56
9.
Growth curve of Salmonella Missouri .......................................................................58
10.
Electropherogram of Salmonella RNA ......................................................................59
11.
Distribution of significantly expressed genes assigned to
functional categories of the observed Salmonella Missouri transcriptome ...............62
12.
Expression patterns of genes involved in polysaccharide
and curli fimbriae synthesis .......................................................................................66
13.
Changes in levels of gene expression in four
Salmonella Pathogenicity Islands (SPI) and
the spv operon on the Salmonella Pathogenicity Plasmid (PSLT) ............................67
14.
Distribution of gene expression on the
Salmonella Pathogenicity Plasmid (PSLT) ................................................................68
ix
LIST OF FIGURES – CONTINUED
Figure
Page
15.
Gene expression patterns in the 1,2-propanediol
utilization operon (pdu), cobalamin synthesis operon
(cbi-cob) and tetrathionate reductase operon (ttr) .....................................................70
16.
Photographs of overnight planktonic cultures of
Salmonella Missouri and Salmonella Typhimurium LT2 .........................................92
17.
Growth curves of Salmonella Typhimurium LT2
and Salmonella Missouri ...........................................................................................93
18.
Venn diagram showing significantly up-regulated genes
in Salmonella Missouri during planktonic growth and
biofilm growth and in Salmonella Typhimurium LT2
during planktonic growth and biofilm growth ...........................................................95
x
LIST OF ABBREVIATIONS
ATCC
American Type Culture Collection
BLAST
Basic Local Alignment Search Tool
CDC
Centers for Disease Control and Preventtion
cDNA
Complementary DNA
CDSC
Communicable Disease Surveillance Center
CFU
Colony Forming Units
CMR
Comprehensive Microbial Database
CT99
Contact x Time to reduce the microbial population by 99%
DNR
Missouri Department of Natural Resources
DOH
Missouri Department of Health
EASE
Expression Analysis Systematic Explorer
ECA
Enterobacterial Common Antigen
EPA
Environmental Protection Agency
EPS
Exopolysaccharide
F99
Fluence required to reduce the microbial population by 99%
FDR
False Discovery Rate
FHL
Fumarate hydrogenlyase
IVET
In vivo Expression Technology
IVS
Intervening Sequences
JCVI
J. Craig Venter Institute
LPS
Lipopolysaccahride
MIDAS
TIGR Microarray Data Analysis System
MO
Missouri
xi
LIST OF ABBREVIATIONS - CONTINUED
MPN
Most Probable Number
NCBI
National Center for Biotechnology Information
NIAID
National Institute of Allergies and Infectious Diseases
OLE
Operon-Linked Expression
ORF
Open Reading Frame
PFGRC
Pathogen Functional Genomics Research Center
PGFE
Pulse Field Gel Electrophoresis
PLG
Phase Lock Gel
PSLT
Salmonella Typhimurium LT2 Pathogenicity Plasmid
RIN
RNA Integrity Number
SAM
Significance Analysis of Microarrays
SCV
Salmonella-Containing Vacuole
SOP
Standard Operating Protocol
SPI
Salmonella Pathogenicity Island
T90
Time taken to reduce the microbial population by 90%
TIGR
The Institute for Genomic Research
TMEV
TIGR Multiexperiment Viewer
TTSS
Type III Secretion System
UASB
Upflow Anaerobic Sludge Blanket
VBNC
Viable But Non Culturable
WHO
World Health Organization
WWTP
Wastewater Treatment Plant
xii
ABSTRACT
The aim of this research was to elucidate the phenotypic adaptation of an
environmental isolate of Salmonella enterica grown in a single species biofilm using
transcriptomic analysis. This environmental isolate was obtained from an outbreak in
Gideon, MO, and was classified as Salmonella enterica serotype Missouri. Gene
expression profiles obtained from this environmental isolate were compared with profiles
of the ATCC type strain Salmonella enterica serotype Typhimurium LT2 grown under
the same conditions. It was shown that there were distinct transcriptional differences in
both of the strains between the biofilm and planktonic phenotypes. Both strains exhibited
the strong up-regulation of several gene pathways that were unique to the biofilm
phenotype. These included genes responsible for the cobalamin-dependent anaerobic
utilization of 1,2-propanediol (cob-cbi-pdu), type III secretion system apparatus and
effector proteins located on Salmonella Pathogenicity Island 2 (SPI-2) and the well
characterized csg operon largely responsible for biofilm formation in Salmonella. A
significant proportion of the genes present on the virulence plasmid PSLT were shown to
be exclusively up-regulated in the biofilm phenotype of Salmonella Typhimurium LT2,
illustrating the tendency of this pathogen to exhibit a promiscuous lifestyle whilst in the
non-host environment. It was further demonstrated that the environmental isolate
exhibited a more tenacious biofilm-forming tendency and overall greater survivability
than the type strain in a low nutrient, non-host environment. It appeared from the
transcriptional profile of Salmonella Typhimurium LT2 during planktonic growth that the
organism struggled to adapt and survive under low nutrient conditions as evidenced by
the increased expression of ribosomal subunit operons rps and rpl and several stressrelated genes including dnaK and htp. The conclusion may be drawn that Salmonella
Missouri has developed several key systems differentiating the biofilm and planktonic
phenotypes and affording it a competitive advantage. While some of these traits have
previously been studied exclusively in the context of host pathogenicity, this research
indicates that perhaps these so-called virulence strategies may afford the pathogen
enhanced survival in non-host environments as well. Therefore, these findings suggest
that the use of excessively sub-cultured laboratory strains may be inappropriate
surrogates for studying the behavior of real-world pathogens.
1
CHAPTER 1
INTRODUCTION
Salmonella has been recognized as a global threat to human health and in the
United States alone is the cause of an estimated USD 3 billion in hospital costs and loss
of revenue (World Health Organization, 2005). Several hundreds of serotypes of
Salmonella may be circulating within the human population at any given time and these
display varying degrees of virulence from causing mild gastric irritation (salmonellosis)
through to full-blown typhoid fever (Centers for Disease Control and Prevention, 2007).
Furthermore, this pathogen tends to cycle between the host and non-host environment
and has been shown to be quite capable of adapting to stressful conditions within both
these settings. In the non-host environment, Salmonella may survive for lengthy periods
of time as part of a microbial consortia termed a biofilm (Armon et al., 1997; Costerton et
al., 1999; Latasa et al., 2005; Leriche and Carpentier, 1995; September et al., 2007).
Chapter 2 of this dissertation summarizes the current state of the literature
available in this field and describes the important advances in Salmonella biofilm and
physiology research and identifies some open questions which were addressed in this
present work.
The goals of this study were to investigate some of the key transcriptional
pathways involved in the switch from the planktonic to the biofilm phenotype using
Salmonella whole-genome microarrays. This method of analysis was first applied to one
serotype of Salmonella enterica, an environmental isolate from a water-related outbreak
in Gideon, MO, and the results of this study are presented in Chapter 3. Subsequently to
2
this, further experiments included an ATCC type strain of Salmonella enterica serotype
Typhimurium LT2 in order to demonstrate the differences between a virulent isolate and
a lesser virulent, frequently passaged strain. The results of this study are presented in
Chapter 4. Each of these two studies will be submitted for publication individually in
order to contribute to the current state of the field. The work demonstrated in Chapter 3
will be published the first submission (to the Society for Applied Microbiology journal
“Environmental Microbiology”) and will form the basis for the second publication (to
“FEMS Microbiology Letters”) covering the work presented in Chapter 4.
The final chapter of this thesis (Chapter 5) communicates the conclusions of this
study and suggests possible directions for future study.
3
CHAPTER 2
LITERATURE REVIEW
Salmonella Background
Salmonella is a gram negative, rod shaped enteric bacterium bearing remarkable
similarity to the well-characterized Escherichia coli. This organism is usually motile by
peritrichous flagella. It is facultatively anaerobic and chemoorganotrophic, exhibiting
both a respiratory and fermentative type of metabolism, depending on environmental cues
and conditions. As such, Salmonella have been isolated from diverse environments
spanning soil, water, invertebrates, reptiles, fish and mammals.
Nomenclature
Salmonella nomenclature has been the source of much contention in the literature
over the years and until January 2003, there were still differing opinions between the
Centers for Disease Control and Prevention and the widely accepted Kauffmann-White
scheme maintained by the World Health Organization (WHO) Collaborating Center for
Reference and Research on Salmonella at the Pasteur Institute, Paris, France (WHO
Collaborating Center). Brenner et al. (2000) published a guest commentary in the Journal
of Clinical Microbiology entitled “Salmonella Nomenclature” in which they discussed
the many issues and points of contention surrounding the naming of this pathogen. At
that time, 2463 serotypes or serovars of Salmonella were defined by the WHO
Collaborating Center. According to the latest published report (Grimont and Weill, 2007),
there are 2579 serovars of Salmonella. Furthermore, it was only in 2005 (Truper, 2005)
4
that the Judicial Commission of the International Committee of Systematic Bacteriology
officially applied the status of Type Strain to Salmonella enterica, replacing the previous
Type Strain Salmonella choleraesius.
Molecular methods have shown that the genus Salmonella consists of only two
species, Salmonella enterica and Salmonella bongori. Of these two species, S. bongori
only contributes 22 serovars to the overall number mentioned previously. According to
the official Kauffmann-White Scheme (Grimont and Weill, 2007), Salmonella enterica is
further divided into six subspecies (Table 1) that can be differentiated by biochemical and
genetic tests. These subspecies are designated by names or Roman numerals, the latter
being simpler and more commonly used.
Table 1. Salmonella enterica subspecies and numerical designations.
Salmonella enterica subspecies
I
enterica
II
salamae
IIIa
arizonae
IIIb
diarizonae
IV
houtenae
VI
indica
Serotyping of Salmonella is based on the immunoreactivity of two surface
structures, the O and H antigens. The O antigen is a carbohydrate that is the outermost
component of lipopolysaccharide. It is a polymer of O subunits, each O subunit usually
composed of four to six sugars, depending on the O antigen. Variations in the O antigen
result from variation in the sugar components, the covalent bonds between the subunits
5
and the nature of the linkages between O subunits. O antigens are designated by Arabic
numerals and are divided into O serogroups (Centers for Disease Control and Prevention,
2007).
The H antigen is the filamentous portion of the bacterial flagella, an organelle
being made up of a complex basal body, a curved hook and a helical filament functioning
as a rotary motor, universal joint and propeller respectively. The filament is a selfassembling polymer made up of thousands of molecules of a single protein termed
flagellin. The ends of flagellin are conserved and give the filament its characteristic
structure. The antigenic variability occurs in the middle region of the flagellin protein
which is surface-exposed. Salmonella is unique among the enteric bacteria in that it can
express two different H antigens which are specified by two genes, fliC and fljB. These
two distinct flagellar antigens are referred to as Phase 1 and Phase 2 antigens
respectively, and the expression of the two genes is coordinated such that only one
flagellar antigen is expressed at a time in a single bacterial cell. Monophasic isolates are
those that express only a single flagellin type. If antigens are composed of multiple
factors, they are designated so and separated by commas (Centers for Disease Control
and Prevention, 2007).
In this study, the serotyping convention of the Kauffmann-White Scheme
described above is adopted. Although Salmonella serotypes can be designated more
precisely by a formula they can also be designated by a name. The typical format for a
serotype formula is:
6
Genus [space] Subspecies Roman numeral [space] O antigen [colon] Phase 1 H antigen
[colon] Phase 2 H antigen.
The two serotypes used over the course of this study can therefore be designated:
Salmonella I 4,5,12:i:1,2 or Salmonella enterica serotype Typhimurium or Salmonella
Typhimurium; and Salmonella I 11:g, s, t or Salmonella enterica serotype Missouri or
Salmonella Missouri.
History of Salmonella Missouri – an
Epidemiology
In early December of 1993, a waterborne disease outbreak was identified in the
town of Gideon, Missouri, USA. The initial report originated with seven cultureconfirmed cases of Salmonella, all patients exhibiting severe diarrhea (Clark et al., 1996).
The patients included three high school students, one child from a day care, two nursing
home residents and one visitor to the nursing home. The Missouri Department of Health
(DOH) conducted preliminary interviews and determined that there were no food
exposures common to the majority of patients and suggested a link with municipal water.
The Missouri Department of Natural Resources (DNR) was subsequently informed and
initiated a sampling of the water supply. Water samples collected by the DNR were
positive for fecal coliforms and on December 18, 1993, the city of Gideon, as required by
the DNR, issued a boil water order. The CDC joined the surveillance on December 22,
1993.
Prior to the outbreak, the Gideon municipal water system, which obtained water
from two adjacent 396 m deep wells, had no form of disinfection in place. The
distribution system consisted primarily of small diameter (5, 10 and 15 cm) unlined steel
7
and cast iron pipe. Tuberculation and corrosion were major problems. Raw water
temperatures were unusually high for a ground water supply (14°C) because the system
was overlying a geologically active fault. There were also regular pressure drops under
high flow or flushing conditions. The municipal system also had two elevated tanks (189
m3 and 378 m3) (Angulo et al., 1997).
On December 23, 1993, a chlorinator was placed on-line at the city well by the
DNR. Prior to switching on the chlorinator, none of the water samples collected
contained chlorine and one sample was positive for the same strain of dulcitol-negative
Salmonella as had been isolated from the initial patients.
A CDC survey indicated that ~44% of the 1104 residents, or almost 600 people,
were affected with diarrhea between November 11 and December 27, 1993 in Gideon,
MO. Through January 8, 1994, the DOH had identified 31 cases with laboratoryconfirmed salmonellosis associated with the Gideon outbreak. Fifteen of the 31 cultureconfirmed patients were hospitalized and two of these 15 patients had positive blood
cultures. Seven nursing home residents died, four of whom were culture-confirmed (the
other three were not cultured) (Clark et al., 1996).
A tank inspector observed birds roosting on the largest city-owned water storage
tank which had a broad, flat roof. Subsequent laboratory study of the persistence of this
Salmonella strain isolated from the Gideon water supply demonstrated that the
pathogenic agent was only reduced in density by 30% during a 4 day period at 15°C
(Clark et al., 1996). The suggestion has therefore been made that, with repeated new
input of Salmonella from infected pigeons, there could have been a continuing high level
8
of this pathogen present in the water storage tank and distribution lines. Since the
infective dose varies from 101 to more than 105 cells of Salmonella depending on strain,
as well as the human condition (age, overall health, lifestyle), an Environmental
Protection Agency (EPA) study concluded that the Salmonella outbreak was largely due
to inadequate disinfection and aged equipment (Clark et al., 1996).
Other Examples of Occurrence and
Abundance in Water
In the natural environment the concentration of Salmonella can be as low as 5
CFU/100 mL (Lemarchand et al., 2004) and as high 103 - 105 organisms/liter such as is
found in raw wastewater in the US (Bitton, 2005) and even higher in developing nations
(September et al., 2007). Removal of Salmonella throughout a typical sewage treatment
system in the US has been measured. Typically there may exist 5 x 103 – 8 x 104 CFU/L
in raw sewage, 102 – 3 x 103 CFU/L after primary treatment only (primary sedimentation
and disinfection), 3 – 103 CFU/L after secondary treatment (including trickling filter or
activated sludge) and 10-6 CFU/L after advanced secondary treatment (including
coagulation, filtration and disinfection) (Maier et al., 2000). These figures however are
merely representative and removal rates can vary greatly. In a study from Spain, raw
water samples showed a high content of Salmonella, with a mean MPN of 266.7/100 mL
while treated water (after decanting and activated sludge) contained a Salmonella MPN
of 45/100 mL, representing a reduction of only 83% (Howard et al., 2004).
In a study conducted in California, effluents from 11 of 12 sewage treatment
plants tested positive for Salmonella when samples were analyzed downstream of a
chlorination/dechlorination site, before effluents merged with the receiving stream
9
(outside the plant). Six hundred and eighty three Salmonella isolations were made from
26 of the 32 sampling sites. Multiple serotypes of Salmonella were represented in the
isolations. During the sampling period, people were observed swimming and fishing in
the sewage treatment plant effluent within 30.5 m (100 ft) of the outfall. Subsequent to
this study, an interesting theoretical exercise was carried out. The daily production of
waste water per capita is estimated to be 400 liters. A person with acute salmonellosis
excretes Salmonella in quantities of 108 - 1011 organisms per gram of feces. In a
community with a population of 100,000 the Salmonella concentration will be: 1011 / 105
x 400 liters = 2.5 x 103 Salmonella per liter of sewage (Kinde et al., 1997).
In 2004, an outbreak of gastroenteritis was investigated on South Bass Island,
OH, an island of 900 residents that is visited by > 500,000 persons each year. Between
May and September 2004, 1450 persons reported illness. Out of 70 stool specimens
tested for bacterial pathogens, Salmonella enterica serotype Typhimurium was identified
in only 1 person. The remaining cases were shown to be due to Campylobacter jejuni,
norovirus and Giardia intestinalis. The environmental assessment demonstrated that
contamination of the karst aquifer beneath the island had occurred from multiple land
uses such as onsite septic systems, land application of septage, infiltration of land run-off,
and, possibly, a direct hydraulic connection with Lake Erie (O'Reilly et al., 2007). While
this study did not show the dominance of Salmonella in the outbreak, it did serve to
illustrate two important points about the pathogen’s modus operandi: first, it is seldom
the only pathogen in a waterborne outbreak and second it is a pathogen capable of
maintaining itself as a virulent agent even at low numbers in the environment.
10
In a study out of Japan, higher incidence of Salmonella in river water than sea
water suggested that salinity is a crucial factor in governing its distribution, but the
occurrence of Salmonella in Fukuyama port marine samples may have arisen from an
increased discharge of polluted waters from an adjacent land or coastal area
(Venkateswaran et al., 1989). In addition to simply the presence of the pathogen in water
systems, regrowth and survival of attached Salmonella has been shown in rural
communities’ storage containers (polyethylene and galvanized steel) at low levels (< 1-15
CFU/cm2) (Momba and Kaleni, 2002), in domestic toilet bowls for up to four weeks after
diarrhea had stopped (Barker and Bloomfield, 2000) and in upflow anaerobic sludge
blanket (UASB) reactors in a wastewater treatment plant (Keller et al., 2003).
Survival in Water and Preferred
Environments
Salmonella discharged in the effluents from municipal wastewater treatment
plants (WWTPs) may be able to survive for an extended time. In an experiment using
non-sterile river water, Salmonella was shown to actually increase 3 logs in the first 21
days and decreased 2 logs in the subsequent 21 days (Armon et al., 1997). Domingo et
al. (2000) showed that Salmonella was able to survive in filtered river water for 31 days,
although the culturable counts only represented about 0.001% of the total counts obtained
by microscopy. Further investigation using direct viable counts and resuscitation studies
showed that this value may have been at least a 4 log underestimate of actual survival,
suggesting the presence of a not immediately culturable state of Salmonella. Several
mechanisms of survival have been suggested, including the adoption of a viable-but-non
culturable (VBNC) state, the integration of the pathogen into an existing biofilm (Barker
11
and Bloomfield, 2000; Esteves et al., 2005; Jones and Bradshaw, 1996; Solano et al.,
2002; Stepanovic et al., 2003) and internalization of the pathogen into a variety of
protozoan hosts (Labrousse et al., 2000; Tezcan-Merdol et al., 2004; Winfield and
Groisman, 2003). Although survival depends on a variety of factors, Salmonella survival
in water and its susceptibility to disinfection have been shown to be similar to those of
coliform bacteria (Health Canada, 2006; McFeters et al., 1974; Mitchell and Starzyk,
1975). As both are of fecal origin, the absence of E .coli should thus adequately indicate
the absence of Salmonella although exceptions are known (Health Canada, 2006) and the
reverse may not necessarily be true.
Several species of Salmonella, including Salmonella Typhimurium, have been
shown to enter the VBNC state after lengthy exposure to oligotrophic fresh and seawater
under ambient temperature (Cho and Kim, 1999; Jimenez et al., 1989; Roszak and
Colwell, 1987). These and many other microbial pathogens for which the VBNC state
has been reported have also been suggested to retain the capacity to cause disease and
therefore still be considered a threat (McDougald et al., 1998). Evidence for a VBNC
state of Salmonella can be found in the following cases:
•
In a study on the survival of pathogens under various storage conditions in bottled
mineral water, Salmonella Typhimurium exhibited greatest survival rates in both
sterile and non-sterile mineral water and persisted up to 60 days in bottled mineral
water stored under dark conditions (Ramalho et al., 2001) Most notable in this
study however was the fact that Salmonella, as well as the other pathogens tested,
exhibited significantly better recovery on non-selective media than on their
12
respective selective media. This observation confirms the notion that injured
pathogens may become susceptible to selective agents and that the dogmatic use
of selective media in microbiological testing laboratories may overlook these
microbes. This is a disconcerting notion considering that some researchers have
shown the ability of injured pathogens to retain their ability to cause disease
(McFeters and LeChevallier, 2000).
•
Santo Domingo et al. (2000) showed that, in 3 of 4 serotypes of Salmonella
enterica inoculated into river water, several resuscitation techniques could be
used to detect viable pathogens over lengthy periods of time. Although the
culturable counts of two bacterial strains in filtered water after 31 days
represented approximately only 0.001% of the total Salmonella counts, direct
viable counts (using a modification of the Kogure-CTC method (Kogure et al.,
1979)) and resuscitation studies (using dilution and enrichment) suggested that the
number of viable bacteria was at least four orders of magnitude higher.
Survival of Salmonella in protozoa has been demonstrated in the following cases:
•
Salmonella Typhimurium in water and sediments was tested using artificially
contaminated aquaria. Water samples remained culture positive for Salmonella for
up to 54 days. Sediment samples were culture positive up to 119 days (Moore et
al., 2003). Larval chironomids (midges) raised in contaminated sediments became
culture positive and the bacteria were carried over to adults after emergence.
Uptake of Salmonella by chironomid larvae and adults suggests that they are
possible vectors in both aquatic and terrestrial environments.
13
•
The ability of Salmonella to become internalized and to survive and replicate in
amoebae was evaluated by using three separate serotypes of Salmonella enterica
and five different isolates of axenic Acanthamoeba species (Tezcan-Merdol et al.,
2004). The survival of Salmonella Typhimurium within Acanthamoeba castellanii
during chlorination was also reported, suggesting a protective intracellular habitat
for the bacteria (King et al., 1988). Results showed that A. rhysodes was able to
ingest Salmonella and that subsequent events included intracellular bacterial
replication. The study also detected a bacterium-mediated cytotoxicity that
appeared to be dependent on documented virulence genes, implying that genetic
determinants of Salmonella used for invasion and intracellular proliferation in
mammals could also be operative in the environment.
Susceptibility to Disinfection
To learn whether cellulose, an important component of Salmonella biofilm
exopolysaccharide (discussed later), might be responsible for chlorine resistance and
therefore the survival of Salmonella within biofilms in water supplies and foodprocessing plants, Solano et al. (2002) carried out survival experiments of wild-type
strains and cellulose-deficient mutants. They used a concentration of NaOCl (30 ppm)
that is 100- to 200-fold higher than the free chlorine concentrations typically obtained in
municipal water supplies, reaching into the concentration range used as a sanitizer for
food processing plants. After a 20 minute exposure period, 75% of the wild-type cells
survived NaOCl exposure. In contrast, only 0.3% of cellulose-deficient mutant cells
survived under the same experimental conditions.
14
Oliver et al. (2005) showed that when asodium hypochlorite (free chlorine)
solution was added to provide a final concentration of 1 mg/L of free chlorine in
wastewater, culturability of control Salmonella Typhimurium cells in the stationary phase
remained at about 106 CFU/mL while log phase cells exposed to this chlorination
protocol typically declined to < 10 CFU/mL after 20 seconds exposure time. Total cell
counts revealed the continued presence of > 106 total cells in all cases. On average,
regardless of the physiological state of the cells, 0.39% of the treated cells responded to
the Kogure-CTC (Kogure et al., 1979) viability assay (as opposed to culturability) after
60 minutes of chlorination, indicating a small portion of the cells were able to resist this
treatment. While such a percentage appeared low, it equated to roughly 103–104 cells/mL.
An often overlooked aspect of the susceptibility of pathogens to disinfection is
their evolutionary ability to survive within the gut of various protozoan species. To show
this, King et al. (1988) performed disinfection experiments on some common waterborne
pathogens including Salmonella Typhimurium which were ingested by a variety of
protozoans. As a baseline, they showed that the CT99 values (i.e. the concentration x
contact time required to inactivate 99% of a population) required to inactivate Salmonella
when free-living are 0.4, 0.5 and 0.5 minutes with free chlorine residuals of 1.0, 0.5 and
0.25 mg/L respectively. However, when ingested by the protozoan Tetrahymena
pyriformis, Salmonella Typhimurium exhibited more than 50-fold greater resistance to
free chlorine. The CT99 values required for inactivation under these protected conditions
were around 90, 90, 80 and 50 minutes at free chlorine residuals of 0.5, 1.0, 2.0 and 4.0
mg/L respectively.
15
Berney et al. (2006) examined the efficacy of sunlight irradiation on the
inactivation of some common waterborne pathogens including Salmonella Typhimurium.
Resistance to sunlight at 37°C based on F99 values (i.e. the strength of radiation or
fluence required to inactivate 99% of a population) was in the following order:
Salmonella Typhimurium > Escherichia coli > Shigella flexneri > Vibrio cholerae. While
F90 values of Salmonella Typhimurium and E. coli were similar, F99 values differed by
60% due to different inactivation curve shapes. These authors also pointed out that T90
values (i.e. the time required to inactivate 90% of a population) are not appropriate for
the determination of irradiation efficacy because they do not take into account different
irradiation intensities. They bemoan the fact that the display of T90 values has become
very common in solar disinfection publications, making comparisons among different
studies very difficult. Keller et al. (2003) showed that viable Salmonella in treated
wastewater effluents could be considerably reduced after UV exposure, although the
degree of inactivation depended on the turbidity of the effluent, with more turbid samples
requiring greater doses. They demonstrated that 2 log reductions in non-filtered effluent
could be achieved at doses of about 30 mWsec/cm2 whereas only 20 mWsec/cm2 doses
were required to achieve the same levels of inactivation in filtered effluent. These
findings were corroborated in a study by Rodriguez-Romo and Yousef (2005) who
demonstrated a 2 log reduction in viable Salmonella on the surfaces of egg shells at doses
of about 24 mWsec/cm2.
The inactivation of Salmonella by ozone has been shown to be an effective means
of controlling surface contamination on food surfaces such as egg shells, fruits and
16
berries (Rodriguez-Romo and Yousef, 2005) and in liquids such as apple cider, orange
juice and water (Lezcano et al., 1999; Restaino et al., 1995; Williams et al., 2004).
According to Restaino et al. (1995) more than 5 log units of Salmonella Typhimurium
cells per mL were killed instantaneously after exposure to ozonated water at a
concentration of around 0.19 ppm. These authors pointed out however that the efficacy of
ozonation was more dependent on the type of organic material present in the water rather
than the amount of the organics as was previously thought. They also indicated that the
currently held hypothesis of determining ozone concentrations for an all-or-none
inactivation may be faulty, showing that death caused by ozone followed a biphasic
pattern. The result of this finding suggested that the high dose-short time, or low doselong time approach may need to be revisited. Lezcano et al. (1999) showed that an
environmental isolate of Salmonella was more resistant in water to ozone than both
ATCC strains and environmental isolates of E. coli and Shigella sonnei. They
demonstrated T90 of 3.44, 3.59, 1.69 and 0.62 minutes and T100 (complete inactivation) of
13, 10, 5 and 3 minutes at 0.48, 0.58, 1.04 and 1.75 mg/L ozone respectively.
The Three C’s of Salmonella Biofilms:
Curli, Cellulose and Cyclic-di-GMP
The natural behavior of bacteria is often multicellular (biofilm state) and yet a
highly regulated transition to the single cell (planktonic state) for spread and distribution
is a prerequisite for survival. The genetic requirements of Salmonella in biofilm
establishment are being currently determined in several laboratories. It would appear
from the current state of the literature available on the genetic analysis of Salmonella
17
biofilms that several pathways and cellular responses are crucial in making the switch
from planktonic to biofilm.
It has been shown that Salmonella harbors genetic information for multicellular
behavior characterized by the expression of cellulose and curli fimbriae (formerly
designated thin aggregative fimbriae (Tafi)). Cellulose and curli fimbriae form the selfproduced extracellular matrix which embeds the cells in a honeycomb-like structure that
enables biofilm formation through cell–cell interactions and adhesion to biotic and
abiotic surfaces. The matrix components also protect against disinfectants and play a role
in bacterial–host interactions (Gerstel and Romling, 2003; Solano et al., 2002; White et
al., 2006; Zogaj et al., 2001).
The csgD gene (curli subunit gene D, previously called agfD in Salmonella
Typhimurium) encodes for a transcriptional regulator of the LuxR superfamily and has
been shown to positively control the extracellular matrix compounds cellulose and curli
(Fig. 1) (Gerstel and Romling, 2003).
18
Figure 1. Sch
hematic overview of the role
r of CsgD
D in biofilm formation (G
Gerstel and
R
Romling,
200
03).
Curli fimbriae aree proteinaceoous, filamenttous appendages with hiighly adhesivve
prroperties. CssgD enables the production of curli fimbriae
f
by transcriptionnal activationn of
thhe divergent csgDEFG-ccsgBAC (form
merly agfDE
EFG-agfBAC
C) operon thhat encodes the
t
sttructural gen
nes of curli fimbriae
f
(Gerstel and Roomling, 20033; Solano et al.,
a 2002).
Cellullose biosynthhesis is also positively reegulated by CsgD whereeby CsgD
sttimulates thee transcriptioon of AdrA (agfD-depen
(
ndent regulattor), a putative inner
m
membrane
prrotein that haarbors a cytooplasmic GG
GDEF domaiin. AdrA activates cellullose
prroduction on
n the post-traanscriptionall level eitherr by direct innteraction wiith one or more
m
19
of the gene products of the bacterial cellulose synthesis operons bcsABZC and bcsEFG
(also sometimes designated yhjOMNL and yhjSTU respectively) (Zogaj et al., 2001) or by
production of a cyclic nucleotide, cyclic-di-GMP, which acts as an activator of cellulose
biosynthesis (Garcia et al., 2004; Romling and Amikam, 2006).
Although cellulose has been identified as the major component of a Salmonella
biofilm exopolysaccharides (EPS) matrix under nutrient deficient conditions, several
other polysaccharides including colanic acid, lipopolysaccharide (LPS) and the
enterobacterial common antigen (ECA) (Solano et al., 2002) have been identified (Fig.
2).
Figure 2. Scheme illustrating the role of different genes in the pathways leading to the
synthesis of polysaccharides involved in the biofilm phenotype. Gene symbols are shown
in boldface italics (Solano et al., 2002).
20
The environment in which a bacterium finds itself undoubtedly influences many
aspects of physiological responses including the formation, maturation and detachment of
biofilms. The majority of these responses occur at the gene level, with signal transduction
systems linking the specific environmental cues to appropriate alterations in bacterial
gene expression. In some of these signal transduction mechanisms, perception of a
primary signal may alter the level of a secondary intracellular signal called a secondary
messenger (Dow et al., 2007). Bis-(3’,5’)-cyclic dimeric guanosine monophosphate
(cyclic-di-GMP) is one such secondary messenger now shown to be involved in the
regulation of a range of functions including developmental transitions, aggregation
behavior, adhesion, biofilm formation and virulence in diverse bacteria. An emerging
trend in current literature is that high cellular levels of cyclic-di-GMP promote biofilm
formation and aggregative behavior while low cellular levels promote motility and
virulence (Fig. 3) (Garcia et al., 2004; Romling and Amikam, 2006).
Research has shown that the expression of genes encoding proteins exhibiting a
GGDEF domain potentially increase the cellular levels of c-di-GMP in several bacteria.
Synthesis of cyclic-di-GMP from two molecules of GTP is catalyzed by the GGDEF
domain and is predicted to occur in two steps, while the degradation of the molecule to
GMP also occurs via a two step reaction. Proteins with an EAL domain have been shown
to catalyze only the first step whereas proteins with an HD-GYP domain have been
shown to catalyze both steps (Dow et al., 2007).
21
Figure 3. Reg
gulatory conccept of cycliic-di-GMP metabolism
m
a signalingg on the
and
population lev
vel. GGDEF
F domains with
w consensuus residues synthesize
s
c--di-GMP froom
tw
wo moleculees of GTP. EAL
E
domainss with conseensus residuees cleave thee c-di-GMP
m
molecule
into
o pGpG (whiile HD-GYP
P domains cleave this to two molecules of GMP)).
H
High
c-di-GM
MP levels proomote sessillity aided byy the producttion of adhessive extracelllular
m
matrix
compo
onents such as polysacchharides (celluulose) and fiimbriae (currli fimbriae).
E
Environmenta
al and host persistence
p
iss also prediccted to be proomoted by high
h
c-di-GM
MP
leevels. Conveersely, low c-di-GMP levvels promotee motility beehavior (swim
mming,
sw
warming and
d twitching motility)
m
andd virulence (Romling
(
and Amikam, 2006).
In Sallmonella, ressearch has shhown that CssgD expression is affected by the
prroduction off cyclic-di-G
GMP throughh several GG
GDEF and EA
AL proteins. STM2123 and
STM3388 aree both di-guaanylate cyclaases involveed in produciing c-di-GM
MP and have both
b
been shown to be involveed in CsgD expression.
e
C
CsgD
subseqquently regullates the
exxpression off agfD-depenndent regulattor, AdrA. Transcription
T
n of this GGD
DEF domainn
prrotein promo
otes cellulosse productionn during Sallmonella biofilm formatiion (Gerstel and
R
Romling,
200
03) and was also shown to
t be responnsible for oveer 60% of thhe cellular c--diG
GMP
producttion in a studdy by Kaderr et al. (20066). In a studyy by Garcia et
e al. (2004),,
reesearchers id
dentified sevven novel prooteins all of which contaained the connsensus GGD
DEF
m
motif
and werre designated Gcp (GGD
DEF domainn containing proteins). Seeveral of theese
22
proteins were also identified as carrying an EAL domain. One of these, GcpE, a putative
phosphodiesterase, appeared to totally abolish biofilm formation and cellulose synthesis
by degrading cyclic-di-GMP. In another study by Hisert et al. (2005), an in vivo screen
for genes required for Salmonella Typhimurium to resist oxidative killing by phagocytes
recovered STM1344 (from ydiV), an EAL-domain protein, as the sole output. The
participation of STM1344 in resistance to phagocytic oxidase was confirmed by in vitro
susceptibility of a ydiV mutant to hydrogen peroxide. However, the ydiV mutant was
concomitantly shown to kill macrophages earlier and was more cytotoxic than the wild
type. It is clear that although there may be a trend indicating that the high cyclic-di-GMP
levels induce biofilm formation and persistence while low levels of cyclic-di-GMP
promote motility and virulence, there are exceptions to every rule and more study is
needed to further the understanding of the role of this molecule in the lifecycle of
Salmonella.
The Hfq Regulon
The bacterial protein, Hfq, has been increasingly recognized as a posttranscriptional regulator of global gene expression in a variety of bacteria, primarily in
response to envelop stress (in conjunction with the specialized σ factor RpoE),
environmental stress (by means of alteration of RpoE) and changes in metabolite
concentrations such as iron levels (via the Fur pathway) (Sittka et al., 2007; Wilson et al.,
2007). Several studies have also revealed that Hfq may be involved in the pathogenic
response of some bacteria including Salmonella (Sittka et al., 2007). Wilson et al. (2007)
have recently demonstrated that Hfq has a role in determining the responses observed in
23
Salmonella during space flight. Furthermore, there are several studies showing that
virulence and biofilm formation are altered under microgravity conditions (Leys et al.,
2004; Mclean et al., 2001) and that these changes may be connected with Hfq activity.
During their study, Wilson et al. (2007) identified a list of space flight-stimulated
genes in Salmonella belonging to the Hfq regulon or involved with iron utilization or
biofilm formation. Because this present study is involved in biofilm formation and
persistence of Salmonella, this list proved helpful in interpreting some of the results of
this study, and the pertinent gene expression patterns from their study are summarized
below in Table 2.
Table 2. Space flight stimulon genes in Salmonella belonging to the Hfq regulon or
involved with iron utilization or biofilm formation (modified from Wilson et al. (2007)).
Gene
ompA
ompC
ompD
Fold change Function
direction
Hfq regulon genes (up‐regulated)
Outer membrane proteins
↑
Outer membrane porin
↑
Outer membrane porin
↑
Outer membrane porin
Plasmid transfer apparatus
Conjugative transfer
Conjugative transfer
Conjugative transfer
Conjugative transfer
Conjugative transfer
Conjugative transfer
Conjugative transfer
Conjugative transfer
Conjugative transfer
Conjugative transfer
Conjugative transfer
Conjugative transfer
Conjugative transfer
traB
traN
trbA
traK
traD
trbC
traH
traX
traT
trbB
traG
traF
traR
↑
↑
↑
↑
↑
↑
↑
↑
↑
↑
↑
↑
↑
rpsL
rpsS
rplD
rpsF
rplP
rplA
rpme2
rplY
Hfq regulon genes (down‐regulated)
Ribosomal proteins
↓
30S ribosomal subunit protein S12
↓
30S ribosomal subunit protein S19
↓
50S ribosomal subunit protein L4
↓
30S ribosomal subunit protein S6
↓
50S ribosomal subunit protein L16
↓
50S ribosomal subunit protein L1
↓
50S ribosomal protein L31
↓
50S ribosomal subunit protein L25
hfq
rpoE
↓
↓
Various cellular functions
Host factor for phage replication
σE (σ24) factor
Gene
adhE
entE
hydN
dmsC
nifU
fnr
fdnH
frdC
bfr
ompW
dps
Fold change Function
direction
Iron utilization/storage genes
↑
Fe‐dependent dehydrogenase
↑
2,3‐dihydroxybenzoate‐AMP ligase
↑
Electron transport (FeS center)
↓
Anaerobic DMSO reductase
↓
Fe‐S cluster formation protein
↓
Transcriptional regulator, Fe‐binding
↓
Fe‐S formate dehydrogenase‐N
↓
Fumarate reductase, anaerobic
↓
Bacterioferrin, iron storage
↓
Outer membrane proteinW
↓
Stress response protein and ferritin
Genes implicated in/associated with biofilm formation
wza
↑
Polysaccharide export protein
wcaI
↑
Putative glycosyl transferase
ompA
↑
Outer membrane protein
wcaD
↑
Putative colanic acid polymerase
wcaH
↑
GDP‐mannose mannosyl hydrolase
manC
↑
Mannose guanylyltransferase
wcaG
↑
Bifunctional GDP fucose synthetase
wcaB
↑
Putative acyl transferase
fimH
↑
Fimbrial subunit
fliS
↓
Flagellar biosynthesis
flgM
↓
Flagellar biosynthesis
flhD
↓
Flagellar biosynthesis
fliE
↓
Flagellar biosynthesis
fliT
↓
Flagellar biosynthesis
cheY
↓
Chemotaxic response
cheZ
↓
Chemotaxic response
24
Iron Utilization Genes
Iron is essential for the multiplication of enterobacteria, since it is a component of
enzymes (e.g., ribonucleotide reductase) which are required for the biosynthesis of
macromolecules (e.g., DNA) and energy-generating electron transport processes.
However, enterobacteria such as Salmonella frequently encounter iron-restricted
conditions both in the host and non-host environments. In order to obtain iron from
insoluble Fe (III) complexes present under aerobic growth conditions, Salmonella may
release low-molecular-weight compounds, designated siderophores, which bind this
metal ion with high affinity(Baumler et al., 1998). The Fe (III)-siderophore complexes
are then internalized by iron-regulated outer membrane receptor proteins which display
substrate specificity. The primary siderophore produced by Salmonella is enterobactin
(enterochelin), a cyclic trimer of N-(2,3-dihydroxybenzoyl)- L-serine (DBS). These
siderophores are usually sequestered back to the bacteria and are transported across the
outer membrane, a process mediated by outer membrane receptor proteins (Fig. 4).
25
Figure 4. Thee struggle forr iron: bacterria vs. host. Within the host
h environnment, most of
o
thhe available iron is bounnd to host prooteins such as
a transferrinn and lactofeerrin. Bacteriial
pathogens acq
quire iron either by prodducing iron chelating
c
ageents such as siderophores
helin) or by utilizing
u
hem
me-binding proteins.
p
Modified from Klemm et al.
(ee.g. enteroch
(22007).
In Sallmonella, sevveral such reeceptor proteeins have been identifiedd, including
FepA and IroN (Rabsch et
e al., 1999). However, Salmonella
S
a possessees several othher
also
ouuter membraane receptors, FhuA, FhuuE and FoxA
A, which aree involved inn utilization of
siiderophores that are not produced byy this pathoggen itself, buut rather reprresent a type of
piracy mechaanism allowing Salmonellla to acquire Fe (III)-sidderophore coomplexes froom
otther microbees (Cornelisssen and Sparrling, 1994)..
26
Another type of system identified in Salmonella is encoded by the feoAB locus
and mediates the transport of iron (II) through the inner membrane. This system does not
require siderophores, as iron (II) is soluble and therefore readily enters the periplasmic
space by diffusion through the porins. Salmonella strains carrying mutations in known
iron uptake systems are either minimally affected in virulence or not affected at all (Hall
and Foster, 1996). This is surprising, as Salmonella are predicted to encounter ironrestricted environments in the course of their pathogenic cycle. The lack of strong
phenotypes associated with mutations in iron uptake systems is therefore most likely due
to the existence of several redundant systems that can mediate the uptake of this critical
nutrient. Evidence of such redundancy came when yet another putative iron transport
system, sitBCD, was identified on the Salmonella Pathogenicity Island 1 (SPI-1). This
system belongs to the ABC family of transporters, is able to restore growth ability to an
enterobactin-deficient strain of E. coli under iron-limiting conditions and is repressed
under iron-rich growth conditions in a fur-dependent manner (Zhou et al., 1999).
1,2-Propanediol Utilization
Salmonella can grow aerobically as well as anaerobically on L-rhamnose, a
common plant-associated sugar, as a sole carbon and energy source (Cocks et al., 1974).
The pathway is mediated by a permease, isomerase, kinase and aldolase, yielding
dihydroxyacetone phosphate and L-lactaldehyde. Aerobically, L-lactaldehyde is
converted to L-lactate by the NAD-dependent lactaldehyde dehydrogenase and pyruvate
via a second enzyme-catalyzed oxidation. Anaerobically, L-lactaldehyde is reduced to
1,2-propanediol by an oxidoreductase, thereby regenerating NAD and allowing the
27
fermentation of rhamnose to proceed. The 1,2-propanediol is then excreted from the
bacterial cell (Fig. 5).
Figure 5. Anaerobic rhamnose catabolism in Salmonella. Modified from Boronat et al.
(1979).
Although the same rhamnose pathway exists in E. coli, the 1,2-propanediol is not
further metabolized under either aerobic or anaerobic conditions. Salmonella, however,
appears to have gained an ecological advantage in being further able to utilize the
excreted product under both conditions. Since it would probably encounter this product in
many of its environmental niches, this ability may be significant. The persistence of
Salmonella in a biofilm may further highlight the usefulness of this pathway. De Beer et
28
al. (1994) showed that within biofilms there exist microniches of aerobic and anaerobic
pockets. Other researchers have also commented on this concept of partitioning within
biofilms, suggesting that within a cluster of cells, several different microenvironments
may exist, each facilitating distinct physiological pathways (Costerton et al., 1994; De
Beer and Stoodley, 2006).
Aerobic metabolism of 1,2-propanediol appears to involve the oxidation to
lactaldehyde through the action of an oxidoreductase. Lactaldehyde is subsequently
metabolized to lactate and pyruvate (Baldoma et al., 1988; Cocks et al., 1974). In
contrast, anaerobic metabolism of 1,2-propanediol has been reported to be mediated by a
coenzyme B12-dependent diol dehydratase (Fig. 6) that yields propionaldehyde which is
immediately metabolized by a dismutation to n-propanol and proprionate (Obradors et
al., 1988). This anaerobic respiration can be carried out by Salmonella using tetrathionate
as a terminal electron acceptor only, as opposed to the more common anaerobic electron
acceptors nitrate, fumarate, trimethylamine-N-oxide or dimethyl sulfoxide (Bobik et al.,
1999). The genes involved in using tetrathionate as a terminal respiratory electron
acceptor are encoded by the divergently described operons ttrSR and ttrBCA. It has been
demonstrated that during anaerobic growth on 1,2-propanediol, Salmonella reduces
tetrathionate to thiosulfate which is then subsequently reduced to hydrogen sulfide.
29
Figure 6. Model of cobalamin-dependent utilization of rhamnose by intracellularly
replicating Salmonella to recruit additional carbon, nitrogen and energy sources modified
from Klumpp and Fuchs (2007).
The pdu genes are contiguous and co-regulated with the cobalamin (cbi-cob)
(vitamin B12) biosynthetic genes, indicating that propanediol catabolism is the primary
reason for de novo B12 synthesis in Salmonella (Ailion et al., 1993; Bobik et al., 1999).
Jeter (1990) showed that de novo synthesis of cobalamin occurs only under anaerobic
conditions. If one includes the cob genes, Salmonella enterica maintains 40 to 50 genes
primarily for the transformation of propanediol. In fact, more than 1% of the Salmonella
enterica genome is devoted to the utilization of propanediol and cobalamin biosynthesis
(Walter et al., 1997). Moreover, nearly all natural isolates of Salmonella tested
synthesized B12 de novo and degraded propanediol (Lawrence and Roth, 1996).
The genes required for 1,2-propanediol degradation cluster at the pdu locus on
centisome 44 of the S. enterica chromosome (Jeter, 1990). This locus includes the
30
positive transcriptional regulator, pocR, and a diffusion facilitator of 1,2-propanediol,
pduF in addition to the genes of the adjacent and divergently transcribed pdu operon
(Bobik et al., 1999). The pdu operon is estimated to include 21 genes. Of these genes,
four have unknown functions (pduLMVX), eight are reported to encode a polyhedral body
(pduABJKNSTU), a distant relative of a carboxysome shell, five encode a diol
dehydratase (pduCDEGH), 3 encode for dehydrogenases (pduOPQ) and one encodes for
a propionate kinase (pduW).
The regulation of the pdu operon has also been investigated. It is co-induced with
the adjacent cob operon in response to 1,2-propanediol and its induction is influenced by
cyclic AMP levels, the redox state of the cell, iron, magnesium, pH, and perhaps the
growth phase (Ailion et al., 1993; Bobik et al., 1999; Heithoff et al., 1999; Rondon and
Escalante-Semerena, 1997). It would appear that the Crp/cAMP complex is the primary
global regulator of pocR (and thus the cob and pdu operons) under aerobic conditions,
while maximal anaerobic induction requires the additive effects of both the Crp/cAMP
complex and the ArcA/ArcB system.
The polyhedral bodies involved in 1,2-propanediol degradation are similar in
structure to carboxysomes. It has been suggested that these structures may be involved in
sequestering toxic aldehydes formed during 1,2-propanediol degradation and in
channeling them to subsequent pathway enzymes (Sampson and Bobik, 2008). It has also
been put forward that polyhedral bodies may protect diol dehydratase from oxygen to
which it is sensitive (Bobik et al., 1999). Whatever the functional purpose of the
polyhedral bodies, due to the number of genes and energy expended in their formation, it
31
is evident that they play an important role in Salmonella survival and niche establishment
among the competitive flora of natural and host environments.
In vivo expression technology (IVET) has indicated that 1,2-propanediol
utilization (pdu) genes may be important for growth in host tissues (Conner et al., 1998)
and competitive index studies with mice have shown that pdu mutations confer a
virulence defect (Heithoff et al., 1999). Bobik et al. (1992) demonstrated a ~10 fold
decrease of intracellular replication of a pocR mutant, affecting both the control of
vitamin B12 synthesis and propanediol degradation, indicating that the cob-cbi-pdu gene
cluster increases the intracellular fitness of Salmonella. More recently, Klumpp et al.
(2007) showed that deletions within this same cluster resulted in attenuated replication in
macrophages. Furthermore, Adkins et al. (2006) found, in acidic minimal medium, a 5fold abundance of Pdu proteins of an environmental isolate of Salmonella enterica in
comparison with the less virulent type strain Salmonella Typhimurium LT2.
Several biotechnologically relevant processes such as unsaturated polyester
resins, liquid laundry detergents, pharmaceuticals, cosmetics, and antifreeze and deicers
depend on the production of 1,2-propanediol via a synthetic process from propylene
oxide, a non-renewable petrochemical derivative(Altaras et al., 2001). Although 1,2propanediol is primarily the result of the breakdown of rhamnose, researchers have also
shown that organisms such as Thermoanaerobacterium thermosaccharolyticum HG-8
(ATCC 31960), a naturally occurring microorganism, is able to ferment common sugars
such as D-glucose and D-xylose to 1,2-propanediol (Cameron et al., 1998). Furthermore,
Salmonella enterica possesses a 1,2-propanediol oxidoreductase (Ros and Aguilar, 1985)
32
which may convert glucose to 1,2-propanediol, albeit at very low levels (Badia et al.,
1985) and which is extremely sensitive to the presence of oxygen.
Glucose may also be converted to acetate via the Embden-Meyerhoff-Parnas
(EMP) or glycolytic pathway in which fructose-l,6-bisphosphate aldolase, as a key
enzyme, splits the glucose backbone symmetrically to ultimately produce two molecules
of pyruvate which in turn may be broken down to acetate via followed methanogenic
acetate cleavage. The EMP pathway is widely distributed among hexose-fermenting
anaerobic bacteria including Salmonella. Once acetate is formed, Starai et al. (2005) have
demonstrated that the eut operon is required for the cobalamin-dependant excretion of
acetate from the cell. This operon has been demonstrated to also form a carboxysome-like
structure thought to contain acetaldehyde for removal from the cell (Rondon and
Escalante-Semerena, 1997).
Pathogenicity
Well over 1000 of the 4330 annotated ORFs of the Salmonella Typhimurium LT2
genome, approximately 25% of all genes, have probably been gained via lateral gene
transfer after the divergence of the Salmonella from E. coli around 100 million years ago,
since close homologs cannot be found in the genomes of E. coli, Yersinia pestis or
Klebsiella pneumoniae (Porwollik and McClelland, 2003). Included in this group of
genes are the four Salmonella Typhimurium LT2 prophages and the Salmonella
Pathogenicity Islands 1–5. However, there are also an additional 24 regions (Table 3)
with 10 or more genes (as well as many smaller clusters) that are not shared with E. coli,
K. pneumoniae or Y. pestis (McClelland et al., 2001). It can be expected that some, if not
33
most, of these regions contain genes that play a role in environmental adaptation and
survival, host infection and disease development.
The biggest cluster of these deviant genes is the cob-cbi-pdu locus, which
encompasses 42 genes and as has been discussed, is involved in de novo biosynthesis of
adenosyl–cobalamin under anaerobic conditions and propanediol utilization as a carbon
and energy source. This cluster is missing in S. bongori and S. enterica subspecies VII
and IV (Porwollik et al., 2002).
The four functional phage genomes present in the Salmonella Typhimurium LT2
chromosome are the P2–like Fels-2, and the lambda-like phages Fels-1, Gifsy-1 and
Gifsy-2 (Figueroa-Bossi et al., 2001). The Fels-1 phage is very restricted in its
distribution and has so far only been detected in Salmonella Typhimurium LT2. Phage
Fels-2 has an effect on the SOS response (an inducible DNA repair system that allows
bacteria to survive sudden increases in DNA damage) of the bacterium, since mutations
within its genome allowed for non-lethality of a lexA null mutation (Bunny et al., 2002).
The Gifsy-2 phage contributes profoundly to the ability of Salmonella Typhimurium to
cause systemic disease in mice. Curing strains of the Gifsy-2 phage has been shown to
render the bacteria over 100-fold attenuated in their ability to establish a systemic
infection in mice, whereas the effect of Gifsy-1 is less pronounced and can only be shown
in cells that lack Gifsy-2 but retain the sodCI gene (Figueroa-Bossi et al., 2001). Recently
it has been shown that the outer membrane porin OmpC is a necessary receptor for Gifsy
phage entry into the bacterial cell. The gene encoding this receptor is present in all
salmonellae (Ho and Slauch, 2001). The lambdoid Gifsy-3 phage is present in Salmonella
34
Typhimurium 14028s and contains the gene sspH1, encoding a leucine-rich substrate of
the type III secretion apparatus of the SPI-1 (Figueroa-Bossi et al., 2001). SspH1 is
suspected to be involved in host adaptation in concert with two other gene products
present in several S. enterica genomes: SlrP and SspH2 (Tsolis et al., 1999).
Table 3. Regions of 10 or more genes recently (ca. 100 million years) acquired by
Salmonella enterica serotype Typhimurium LT2. Modified from Porwollik et al. (2003).
Region
(Locus) start
Number of
genes
Prominent genes/operons
Function
STM0014
STM0266
25a
43
bcf
saf, sinR
Fimbriae
Fimbriae, transcriptional regulator, virulence proteins?
STM0328
37a
stb, mod, res
Fimbriae, transport proteins? DNA restriction/modification, transcriptional regulators?
STM0514
19b
all, glx
Allantoin metabolism, glycerate kinase
STM0543
STM0715
STM0893
STM1005
24a
13
40
52
fim, rfbI
sodCIII, nanH
sodCI, grvA, gtgE
Fimbriae, glucosyl transferases, transcriptional regulator?
Glucosyl transferases, cell wall biogenesis
Prophage Fels-1: super oxide dismutase, neuraminidase
Prophage Gifsy-2: superoxide dismutase, virulence genes
STM1087
11a
pip, sopB
SPI-5: virulence genes, effector protein
STM1239
30a
pag, env, msgA
Virulence genes, PhoP regulated genes, ABC transport system
STM1350
13b
ydi
Energy metabolism
STM1379
44a
ttr, sse, ssa
SPI-2: type III secretion system
STM1528
STM1610
STM1629
STM1664
STM1853
35a
12
10
11
21
pqa
sopE2, pagK, mig-3, pagO
Hydrogenases, PhoPQ regulated gene, transporters, transcriptional regulator?
PTS system
ABC transport
Transcriptional regulators?
Phage genes, effector proteins, PhoPQ regulated genes, virulence genes
STM2019
STM2082
STM2230
STM2584
STM2689
40c
16
16
54
100a
cbi-cob-pdu
rfb
sspH2, oafA
gipA, gogB
iro, fljAB, hin, tct, virK, mig-14
Vitamin B12 synthesis, 1,2-propanediol utilization
LPS side chain biosynthesis
Phage genes, effector protein
Prophage Gifsy-1
Prophage Fels-2, PTS system, phase 2 flagellin, H inversion, virulence genes, transporters, siderophores?
STM2865
STM3025
STM3117
43a
12
18
hil, spa, inv, sip
std
SPI-1: type III secretion system and effectors, transporter
Fimbriae
Transcriptional regulators?
STM3752
STM3766
STM4195
STM4305
STM4417
13a
10
25
16
20
mgt, sugR
SPI-3 (part): Mg transport
PTS system
Prophage
Phage genes, DMSO reductase complex
Sugar transport, kinases
STM4440
11c
STM4488
23
a
PTS component?
DNA repair?
a
Polyphyletic origin likely.
Present in E. coli, absent in S. bongori and five S. enterica subspecies.
c
Present in K. pneumoniae.
b
Type III Secretion Systems
Type III secretion systems (TTSS) are specialized structures found in several
Gram-negative bacterial pathogens, including Salmonella, that deliver effector proteins to
35
host cell membranes and cytosol (Hueck, 1998). The TTSS apparatus is a needle-like
structure which spans the inner and outer membranes of the bacterial envelope and
secretes translocator and effector proteins. There are structural similarities between the
needle complex and flagellar basal body, and some of its proteins, including those which
form the core of the central channel. Translocon proteins allow access of effector proteins
to the eukaryotic cell, probably by forming pores in the host cell membrane. Since TTSS
are involved in direct cell-cell contact transfer and in some cases a connecting channel
between the bacterium and the eukaryotic membrane may even be formed (Frankel et al.,
1998). The effector proteins subvert different aspects of host cell physiology and
immunity, thereby promoting bacterial virulence (Galan and Wolf-Watz, 2006).
Salmonella Pathogenicity Island 1
Salmonella encodes two distinct virulence-associated TTSS within SPI-1 and SPI2. Salmonella Pathogenicity Islands are characterized by their absence from the E. coli
genome, a G + C content which is different from the average of the Salmonella genome,
and the presence of distinct genes, the impact and effects of which have been shown in
different stages of the infection process (Porwollik and McClelland, 2003).
The former of these pathogenicity islands found in Salmonella spp. was first
demonstrated to contain genes required for the invasion phenotype by Mills et al. (1995).
The ability of Salmonella to enter epithelial cells has been reported to depend on growth
phase, low oxygen tension, pH and high osmolarity (Bajaj et al., 1996). Thus these
conditions may be important drivers in controlling gene expression of the SPI-1.
36
The SPI-1 TTSS of Salmonella Typhimurium delivers several effector proteins
(e.g. SipB, SptP and AvrA) through the host cell plasma membrane. Most of these
effector proteins are involved in actin cytoskeleton rearrangements, leading to membrane
ruffling and subsequent Salmonella invasion (Galan, 1999). SPI-1 effectors also induce
IL-8 and pathogen-elicited epithelial chemoattractant secretion in intestinal epithelial
cells, resulting in transmigration of neutrophils (Lostroh and Lee, 2001). The invasion
mechanism displayed by Salmonella (Fig. 7) and a description of this SPI-1-mediated
invasion follows.
Figure 7. Invasion of Salmonella into the host epithelium as the initial stage of
establishing infection (BioCarta, 2008).
37
Pathogenic Salmonella enter cells such as those of the intestinal epithelium by
altering cellular cytoskeletal structure and inducing membrane ruffling of the infected
cell. Salmonella is able to alter the cytoskeleton and membrane through the action of SPI1 TTSS-mediated bacterial Sip proteins, SopE, SopB, and SptP that are inserted into the
cytosol of the infected cell. Although not all of these effector proteins are encoded on the
SPI-1, their secretion is mediated by SPI-1 TTSS (Wang et al., 2004). Sip proteins
encoded by Salmonella are required for the action of SopE and for the invasion of
epithelial cells. SipA stabilizes actin filaments, inducing membrane ruffling and perhaps
focusing membrane changes where bacteria are localized to allow their entry. The SPI-1
translocon protein SipB binds to and activates caspase-1, leading to the induction of
apoptosis in macrophages (Hersh et al., 1999). SipC produces a similar effect on actin
filaments and cytoskeletal structure. SopE acts as an exchange factor on Rac1 and Cdc42,
two GTPases in the Rho family that regulate actin cytoskeleton. The activation of Rac2
and Cdc42 by Salmonella SopE induces changes in cytoskeleton structure that allow
bacterial entry into the cell. SopB is another Salmonella protein that acts as an inositol
polyphosphate phosphatase and also stimulates Cdc42 and Rac1. One of the cellular
targets of both Cdc42 and Rac1 that affects actin structure is the Arp2/3 complex. Cdc42
and Rac1 activate Wasp, which activates Arp2/3. Activated Arp2/3 induces the formation
of actin Y branches, which in combination with changes in actin caused by SipA and
SipC help to form lamellipodia, and causes membrane ruffling, leading to entry of
Salmonella into the affected cell (Galan and Zhou, 2000).
38
After the initial infection, cells quickly return to their normal morphology, a
process that depends on the action of the bacterial protein SptP. While SopE acts as an
exchange factor, SptP acts as a GTPase activating protein to inactivate Rac1 and Cdc42
once again. This inactivation of the original entry mechanism provides an example of the
delicate balance between infectious organisms and their host (Galan and Zhou, 2000).
Mutations which prevent secretion through the SPI-1 TTSS lead to a 10- to 100fold increase in attenuation in the mouse model of systemic infection when the bacterial
inoculum was administered orally (Baumler et al., 1997; Galan and Curtiss, 1989; Jones
et al., 1994). Evidently the lack of complete attenuation of SPI-1 null mutants reflects the
ability of Salmonella to disseminate to the liver and spleen from the intestinal tract via an
alternative route: carriage within transmigrating, CD-18 expressing phagocytic cells
(Vazquez-Torres et al., 1999). After the bacteria reach the spleen and liver, they replicate
within membrane-bound compartments, called Salmonella-containing vacuoles (SCVs),
inside macrophages (Richter-Dahlfors et al., 1997; Salcedo et al., 2001).
Salmonella Pathogenicity Island 2
One main function of the SPI-1 is to aid bacterial translocation from the intestinal
lumen to the basolateral side of the intestinal mucosal membrane. This process also
involves yet another drastic change in the surrounding environment of the infecting
bacteria, requiring the pathogen to withstand the host antibacterial responses such as
professional phagocytic cells aimed at ingesting and killing the bacteria. The SPI-2 TTSS
is a multifunctional virulence system that is activated following entry of bacteria into
eukaryotic cells and facilitates bacterial multiplication in all cell types that have been
39
tested (Beuzon et al., 2002; Cirillo et al., 1998; Hensel, 2000). SPI-2 gene products are
thought to be induced by Mg2+ deprivation, phosphate starvation, low pH and oxidative
stress (Hensel, 2000) and in bacterial growth experiments, genes are not induced until
cells enter stationary phase (Monack et al., 2001).
Related in behavior to the SPI-2 is the expression of the spv operon located on a
96kb virulence plasmid in Salmonella Typhimurium (Eriksson et al., 2003; Gulig et al.,
1993; Rhen et al., 1993). Because intracellular growth and bacterial proliferation in
cultured cells is correlated with systemic growth in the host (Salcedo et al., 2001), this
explains the profound attenuation of SPI-2 or spv null mutants in vivo (Hensel, 2000;
Shea et al., 1996).
Although SPI-2 is almost 40 kb in length, genes encoding the type III secretion
system are localized to a region of approximately 26 kb beginning at the centisome 30
end of the island. Here, 31 genes are organized in four operons termed (1) regulatory, (2)
structural I, (3) structural II and (4) effector/chaperone (Cirillo et al., 1998; Hensel et al.,
1998). In addition to several genes encoding evolutionarily conserved structural
components of the secreton machinery (Aizawa, 2001) and the translocon proteins SseB,
SseC and SseD, there are a few genes that appear to be unique to SPI-2, such as sseE,
whose functions are unknown. SseB is similar to EspA of enteropathogenic E. coli, and
might therefore link the secretion needle to the translocon pore (Beuzon et al., 1999).
SseB, SseC and SseD are not required for secretion of effectors, but are necessary for
their translocation across the vacuolar membrane (Waterman and Holden, 2003). Hence,
these proteins can be operationally defined as translocon components, although their
40
presence in the vacuolar membrane has not been demonstrated directly. In addition to the
components of the secreton and translocon, SPI-2 also encodes at least three chaperones:
SscA, SscB and SseA. The partners of SscA and SscB have not been defined, but SseA is
a chaperone for SseB and SseD (Ruiz-Albert et al., 2003; Zurawski and Stein, 2003). The
SPI-2 also encodes a two-component regulatory system which is required for expression
of all SPI-2 TTSS genes (Cirillo et al., 1998) as well as several genes located outside SPI2 which encode effector proteins (Beuzon et al., 2000; Knodler et al., 2002; Worley et al.,
2000). In other TTSS’s, some translocon proteins have been shown to function as
effectors, but there is no evidence yet to indicate whether this might be the case for SseB,
SseC or SseD. SpiC, SseF and SseG are proposed to be effector proteins encoded within
SPI-2 (Freeman et al., 2002; Kuhle and Hensel, 2002).
41
CHAPTER 3
A TRANSCRIPTIONAL STUDY OF AN ENVIRONMENTAL SALMONELLA
ENTERICA ISOLATE BIOFILM
Introduction
Salmonella enterica, like Escherichia coli, is an enteric pathogen belonging to the
family Enterobacteriaceae and has been identified as the second most common cause of
gastroenteritis in children under five years of age in the United Kingdom (Crowley et al.,
1997). This organism is responsible for salmonellosis, the second most common cause of
bacterial food poisoning reported to the Communicable Disease Surveillance Center
(CDSC) (Evans et al., 1998) and accounts for 60% of all bacterial disease outbreaks in
the US. It is estimated that over 4 million cases of Salmonella infection and 1000 related
deaths occur in the United States annually (Feng, 1992). Individuals infected with
Salmonella shed the organisms in their feces, which can enter domestic sewage and
consequently may contaminate drinking water sources.
Although the primary cause of salmonellosis is consumption of Salmonellacontaminated foods, there is increasing evidence that this pathogen may be associated
with biofilms on materials of different nature and under different growth conditions
(Solano et al., 2002; Stepanovic et al., 2003) and may be important in drinking water
distribution systems (Jones and Bradshaw, 1996). Salmonella discharged in the effluents
from municipal wastewater treatment plants have been reported to survive for an
extended time in nutrient-rich river water (Winfield and Groisman, 2003). Several
42
mechanisms of survival have been suggested, including the adoption of a viable-but-non
culturable (VBNC) state (Roszak et al., 1984), the integration of the pathogen into an
existing biofilm (Barker and Bloomfield, 2000; Jones and Bradshaw, 1996; Solano et al.,
2002; Stepanovic et al., 2003), internalization of the pathogen into a variety of protozoan
hosts (King et al., 1988; Moore et al., 2003; Tezcan-Merdol et al., 2004) and adaptation
via lateral gene transfer (Porwollik et al., 2002) whereby the pathogen gains a strategic
advantage over other microbes in the biofilm community to exploit a particular
microniche.
Disease is caused by the penetration of the Salmonella bacteria into the epithelium
of the small intestine and subsequent enterotoxin production resulting in electrolytic
imbalance. It has been suggested that biofilm formation which may aid in survival of
bacteria under various conditions might be related to increased virulence (Wilson et al.,
2007). Indeed, the formation of Salmonella biofilm on epithelial cells and its ability to
outcompete E. coli in heterologous infections supports the notion that biofilm growth
may be related to increased virulence (Esteves et al., 2005). Transcriptional profiling in
related infectious models and biofilm communities may provide some clues to these
methods of survival. However, due to the spatial and physiological heterogeneity within
microbial biofilms (Costerton, 2000; De Beer and Stoodley, 2006), it is often technically
challenging to isolate and purify mRNA from discrete populations within a biofilm
community. Advances in laser dissection microscopy and mRNA stabilization may in the
future offer the means with which to investigate physiological behavior of single cells
43
within discrete microniches of a biofilm, but for this present study, the entire
monoculture biofilm was regarded as a single unit.
It is traditionally thought that Salmonella has acquired various virulenceassociated genes through lateral gene transfer to allow it to evade host defense
mechanisms and increase its survival and persistence within the host. Such genes include
those operons located on Salmonella Pathogenicity Islands (SPIs) 1 and 2 which are
usually associated with enterocyte invasion (Ellermeier and Slauch, 2007) and
intracellular replication (Hensel, 2000) respectively. An additional pathway apparently
gained via lateral gene transfer is the cob-cbi-pdu operon which allows Salmonella to
utilize 1,2-propanediol as a sole carbon and energy source under anaerobic conditions
(Klumpp and Fuchs, 2007) in a cobalamin-dependent fashion (Sampson and Bobik,
2008). Induction is mediated by a positive regulatory protein (PocR) encoded by a gene
(pocR) that maps between the cob and pdu operons (Bobik et al., 1992). The proximity of
these operons and their coordinate control probably reflect the fact that vitamin B12 is an
essential cofactor for propanediol dehydratase, the first enzyme of propanediol
degradation (Jeter, 1990). The coregulation also supports the idea that the major function
of de novo vitamin B12 synthesis in Salmonella is in propanediol degradation (Ailion et
al., 1993). However, this regulon appears to be a paradox since PocR has been
demonstrated to induce expression of the divergent pathways both aerobically and
anaerobically, but de novo synthesis of vitamin B12 (a necessary co-factor in the
utilization of 1,2-propanediol) only occurs under anaerobic conditions (Bobik et al.,
1992). It is suggested that this apparently paradoxical pathway may represent a
44
significant advantage for Salmonella within a biofilm community where it may encounter
both aerobic and anaerobic microniches (Costerton et al., 1994; De Beer et al., 1994;
Price-Carter et al., 2001).
Winfield and Groisman (2003) suggest that Salmonella, unlike E. coli, has
actually evolved to actively cycle through host and non-host environments. These authors
suggest that E. coli does not persist in non-host environments and that its presence in
such locations results from recent excretion of waste by animal hosts. They report that
this is essentially the logic behind the use of E. coli as the indicator organism for
environmental fecal contamination, that is, as an indicator species, E. coli is assumed not
to be a permanent resident of soil and water environments. It is suggested here that
several systems generally only associated with the host environment and/or virulence are
indeed activated in the non-host biofilm environment. These findings suggest that
Salmonella may have alternative uses for the so-called virulence genes and may be
adapted to persisting as a biofilm in the external environment.
Materials and Methods
Strains and Growth
The strain of Salmonella used in this study was an environmental pathogen
isolated from an outbreak in Gideon, MO, USA in 1993 (Clark et al., 1996). This highly
virulent strain of Salmonella was typed by pulsed gel field electrophoresis (PGFE) at the
CDC in Atlanta, GA, USA and is designated Salmonella Missouri in this paper. Sequence
analysis of the 16S rDNA gene was also performed (Research Technology Support
Facility, Michigan State University using a Perkin Elmer/Applied Biosystems 3100
45
capillary sequencer) to confirm the identity of this organism. Primers used to amplify a
highly conserved region of the 16S rDNA gene covered an area of approximately 1500
base pairs. These primers have been used regularly in this lab and are designated 8F and
1492R (Burr et al., 2006).
Planktonic growth rates were determined in M9 Minimal Media (BectonDickinson, MD) with the addition of 0.4% glucose (Fisher Scientific, NJ) as the carbon
source (Ren et al., 2005). This was the defined medium used in all subsequent
experiments unless otherwise indicated. All cultures, both planktonic and biofilm, were
grown at an ambient temperature of 23°C. For each new experiment, Salmonella
Missouri was freshly prepared from a cryostock which had been maintained at -80°C
with minimal passaging. The ATCC type strain No. 700720, Salmonella enterica
serotype Typhimurium LT2, was cultured as a reference strain to provide a comparison of
growth rate.
In order to determine growth rates, a starter culture of the organism was prepared
by inoculating an overnight colony grown on XLD agar (EMD, NJ) into 100 mL volumes
of M9 + glucose in 250 mL baffled flasks (Pyrex, USA) with orbital shaking of 180 rpm.
These starter cultures were allowed to grow up for 24 hours at which point 100 µL was
inoculated into 100 mL fresh media in a 250 mL Nephelo flask (Wheaton, USA) and
these flasks were returned to the orbital shaking platform at 180 rpm. Optical density was
determined every 4 hours using a Spectronic 20D+ spectrophotometer (Thermo Electron
Corporation, MA) reading at a wavelength of 600 nm.
46
Planktonic cultures were grown under the same conditions as used in determining
experimental growth rates. For microarray experiments, cultures were harvested at 12
hours (empirically determined to be mid- to late-logarithmic phase for both strains of
Salmonella).
Biofilms were grown using the CDC biofilm reactor (www.biofilms.biz) with
glass coupons serving as surfaces for attachment. CDC reactors were preconditioned with
sterile M9 + glucose for 24 hours in batch mode to ensure sterility of the media and
equipment. An inoculum of 1mL Salmonella grown up as described previously for the
preparation of a growth curve experiment was aseptically introduced through a rubber
injection septum and an 18 hour batch mode was allowed in order to facilitate
establishment of the culture in the reactor. This period of batch growth was followed by
switching on the pump and allowing fresh media to flow into the reactor with a hydraulic
retention time of 7.6 hours to ensure that planktonic bacteria were washed out and the
biofilm bacteria predominated.
Biomass Harvesting
For planktonic samples, 50 mL of a 12 hour culture was centrifuged at 4°C for 10
minutes at 10,000 x g. The supernatant was removed and the pellet was resuspended on
ice in a 1:1 mixture of 400 µL RNA Buffer A (50 mM sodium acetate, pH 5.5; 10 mM
EDTA, pH 8.0; 1% SDS) and 400 µL acidic phenol:chloroform (pH 4.5) (Ambion, TX).
For biofilm samples, biofilm material was scraped off three coupon surfaces using
a cell scraper (Fisher Scientific, NJ) into equal volumes of RNA Buffer A and acidic
phenol:chloroform.
47
RNA Purification
Several methods of RNA purification were attempted, including TRIzol
(Invitrogen, CA), RNA Power Kit for Soils (MoBio, CA) and RNeasy (QIAGEN, MD),
before settling on the following optimized technique.
The phenol mixtures were transferred to Lysing Matrix Tube E (MPBio, OH) and
treated in a FastPrep Bead Beater FP120 (Bio101 Savant, NY) for 30 seconds at 5.5 rpm.
Samples were centrifuged at 4°C for 30 minutes at 14,000 x g.
Phenol was removed using successive chloroform extractions in 2 mL Phase Lock
Gel (PLG) Heavy tubes (Eppendorf, NY). All steps were subsequently performed quickly
and at room temperature. Briefly, the aqueous (top) phase of each sample was transferred
into a prespun (13,000 x g for 2 minutes) PLG Heavy tube to which 200 µL acidic
phenol:chloroform and 200 µL chloroform:isoamyl alcohol (Amresco, OH) were added.
The tubes were inverted gently to mix and incubated on ice for 10 minutes. Tubes were
then centrifuged at 13,000 x g for 5 minutes. A further 400 µL chloroform:isoamyl
alcohol was added, the tube was inverted to mix and centrifuged at 13,000 x g for 5
minutes.
The aqueous phase was then transferred to a new RNase-free tube and finally
treated with TURBO DNase (Ambion, TX). Briefly, a 0.1 volume of 10x TURBO DNase
Buffer was added to the sample followed by the addition of 5 µL TURBO DNase.
Samples were mixed gently by flicking the tubes and incubated at 37°C for 20 minutes.
Activity of the enzyme was inhibited by the addition of 0.1 volumes of resuspended
DNase Inactivation Reagent (Ambion, TX). The sample was incubated at room
48
temperature for 2 minutes with regular, gentle mixing and finally centrifuged at 10,000 x
g for 1 ½ minutes to pellet out the DNase Inactivation Reagent. The supernatant was
transferred to a fresh RNase-free tube.
Finally the sample was cleaned up using a modified protocol of an RNeasy Cleanup Reaction (QIAGEN, MD). Briefly, aliquots of 200 µL RNA were mixed with 700 µL
RLT Buffer (QIAGEN, MD) followed by the addition of 500 µL absolute ethanol.
Volumes of 750 µL were loaded onto an RNeasy Column (QIAGEN, MD) and
centrifuged at room temperature for 15 seconds at 10,000 x g. The eluate was discarded
and subsequent volumes of RNA were loaded onto the same column until all the sample
had been run through. The columns were then washed twice with Buffer RPE (QIAGEN,
MD) and RNA was eluted in two successive 50 µL volumes of RNase-free water. Yield
was determined by spectrometry on a Nanodrop 1000 (Nanodrop Technologies, DE) and
quality assayed with a 2100 Bioanalyzer (Agilent, CA).
DNA Microarray Transcriptional Profiling
RNA was reverse transcribed into cDNA and indirectly labeled according to
SOP#: M007 released by Pathogen Functional Group Research Center (PFGRC), J. Craig
Venter Institute (JCVI) (http://pfgrc.jcvi.org/index.php/microarray/protocols.html).
Briefly, 5 µg RNA was reverse transcribed using SuperScript III (Invitrogen, CA) with a
0.5 mM 5-(3-aminoallyl)-dUTP:dTTP (Sigma, MO) for 18 hours. The optimal ratio of
aa-dUTP to dTTP varies depending on the GC content of the organism in question.
Organisms with high GC content, such as Pseudomonas aeruginosa PAO1 which has a
GC content of 66%, generally require a lower aa-dUTP to dTTP ratio. Organisms with
49
low GC content, such as Streptococcus pyogenes M1 GAS and Bacillus anthracis strain
Sterne which have GC contents of 38% and 35% respectively, usually require a higher
aa-dUTP to dTTP ratio. Since Salmonella Typhimurium LT2 has a GC content of 52%
(compared with the E. coli K12 GC content of 50%), a 2:1 ratio of aa-dUTP:dTTP was
decided on. This first strand cDNA synthesis reaction was stopped and remaining RNA
degraded by alkaline hydrolysis with sodium hydroxide and neutralization with TRIS.
Removal of unincorporated aa-dUTP and free amines was achieved using a
modified protocol from the QIAGEN MinElute PCR purification kit (QIAGEN, MD).
These modifications included the substitution of a 5 mM phosphate wash buffer pH
8.5/80% ethanol for the kit wash buffer and nuclease-free water for the elution buffer.
These substitutions were made to avoid contamination with free amines which compete
with the aa-dUTP in the subsequent Cy-dye coupling reaction.
The clean-up step was followed by drying for 35 minutes at 60°C in a CentriVap
DNA Vacuum Concentrator (Labconco, MO). Dried probes were then indirectly labeled
with Cy3 or Cy5 (Amersham, NJ). Briefly, aminoallyl-labeled cDNA was resuspended in
4.5 µL 0.1 M sodium carbonate buffer, pH 9.3. This was followed by the addition of the
appropriate DMSO-resuspended Cy dye and an incubation of between 1 and 2 hours at
room temperature in the dark. After coupling was complete, 20 µL 4.5 M sodium acetate
pH 5.2 (Ambion, TX) was added. Two important aspects of this step to note include the
thorough resuspension of the dried probe before the addition of the Cy dye as well as
adhering to the prescribed pH 9.3 of the sodium carbonate buffer to ensure optimum
coupling of the aminoallyl-labeled cDNA to the Cy dye ester.
50
Labeled cDNA was purified using the MinElute PCR Purification kit (QIAGEN,
MD) according to manufacturer’s instructions. Analysis was performed to ensure
optimum yield and labeling efficiency using the “Microarray” function of a Nanodrop
1000 (Nanodrop, DE). For each sample, the total picomoles of cDNA synthesized was
determined using the following formula:
μ
324.5
37
/
/μ
1000
/
For each sample the total picomoles of dye incorporation (Cy3 or Cy5) was
determined using the following formula:
3
5
μ
0.15
μ
0.25
And finally, the incorporation ratio of cDNA to dye was determined using the
formula:
#
Theoretically required limits were set at > 800 pmol of dye incorporation per
sample and a dye incorporation ratio of < 20 in order to obtain optimal microarray
hybridizations.
51
Following analysis, the two differentially labeled cDNA’s (Cy3 and Cy5) were
mixed and dried for 35 minutes at 60°C in a CentriVap DNA Vacuum Concentrator
(Labconco, MO). Dried probes were stored at -80°C.
Hybridization was performed according to SOP#: M008
(http://pfgrc.jcvi.org/index.php/microarray/protocols.html) using 70-mer spotted
Salmonella Typhimurium/Typhi Version 5 arrays from the PFGRC, JCVI. These
microarrays were designed on Salmonella enterica serotype Typhimurium LT2,
Salmonella enterica serotype Typhi CT18 and Ty2. Oligonucleotides (single stranded 70mers) were designed based on open reading frame sequences across all three genomes of
the microarray and did not necessarily represent a single oligo from a single strain. The
oligonucleotides were designed to provide coverage across all the organisms used in the
creation of the microarray. The number of open reading frames used in the design of the
microarray were 4553, 4395 and 4323 and the number of oligonucleotide sequences
designed were 4504, 926 and 32 for the LT2, CT18 and Ty2 respectively. This yielded a
total number of oligonucleotide sequences of 5462. Each oligo was replicated four times
on the slides. Additionally, each slide contained 10 Arabidopsis thaliana amplicons and
500 A. thaliana 70-mers as controls. The total number of elements on the array (minus
empty spots) was 23888. The PFGRC Universal Microarray Standard Set was used as an
internal control. These standards consisted of a mix of 1000 Cy-dye end labeled 40-mer
probes (500 Cy3 and 500 Cy5) complementary to the 500 A. thaliana 70-mer control
spots. The control probe mix was routinely spiked into the experimental probe mix
immediately before hybridization to the microarray. Spots associated with the PFGRC
52
Universal Microarray Standard Set have the designation “Atg1” on the annotation sheets
used during data analysis.
Hybridized slides were incubated at 42°C overnight, washed in increasing
stringency buffers and finally scanned using a GenePix 4000B microarray scanner
(Molecular Devices, CA) to generate 2-color 16-bit TIFF images. If slides could not be
scanned immediately, they were stored in the dark in the final high stringency wash
buffer with 10 mM DTT (to act as an ozone scavenger), however it was observed that
storage in this manner only yielded acceptable results for up to 3 hours before washout of
the dye occurred. Five hybridizations were performed from each of three biological
replicate planktonic/biofilm pairs with two of these hybridizations (technical replicates)
being dye swaps (flip dyes), performed as part of overall quality assurance.
Data Analysis
Processing of the 16-bit TIFF images from hybridized arrays was performed with
the TIGR TM4 package (Saeed et al., 2003). Intensity values for Cy3 and Cy5 channels
were obtained using TIGR Spotfinder software. Normalization was performed with the
LOWESS algorithm available in TIGR MIDAS, using the global mode and a smoothing
parameter of 0.33. All intensity values less than two times greater than background were
removed from subsequent analysis, and quadruplicate in-slide replicate intensities on
each slide (considered a further one technical replicate) were reduced to a single value by
computing the geometric mean.
To determine genes whose expression was significantly different from zero,
significance analysis of microarrays (SAM) software (incorporated within the TIGR TM4
53
package) was employed using the one-class response with 8 unique permutations. While
the three biological replicates were used for final analysis, two additional flip dye
technical replicates were also compared to observe any irregularities. None were
observed. Significant genes were determined by setting the number of median falsely
called genes to less than one. At these levels, the q-values (a measure of significance in
terms of the false discovery rate) for all biological replicates were less than 0.1%.
Significantly different genes were then sorted according to the observed score (d) which
represents the relative difference of a gene between the samples.
Each SAM plotsheet contains all the genes plotted by their observed scores and
expected scores. The observed score is the relative difference in gene expression. It is
calculated by dividing the difference between gene relative abundances in the biofilm and
planktonic samples by the pooled standard error of repeated measurements of that gene in
the two samples. The expected score is calculated using the large set of permutations of
gene relative abundance data of the biological replicates from the biofilm and planktonic
samples.
The observed score provides a control over random fluctuation, while the
expected score allows assignment of statistical significance. The correlation of these two
scores is used for identifying genes with potentially significant differential expression. If
a gene has absolutely no differential expression, the observed relative difference would
be the same as the random fluctuation that is represented by the expected score. The data
point of such a gene in the SAM plotsheet would fall on the 45° line through the origin.
Data points representing differentially expressed genes will deviate from this 45° line.
54
The point displacement of a gene from the 45° line through the origin is quantitatively
measured by a delta (Δ) value in SAM. Genes with Δ values beyond a certain threshold
are called significant. The 45° upper and lower Δ lines indicate the boundary defined by a
selected Δ value.
A fold change limit of 1.5 was also applied to significant genes (subsequent to
SAM-applied Δ values) in order to further gauge the magnitude of change. However,
since fold change is somewhat arbitrary, especially when attempting to ascertain
significant biological roles, imposing a typical 2-fold criterion which removes from
consideration a gene with a 1.9 fold change that is really key to a biological mechanism,
could alter the interpretation of a study. Therefore thedata before fold change limits were
applied is the primary data presented.
Expression Analysis Systematic Explorer (EASE) (incorporated within the TIGR
TM4 package) was used on the subset of genes determined to have significant changes in
expression as identified by the SAM analysis. EASE uses a modified Fisher exact test
(EASE score) to estimate the significance of classes of biological function present in a
subset of significant genes relative to the total as represented on the array (Hosack et al.,
2003). TIGR role categories (http://cmr.jcvi.org) determined as part of the whole-genome
annotations of Salmonella enterica serotype Typhimurium LT2, Salmonella enterica
Typhi CT18 and Ty2 were used as the biological classes examined for overrepresentation in the lists of significant genes and for all annotation referred to in this
study. Only biological classes with EASE scores of ≤ 10-3 were determined to be
significant.
55
Results and Discussion
Bacterial Characterization
The environmental isolate of Salmonella used in this work had been isolated from
an outbreak in Gideon, Missouri, USA in 1993 and had originally been typed at the CDC,
Atlanta, Georgia, USA by PFGE. At that time, the CDC was still using non-standardized
nomenclature for Salmonella and they identified that organism as Salmonella serovar
typhimurium. Subsequent phylogenetic analysis (Fig. 8) of PCR-amplification and
sequencing of a portion of the 16S rDNA gene revealed that the strain bore a 99%
homology with various subspecies of S. enterica including S. enterica serotype
Typhimurium, Typhi and Paratyphi as well as S. enterica subsp. arizonae (Table 4).
According to the NCBI Taxonomy Browser, although over 200 serotypes of S. enterica
subsp. enterica are listed, from Aberdeen to Zanzibar, the Missouri isolate has to date not
been deposited within this database.
Table 4. Top six sequences producing significant alignments (NCBI-BLAST) to a 702 bp
sequence obtained by PCR amplifying a portion of the 16S rDNA gene of Salmonella
Missouri (Zhang et al., 2000).
Accession #
AE008820.1
AF332600.1
EU118108.1
EU118101.1
EU118091.1
EU118085.1
Description
Salmonella Typhimurium LT2, section 124 of
220 of the complete genome
Salmonella enterica subsp. enterica 16S
ribosomal RNA gene, partial sequence
Salmonella Typhi strain T1 16S ribosomal
RNA gene, partial sequence
Salmonella enteritidis strain E2 16S
ribosomal RNA gene, partial sequence
Salmonella enterica subsp. enterica serovar
Paratyphi C strain C2 16S ribosomal RNA
gene, partial sequence
Salmonella enterica subsp. enterica serovar
Paratyphi B strain B4 16S ribosomal RNA
gene, partial sequence
Max score
Total
score
Query
coverage
E value
Max ident
1280
1280
100%
0
99%
1279
1279
99%
0
99%
1275
1275
100%
0
99%
1275
1275
100%
0
99%
1275
1275
100%
0
99%
1275
1275
100%
0
99%
56
Figure 8. NCB
BI-BLAST phylogenetic
p
c tree using the
t neighborr-joining alggorithm
inndicating relatedness of Salmonella
S
M
Missouri
(inndicated by query
q
ID lcl|13935) to otther
prrokaryotic organisms
o
baased on a 7022 bp sequencce obtained by
b PCR ampplifying a poortion
of the 16S rD
DNA gene (Z
Zhang et al., 2000).
It is in
nteresting to note that acccording to itts relatednesss based on 16S
1 rDNA
seequence dataa, the Salmonella Missouuri strain borre similarityy to the moree virulent
seerotypes of Salmonella
S
e
enterica,
nam
mely Typhi and
a Paratyphhi. This is noot surprisingg,
57
considering the virulence this pathogen demonstrated during the Gideon outbreak, which
affected about 44% of the town, hospitalizing 15 patients and causing mortality in seven
nursing home residents (Clark et al., 1996).
Subsequent to initial typing by PFGE, the CDC agreed to conform to the
Kauffman-White nomenclature scheme for Salmonella phylogeny, and this isolate was
re-categorized as Salmonella enterica serotype Missouri. It is noteworthy that even such
a subtle change can highlight potential elevation in virulence of a pathogen, considering
that most clinicians do not associate the Salmonella Typhimurium serotype with such
virulent pathology.
In order to characterize the experimental strain further based on growth
characteristics, a standard growth curve (Fig. 9) was performed in M9 minimal media
with 0.4% glucose as a carbon source at ambient temperature (ca. 23°C). The growth rate
was relatively rapid, considering the minimal conditions and low temperature. The
majority of microbiology texts would list Salmonella as having an optimal growth
temperature at 37°C based on the traditional notion that it is an enteric pathogen.
58
0.7
0.6
Absorbance
0.5
0.4
0.3
0.2
0.1
0
0
5
10
15
20
25
Time (hours)
OD600nm Salmonella Missouri
OD600nm Salmonella Typhimurium LT2
Figure 9. Growth curve of Salmonella Missouri (blue) based on absorbance at an optical
density of 600 nm. The growth curve of the ATCC type strain Salmonella enterica
Typhimurium LT2 (red) is shown for comparison.
The doubling time (g) of the strain Salmonella Missouri was determined, using
the specific growth rate from the slope of the exponential portion (µ = 0.0778) of the
growth curve, to be 8.91 hours when grown at ambient temperature in M9 + 0.4%
glucose with constant shaking. The equivalent doubling time for the ATCC type strain
Salmonella Typhimurium LT2 was determined to be 13.84 hours under the same growth
conditions.
ln 2
59
RNA Purification
During attempts to isolate high quality RNA from the biofilm and planktonic
cultures for the microarray experiments, a third, seemingly spurious, band appearing on
agarose gels and in BioAnalyzer electropherograms of total RNA extractions (Fig. 10)
was noticed. Initially it was thought that the purification procedure was causing
degradation of the RNA. However, after multiple attempts at RNA purification via
numerous different methods, as well as the observation that the additional band always
seemed to appear at the same distance relative to the other two bands, older literature was
discovered with a possible explanation.
Figure 10. Electropherogram of Salmonella RNA used to check the quality of purified
nucleic acid. L = 6000 RNA Ladder (Ambion, TX); 7 = purified RNA from
Pseudomonas aeruginosa PAO1; 8 = purified RNA from Salmonella Missouri.
Burgin et al.(1990) discovered novel, approximately 90 bp intervening sequences
(IVSs) within the 23S rRNA genes of Salmonella. These non-rRNA sequences appear to
60
be transcribed and then excised by RNase III during rRNA maturation. The rRNA
fragments that result from the excision of the extra sequences are functional but not
relegated (Mattatall and Sanderson, 1996). This results in fragmented 23S rRNAs. They
showed that the fragmentation patterns can be understood as the result of two breakage
points (at helix-25 and helix-45) in the 23S rRNA. One type of fragmented 23S rRNA
(normally approximately 2.9 kb total) would consist of 0.5 kb and 2.4 kb fragments,
another of 1.2 kb and 1.7 kb fragments (as was regularly observed in this study), and a
third of 0.5 kb, 0.7 kb and 1.7 kb fragments. For this reason, the RNA Integrity Number
(RIN) generated by the BioAnalyzer, usually used to indicate acceptable RNA purity
(DNA- and protein-free) and quality (free from RNase degradation), was inappropriate
for use in this study and is not reported here.
Data Analysis
After normalization and statistical analysis, the total number of significantly
expressed genes was determined to be 857. This equated to 410 up-regulated biofilmassociated genes (11% of 3839 total genes analyzed) and 447 up-regulated planktonicassociated genes (12% of 3839 total genes analyzed). These genes were determined to be
significant by applying a SAM delta (Δ) of 0.86190873, yielding the number of falsely
significant genes (median) as 0.73978, a false discovery rate (FDR) median of 0.08572%
and q-values ≤ 0.1%.
Since the ultimate goal of any molecular microbial ecologist carrying out
transcriptomic studies is to assign biological relevance to a set of gene expression data,
the first iteration of analyses was implanted to determine whether there were any
61
functional role categories into which a significant portion of the expressed genes fell, and
if they were primarily associated with the planktonic or biofilm phenotype. To this end,
the use of the EASE algorithm was implemented. Since the entire genomes of Salmonella
Typhimurium, Typhi CT18 and Typhi Ty2 have been sequenced and mostly annotated,
gene expression data was deciphered into the cellular role categories according to The
Institute of Genomic Research (now called JCVI) Comprehensive Microbial Database
(CMR). Several flaws were noticed in using this annotation scheme, but owing to the fact
that it is the most complete database available, these values herein but are submitted with
the following caveat: of the 3839 total genes available in the dataset, only 2701 have been
annotated and classified (1138 genes have not even been classified into “Unclassified” or
“Unknown function” categories). Similarly, of the 447 significant genes associated with
the planktonic phenotype, only 302 have been annotated and classified; and of the 410
significant genes associated with the biofilm phenotype, only 303 have been annotated
and classified. It is largely for this reason that the EASE scores were uncharacteristically
high for such a global gene expression study (one usually considers EASE scores ≤ 10-3
to be significant for global gene expression studies).
Based on the completely annotated dataset available, it is demonstrated that there
are only minor differences between the functional category breakdowns of the planktonic
and biofilm phenotypes (Fig. 11). Most noticeably, the categories “Energy Metabolism”
and “Protein Fate” were determined to be significant (EASE scores ≤ 10-3) in the biofilm
phenotype while “Unclassified” genes were somewhat important but not significant
(EASE score 7.9 x 10-2). “Amino Acid Biosynthesis” and “Cell Envelope” associated
62
genes were deetermined too be noteworrthy but not significant (EASE scorees 1.2 x 10-3 and
pectively) inn the planktoonic phenotyype.
3.2 x 10-2 resp
Planktonnic
Biofilm
Figure 11. Diistribution off significantlly up-regulaated genes asssigned to fuunctional
caategories of the observedd Salmonellaa Missouri trranscriptome. Functionaal categories are
acccording to the
t JCVI Coomprehensivve Microbial Database (C
CMR) Annottation Schem
me.
V
Values
indicaated are perccentages.
Threee noticeable pathways
p
maaking up thee bulk of the genes in thee “Energy
M
Metabolism”
category weere the 1,2-ppropanediol utilization
u
opperon (pdu),, the H2-evolving
hyydrogenase 3 complex (hyc) and thee NADH dehhydrogenase I operon (nuuo). Althouggh
genes categorrized as “Unnclassified” in
i the biofilm
m phenotypee fell below the
t significaance
thhreshold set for EASE sccores, they were
w almost entirely assoociated with the
63
aforementioned pathways falling in either the “Energy Metabolism” or “Protein Fate”
categories above.
The most abundant genes in the “Energy Metabolism” category were those genes
associated with the 1,2-propanediol utilization operon. Associated genes such as the
tetrathionate reductase complex (ttr), shown to be the terminal electron acceptor in the
anaerobic utilization of 1,2-propanediol, and further pdu and cbi genes were found in the
“Unclassified” category. Collectively these genes encode for a pathway which has
afforded Salmonella tremendous ecological niche advantages over evolutionally-related
E. coli in that Salmonella is able to produce vitamin B12 de novo under anaerobic
conditions and ferment 1,2-propanediol, a breakdown product of the common plant sugar,
rhamnose.
The hyc/hyp operon of Salmonella encodes the H2-evolving hydrogenase 3
complex that, in conjunction with formate dehydrogenase H (fdh), constitutes a
membrane-associated formate hydrogenlyase (FHL) catalyzing the disproportionation of
formate to CO2 and H2 during fermentative growth at low pH. Categorization of this
operon was scattered between the “Energy Metabolism”, “Protein Fate” and
“Unclassified” categories. Several hyc, hyp and fdh genes were found in these categories.
The formate hydrogenlyase reaction is thought to relieve the buildup of reducing
equivalents and, in addition, to offset acidification of growth media during fermentative
growth. Although other hydrogenase isoenzymes are known in Salmonella and are
thought to be involved in the second mode of hydrogen metabolism, namely hydrogen
uptake where hydrogen is oxidized and energy liberated to support anaerobic growth, no
64
evidence that these genes were up-regulated in the biofilm phenotype came from the
EASE analysis.
The membrane-bound NADH dehydrogenase in Salmonella, NADH:ubiquinone
oxidoreductase, is encoded by multiple genes on the nuo operon. Dekkers et al. (1998)
observed a competitive plant root colonization defective mutant of Pseudomonas
fluorescens with a mutation in the nuoD gene homolog. They suggest that NADH
dehydrogenase I plays a role in root colonization in this plant-associated pathogen. More
than half the genes of this operon were significantly expressed in the biofilm phenotype
and fell under the “Energy Metabolism” category identified by EASE analysis.
The “Protein Fate” category contained multiple genes associated with the SPI-2
TTSS, primarily the ssa, ssc and sse genes. Other genes in this category included the
stress response protein chaperones dnaK and hscC.
For the two noteworthy functional categories in the planktonic phenotype, namely
“Amino Acid Biosynthesis” and “Cell Envelope”, the genes did not seem to be highly
related to any one particular pathway. The only exceptions were the rfa and rfb genes
known to be involved in lipopolysaccharide (LPS) O-antigen biosynthesis. LPS has been
extensively studied as one of the main virulence factors of Gram-negative bacteria where
it is a major component of the outer membrane. It consists of three parts: the lipid A,
which is hydrophobic and forms the outer leaflet of the outer membrane bilayer; the core
oligosaccharide; and the O side chain also called the O-antigen. The lipid A part is
responsible for the endotoxin activity and is involved in the interaction of the cell with
the host (Khan et al., 1998). The O-antigen has been shown to function as a barrier
65
against complement mediated lysis (Hackett et al., 1987) and also plays a role in
resistance to killing by the microbiocidal intracellular granules of polymorphonuclear
leukocytes (Stinavage et al., 1989). The lipid A and core are highly conserved structurally
and genetically within a genus. The O-antigen comprises chains of repeat units of either
the same or different sugars and varies considerably among bacterial species with respect
to chemical composition, structure, and antigenicity. The genes directing O-antigen
biosynthesis are clustered mainly in the rfa, rfb and rfc regions of the bacterial
chromosome.
In an attempt to discern further metabolically-related differences, significantly
expressed genes were sorted according to locus position and scanned for clustering
patterns which potentially signified unified operon expression (Sabatti et al., 2002).
Although this technique was not strictly performed according to the Bayesian
classification technique implemented by Sabatti et al. (2002), it did prove to be a useful
analysis method and several additional pathways were identified which the EASE
functional category analysis was unable to resolve.
The first pathway found to be significantly up-regulated in the Salmonella
Missouri biofilm phenotype was the well known central mechanism involved in biofilm
formation through curli and cellulose synthesis via the regulation of CsgD (Fig. 12).
Using the operon-linked expression (OLE) technique, it was confirmed that the csg
operon was highly up-regulated in the biofilm phenotype, including the gene coding the
GGDEF domain-containing protein AdrA. From here, the search parameters were
66
widened to detect operons associated with the synthesis of exopolysaccharides in
Salmonella (refer to Fig. 2).
Figure 12. Expression patterns of genes involved in polysaccharide and curli fimbriae
synthesis. Also included is a gene thought to be associated with cyclic-di-GMP levels in
the cell where this molecule has impact on CsgD regulation. Red bars indicate upregulation during planktonic growth while green bars represent up-regulation during
biofilm growth. The degree of differential expression is shown by the observed d-score as
determined by SAM. The SAM Δ was 0.14365146, false significant genes (median) was
584.05314 and FDR (median) was 18.64198%. Black dividing lines separate genes
occurring within distinct operons. A = succinate dehydrogenase (sdh); B = fructose
bisphosphate aldolase (fba); C = glucose phosphate isomerase and mutase (pgi and pgm
respectively); D = mannose dehydratase (gmd); E = colanic acid synthesis (wca); F =
enterobacterial common antigen and lipopolysaccharide synthesis (wec and rff
respectively); G = cellulose synthesis (yhj or bcs); H = curli subunit genes (csg); I =
agfD-dependent regulator (adrA); J = glycine activity (gly).
67
In contrast to experiments mentioned previously in which Salmonella has been
studied in the biofilm mode of growth where cellulose appears to be the predominant
component of the EPS, it was found that succinate dehydrogenase genes (sdh) in the
tricarboxylic acid cycle and subsequent genes involved in the mannose degradation
pathway, gmd, and synthesis of colanic acid, wca operon, were more highly expressed in
the biofilm. Genes involved in cellulose biosynthesis (bcs or yhj) were primarily upregulated in planktonic cells. These results also confirmed the EASE-identified results
that genes involved in LPS (rfa, rfb and rff) and ECA (wec) were up-regulated in
planktonic cells.
The next major operons examined were those known to be associated with
virulence in Salmonella. It was observed that multiple operons previously shown to be
involved in the initial stages of virulence in murine models, namely the SPI-1, were upregulated in planktonic cells while the virulence genes on SPI-2, involved in systemic
persistence, were up-regulated in the biofilm phenotype (Fig. 13).
68
Figure 13. Changes in levels of gene expression in four Salmonella Pathogenicity Islands
(SPI) and the spv operon on the Salmonella Pathogenicity Plasmid (PSLT). Red bars
indicate up-regulation during planktonic growth while green bars represent up-regulation
during biofilm growth. The degree of differential expression is shown by the observed dscore calculated by SAM. The SAM Δ was 0.14365146, false significant genes (median)
was 584.05314 and FDR (median) was 18.64198%. Black dividing lines separate genes
occurring within distinct operons. A = spv; B = SPI-5; C = SPI-2; D = SPI-1; E = SPI-3.
The OLE search was broadened to include genes on the PSLT (Fig. 14). A
striking predominance (52%) of highly up-regulated genes was observed under
planktonic culture conditions while only 21% of genes on the PSLT were associated with
the biofilm phenotype. Curiously, the spv operon, located on the PSLT and normally coregulated with SPI-2, was up-regulated in the planktonic phenotype (Fig. 13). The
majority of significantly expressed (FDR 0.08572%) genes within the PSLT up-regulated
69
under planktonic growth conditions were associated with DNA replication, plasmid
partitioning and conjugative transfer.
Figure 14. Distribution of gene expression on the Salmonella Pathogenicity Plasmid
(PSLT). Significance was determined by SAM observed d-scores with q-values of less
than 5% (except 4 genes included in the biofilm count and 6 genes included in the
planktonic count). The SAM Δ was 0.14365146, false significant genes (median) was
584.05314 and FDR (median) was 18.64198%. The total number of genes currently
identified on the PSLT is 111. Of these 9 genes are not yet annotated but are included as
insignificant for the sake of completeness.
Possibly the most interesting result discovered using the OLE technique was the
significance of the cbi-cob-pdu operon (Fig. 15). Although it was found some of these
genes using the EASE functional category analysis, most of the genes associated with this
pathway were unaccounted for. Since more than 1% of the entire Salmonella genome is
devoted to genes involved in this pathway, one would expect there to be great importance
of these genes in the survival of this pathogen in the environment. Furthermore, since
Salmonella is likely to spend more of its time associated as a biofilm in the natural
70
environment, one would expect this pathway to be strongly up-regulated in the biofilm
phenotype, as identified here.
2.5
1.5
ttrA
ttrC
ttrB
ttrS
cobT
cobS
cobU
cbiP
cbiO
cbiQ
cbiN
cbiM
cbiL
cbiK
cbiJ
cbiH
cbiG
cbiF
cbiT
cbiE
cbiD
cbiC
cibB
cbiA
pocR
pduF
pduA
pudB
pduC
pduD
pduE
pduG
pduH
pduJ
pduK
pduL
pduM
pduN
pduO
pduP
pduQ
pduS
pduT
pduU
pduV
pduW
pduX
ackA
pta
fucO
fucA
fucP
fucI
fucK
fucU
fucR
prpD
prpE
SAM Observed Score
0.5
B
C
D
E
F
G
‐0.5
‐1.5
‐2.5
‐3.5
A
‐4.5
Figure 15. Gene expression patterns in the 1,2-propanediol utilization operon (pdu),
cobalamin synthesis operon (cbi-cob) and tetrathionate reductase operon (ttr). The
transcriptional regulator pocR and 1,2-propanediol diffusion facilitator pduF are also
included although these genes were not significantly expressed in either the biofilm or
planktonic cultures. Also included are two additional operons encoding enzymes
(phosphotransacetylase propionate kinase and propionyl-CoA synthetase) involved in
1,2-propanediol degradation. Red bars indicate up-regulation during planktonic growth
while green bars represent up-regulation during biofilm growth. The degree of
differential expression is shown by the observed d-score calculated by SAM. The SAM Δ
was 0.14365146, false significant genes (median) was 584.05314 and FDR (median) was
18.64198%. Black dividing lines separate genes occurring within distinct operons. A =
propionyl-CoA synthetase (prp); B = tetrathionate reductase (ttr); C = cobalamin
synthesis (cob-cbi); D = propanediol utilization transcriptional regulator (pocR) and
propanediol diffusion facilitator (pduF); E = propanediol utilization and polyhedral body
formation (pdu); F = housekeeping enzymes; G = L-1,2-propanediol oxidoreductase and
fucose genes (fuc).
71
Using the OLE technique, it was demonstrated that all the genes involved in the
anaerobic utilization of 1,2-propanediol via the cobalamin-dependent reaction were
almost exclusively up-regulated in the biofilm phenotype. These included the pdu genes
with dehydratase activity as well as those involved in polyhedral body formation; the cbicob vitamin B12 adenosyl cobalamide precursor biosynthetic genes; the prp putative
acetyl-CoA synthetase genes; the ttr tetrathionate reductase genes involved in making
tetrathionate available as an electron acceptor through the reduction to thiosulfate; and
housekeeping genes ackA and pta. It was not demonstrated that the transcriptional
regulators pocR and pduF were significantly expressed under either growth condition. In
addition, several of the key genes involved in the ethanolamine (eut) degradation
pathway were up-regulated (data not shown) as were genes in the fucose-related (fuc)
operon.
Conclusions
In the current study, a full genome transcriptional analysis of an environmental
isolate, Salmonella enterica serotype Missouri, was undertaken to determine whether
significant gene expression pattern differences could be identified between the biofilm
and planktonic phenotypes. Previous studies have indicated that Salmonella is
successfully able to regulate its response to environmental fluxes by altering
transcriptional control of discreet biochemical and physiological pathways (Adkins et al.,
2006). In particular, the response to changing conditions during host infection has been
studied and several key pathways have been identified as being central to Salmonella’s
pathogenicity and ability to survive within the host and persist under adverse conditions
72
(Bajaj et al., 1996; Hautefort et al., 2008). However, the lifecycle of Salmonella is not
limited to host infections and this pathogen has demonstrated a ubiquitous nature within
the environment. And although Salmonella is classified within the Enterobacteriaceae,
this pathogen appears to spend a major portion of its existence in non-host environments
(Labrousse et al., 2000; Pagnier et al., 2008; Tezcan-Merdol et al., 2004) and has
developed several key traits which allow it to persist and grow under potentially stressful
conditions (Leriche and Carpentier, 1995; Reissbrodt et al., 2002; Smith and Oliver,
2006).
Salmonella Missouri was the pathogenic agent responsible for an outbreak of
waterborne salmonellosis in Gideon, MO during the Christmas of 1993 (Clark et al.,
1996). This pathogen demonstrated tenacious pathogenicity, causing illness in over 40%
of the population and mortality in 7 people. An epidemiological study determined that the
source of contamination was an uncovered water storage tank which had been
contaminated by pigeon stool. That this pathogen was able to survive in the drinking
water distribution system and cause infection over several weeks is evidence of its
adaptation to survive in certain ecological niches.
It was observed that this strain of Salmonella exhibited a rapid growth rate under
minimal, suboptimal growth conditions and that it was able to establish an observable
biofilm in overnight cultures, a trait not usually observed in typically less virulent enteric
pathogens (Andersson et al., 2008; Mohamed et al., 2007). On subsequent transcriptional
analysis of this organism grown either as a planktonic or biofilm culture, distinct patterns
73
were observed which may explain the ability of this organism to survive in the non-host
environment.
Initial analysis using EASE to distinguish biologically relevant pathways in the
two phenotypes was not particularly useful owing to the apparent inability of the EASE
algorithm to resolve important functional categories in Salmonella. This may be due to
the large number of genes on the Salmonella genome which have yet to be assigned to
descriptive functional categories. Although the microarray used in this study was based
on the combined annotated genomes of Salmonella Typhimurium LT2 and Salmonella
Typi CT18 and Ty2, there is still 5.92%,
7.93% and 4.51% respectively of each of
the genomes which have not yet been assigned to functional categories (not even
“Unclassified” or “Unknown function”). Nevertheless, the observation that the genes
within the categories “Energy Metabolism”, “Protein Fate” and “Unclassified” were for a
large part interrelated, and this method served as a launchpad for analysis.
Most interesting was the observation that the 1,2-propanediol utilization pathway
was strongly up-regulated in the biofilm phenotype. This pathway has been the subject of
several studies (Bobik et al., 1999; Chen et al., 1994; Jeter, 1990; Obradors et al., 1988;
Roth et al., 1996) and has been suggested to confer strategic niche advantage to this
pathogen in terms of outcompeting natural host intestinal flora and survival in the
fermentative environment of the gut (Korbel et al., 2005; Scott et al., 2006). In addition,
the ability of an organism to utilize this breakdown product of the ubiquitous plant sugar,
rhamnose, as the sole carbon and energy source under anaerobic conditions may reflect
an important survival strategy in the non-host environment. However, since the only
74
carbon source made available in these experiments was glucose, it is suggested that
Salmonella Missouri has the ability to convert glucose to 1,2-propanediol via glycolysis
(Altaras et al., 2001; Cameron et al., 1998; Ros and Aguilar, 1985) under the largely
anaerobic conditions of the biofilm (Costerton et al., 1994; De Beer and Stoodley, 2006).
Evidence for this glucose to 1,2-propanediol conversion may be demonstrated by the upregulation of the fuc operon which includes genes responsible for encoding a propanediol
oxidoreducatse and some of the eut operon, highly similar to the pdu operon in that it
encodes a carboxysome-like structure to protect the cell from acetaldehyde during the
fermentation of ethanolamine (Price-Carter et al., 2001; Starai et al., 2005).
Furthermore, the apparent co-evolution of the pdu and eut operons with the ability
of Salmonella to synthesize vitamin B12 de novo under anaerobic conditions may
represent a further important niche advantage (Roth et al., 1996; Sampson and Bobik,
2008). Biofilms also represent a competitive strategy by microbes in the environment
(Boe-Hansen et al., 2002; Esteves et al., 2005). Taken together with the observations that
these operons were significantly up-regulated in the biofilm phenotype strongly suggests
that Salmonella has developed the ability to form a biofilm in the environment and may
outcompete other microbes including the closely-related E. coli by accessing specialized
biochemical pathways for carbon utilization.
Although by no means involved in biofilm-exclusive physiology, that an almost
complete complement of hydrogenase 3 (hyc/hyp) complex was expressed in the biofilm
phenotype indicates the advantage of this energy-generating complex. In addition, since
the buildup of reducing equivalents and acidification in microniches in the biofilm may
75
represent disastrous consequences for the microbe, the ability of hydrogenase to mitigate
this stress may be highly beneficial. Biocorrosion as a result of hydrogenase activity in
biofilm communities has been reported (Vignais and Colbeau, 2004). Since Salmonella
has been conclusively demonstrated to inhabit aquatic environments and be entrained in
biofilms in drinking water distribution systems (Camper et al., 1998) and wastewater
treatment plants (Berge et al., 2006), this biocorrosion aspect of its physiology may
represent another area of necessary investigation.
Similarly, the orchestrated expression of NADH dehydrogenase I (nuo) genes
may represent an important biofilm-associated feature of Salmonella physiology and
virulence. Since it has been demonstrated that nuo plays a critical role in biofilm
formation and virulence of the plant pathogen, Pseudomonas fluorescens (Carvajal et al.,
2002), it is suggest that Salmonella may also use this energy-generating oxidoreductase
to promote its survival in the biofilm phenotype in the non-host environment.
Corroboratory data that may be viewed as confirmation of the effectiveness of this
microarray study to elucidate pathways within the biofilm and planktonic phenotypes
come from the observations of the up-regulation of the csgD gene and related pathways.
Far and away the bulk of genetic studies carried out on Salmonella biofilms have
centered around the activity of this gene and related operon (Brombacher et al., 2006; Da
Re and Ghigo, 2006; Gerstel and Romling, 2003; Gibson et al., 2006; Kader et al., 2006;
Latasa et al., 2005; Prigent-Combaret et al., 2001). That the up-regulation of this operon
during biofilm growth of Salmonella Missouri was observed confirms its almost global
relatedness to the biofilm phenotype. However, more interesting was the fact that the
76
expression of cellulose synthetic genes were not observed in the biofilm phenotype but
rather in the planktonic cultures of Salmonella Missouri, indicating that perhaps in this
strain of the pathogen, cellulose may not be the predominant component of EPS in the
biofilm matrix. This was further demonstrated when the search for known EPS matrix
components was broadened and the up-regulation of genes in the mannose and colanic
acid operons was demonstrated. This may be understood in the context of a pH-related
shift, colanic acid being more stable under conditions found in the gastrointestinal tract
than cellulose (Mao et al., 2006).
Although no assays for cyclic-di-GMP levels in the cells growing in the two
different phenotypes were performed, it is suggested that cyclic-di-GMP levels were
elevated in the biofilm cells. This is based on current opinions in the biofilm literature
(Romling and Amikam, 2006; Tamayo et al., 2007) and the fact that the up-regulation of
adrA which encodes a GGDEF domain protein was observed.
The significantly observed “Protein Fate” category in EASE analysis of the TIGR
biological roles contained several proteins which are located on the SPI-2, namely those
effector and structural proteins associated with the second TTSS in Salmonella. In vivo,
this pathogenicity island has been demonstrated to enhance persistence of the pathogen
and establish systemic infection. Mutational analysis has revealed that knockouts within
this island attenuate virulence and the infection was cleared by the immune system more
rapidly than in wild-type infections (Cirillo et al., 1998; Rytkonen et al., 2007).
Furthermore, several aspects of the establishment of a systemic infection reflect the
biofilm lifestyle, including protection from oxidative stress, competition for limiting
77
nutrients such as iron and magnesium, and long-term survival. It is suggested that
perhaps this horizontally-acquired pathogenicity island may confer more than simply a
virulence ability upon Salmonella within the host. Considering the metabolic tax involved
in expressing this pathway, and the space occupied on the genome by this suite of genes,
it is unlikely that Salmonella has maintained functionality of this complex exclusively for
its survival in the host environment. Rather it is conceivable that there is a multipurpose
usefulness for this island. Tezcan-Merdol et al. (2004) showed that while hilA, a key
regulator in SPI-1-mediated invasion, was not required to establish persistence of
Salmonella in Acanthamoeba rhysodes, they suggest that SPI-2 may play a role in
survival in the amoeba. More directly, Labrousse et al. (2000) have demonstrated that
SPI-2 does plays a role in the ability of Salmonella to exist within the model host
Caenorhabditis elegans, where the pathogen forms a biofilm-like structure in the
intestine and terminal bulb of the pharynx of the nematode. In addition, Chakravortty et
al. (2002) demonstrated that SPI-2 played a direct role in protecting Salmonella from the
deleterious effects of reactive nitrogen intermediates synthesized by inducible nitric oxide
synthase and which are involved in the control of intracellular pathogens, including
Salmonella. Furthermore, localization of nitrotyrosine residues in the surroundings was
observed for SPI-2 mutant strains but not wild-type Salmonella, indicating that
peroxynitrite, a potent antimicrobial compound, is excluded from Salmonella-containing
vacuoles (SCV) by action of SPI-2. Since Salmonella may encounter similar reactive
nitrogen intermediates in the natural environment as well as in food processing plants
where nitric oxide is gaining popularity as a preservative (Fan et al., 2008), and
78
considering that the results show SPI-2 up-regulated in the biofilm phenotype, an
intrinsically recalcitrant lifestyle for any pathogen, this may prove to be an interesting
niche adaptation worth future study.
Concomitantly with the expression of SPI-2 in the biofilm phenotype, expression
of other pathogenicity islands (SPI-1, -3 and -5) in the planktonic phenotype was
observed. Since the primary function of SPI-1 during host infection is to attach to and
invade epithelial cells lining the gut, intuition would suggest that this set of genes would
be more likely expressed in the biofilm phenotype. However, it may be that these genes
were switched on under the iron-limiting conditions of the M9 minimal media and are not
necessarily a true planktonic phenotype expression. An alternative explanation is that
SPI-1 effector proteins may play a tactic role in Salmonella, aiding in locating a suitable
attachment surface. Curiously, the spv operon which is usually concomitantly expressed
with SPI-2, was up-regulated in the planktonic phenotype, while the SPI-2 was downregulated. However, too little is still known about this operon to comment on its
biological significance (Tezcan-Merdol et al., 2007).
In conclusion, this transcriptional study of Salmonella Missouri in the biofilm and
planktonic phenotypes may reveal an accurate representation of the behavior of a virulent
isolate of Salmonella in the non-host environment. The identification of some of the key
biological pathways characterizing the biofilm phenotype of Salmonella may hold clues
to better understanding the ability of this pathogen to survive in the environment and
persist outside of the host for long periods of time, competing for nutrients, dealing with
79
oxidative stress and overcoming predation, all of which mirror similar traits demonstrated
by this organism in establishing infection in the human host.
80
CHAPTER 4
A TRANSCRIPTIONAL COMPARISON OF SALMONELLA TYPHIMURIUM LT2
AND AN ENVIRONMENTAL ISOLATE OF SALMONELLA ENTERICA
Introduction
The recent surge of Salmonella outbreaks in the United States associated with
improperly handled foodstuffs has highlighted the need for more research into the
environmental reservoirs, lifestyle and survival of this pathogen (Kaye, 2008;
McDonough et al., 1999). Several divisions within the National Institute of Allergy and
Infectious Diseases (NIAID) currently support programs under the banner “emerging
infectious diseases” (EIDs). Emerging diseases include outbreaks of previously unknown
diseases or known diseases whose incidence in humans has significantly increased in the
past two decades. Re-emerging diseases are known diseases that have reappeared after a
significant decline in incidence. Re-emergence may be due to several factors including
the development of multidrug resistance by the pathogen and human behavior in terms of
reckless regard for the environment (Vidaver, 1996). In the NIAID strategic plan (2008),
NIAID: Planning for the 21st Century, it was documented that NIAID had recently joined
with several other US Government agencies to support research on the relationship
between man-made environmental changes and transmission of infectious diseases. The
intent was that future NIAID-supported studies would focus on whole-genome
approaches to pathogen research, including large-scale sequencing, bioinformatics and
functional genomics. Such investigations would hopefully provide tools critical to the
81
study of microbial evolution, adaptation and pathogenicity. Salmonella is listed as one of
these re-emerging infections
(http://www3.niaid.nih.gov/research/topics/emerging/list.htm) and the primary focus of
most of this research is in keeping with the NIAID directive to understand the
pathobiology of Salmonella within the context of the non-host environment.
Interest in comparing the well-studied and characterized ATCC type strain of
Salmonella enterica serotype Typhimurium LT2 with a closely related environmental
isolate Salmonella enterica serotype Missouri arose from observations of the differences
in growth behavior of the two organisms. In addition, current thinking suggests that
frequently passaged laboratory reference strains might have lost important
pathophysiological characteristics and therefore might be inadequate to document ‘realworld’ pathogenesis (Fux et al., 2005; Nilsson et al., 2004; Somerville et al., 2002).
Furthermore, the close link between horizontal gene transfer and biofilm formation is
being increasingly recognized (Schwartz et al., 2003). These observations of impaired
biofilm formation by laboratory reference strains compared with clinical strains might
indicate further-reaching genetic alterations affecting bacterial virulence on a broader
level.
Materials and Methods
Strains and Growth
The strains of Salmonella used in this study were the ATCC type strain No.
700720, Salmonella enterica serotype Typhimurium LT2 and an environmental isolate
from an outbreak in Gideon, MO, USA in 1993 (Clark et al., 1996). The latter was a
82
highly virulent strain of Salmonella enterica, typed by PGFE at the CDC in Atlanta, GA,
USA and has been designated Salmonella Missouri in this paper. Sequence analysis of
the 16S rDNA gene was also performed (Research Technology Support Facility,
Michigan State University using a Perkin Elmer/Applied Biosystems 3100 capillary
sequencer) to confirm the identities of both these organisms. Primers used to amplify a
highly conserved region of the 16S rDNA gene covered an area of approximately 1500
base pairs. These primers have been used regularly in this lab and are designated 8F and
1492R (Burr et al., 2006).
Planktonic growth rates were determined in M9 Minimal Media (BectonDickinson, MD) with the addition of 0.4% glucose (Fisher Scientific, NJ) as the carbon
source (Ren et al., 2005). This was the defined medium used in all subsequent
experiments unless otherwise indicated. All cultures, both planktonic and biofilm, were
grown at an ambient temperature of 23°C. For each new experiment, the relevant strain of
Salmonella was freshly prepared from a cryostock which had been maintained at -80°C
with minimal passaging.
In order to determine growth rates, a starter culture of the organism was prepared
by inoculating an overnight colony grown on XLD agar (EMD, NJ) into 100 mL volumes
of M9 + glucose in 250 mL baffled flasks (Pyrex, USA) with orbital shaking of 180 rpm.
These starter cultures were allowed to grow up for 24 hours at which point 100 µL was
inoculated into 100 mL fresh media in a 250 mL Nephelo flask (Wheaton, USA) and
these flasks were returned to the orbital shaking platform at 180 rpm. Optical density was
83
determined every 4 hours using a Spectronic 20D+ spectrophotometer (Thermo Electron
Corporation, MA) reading at a wavelength of 600 nm.
Planktonic cultures were grown under the same conditions as used in determining
experimental growth rates. For microarray experiments, cultures were harvested at 12
hours (empirically determined to be mid- to late-logarithmic phase for both strains of
Salmonella).
Biofilm cultures of each of the strains of Salmonella were obtained using the
CDC biofilm reactor (www.biofilms.biz) with glass coupons serving as surfaces for
attachment. CDC reactors were preconditioned with sterile M9 + glucose for 24 hours in
batch mode to ensure sterility of the media and equipment. An inoculum of 1mL
Salmonella grown up as described previously for the preparation of a growth curve
experiment was aseptically introduced through a rubber injection septum and an 18 hour
batch mode was allowed in order to facilitate establishment of the culture in the reactor.
This period of batch growth was followed by switching on the pump and allowing fresh
media to flow into the reactor with a hydraulic retention time of 7.6 hours to ensure that
planktonic bacteria were washed out and the biofilm bacteria predominated.
Biomass Harvesting
For planktonic samples, 50 mL of a 12 hour culture was centrifuged at 4°C for 10
minutes at 10,000 x g. The supernatant was removed and the pellet was resuspended on
ice in a 1:1 mixture of 400 µL RNA Buffer A (50 mM sodium acetate, pH 5.5; 10 mM
EDTA, pH 8.0; 1% SDS) and 400 µL acidic phenol:chloroform (pH 4.5) (Ambion, TX).
84
For biofilm samples, biofilm material was scraped off three coupon surfaces
using a cell scraper (Fisher Scientific, NJ) into equal volumes of RNA Buffer A and
acidic phenol:chloroform.
RNA Purification
Several methods of RNA purification were attempted, including TRIzol
(Invitrogen, CA), RNA Power Kit for Soils (MoBio, CA) and RNeasy (QIAGEN, MD),
before settling on the following optimized technique.
The phenol mixtures were transferred to Lysing Matrix Tube E (MPBio, OH) and
treated in a FastPrep Bead Beater FP120 (Bio101 Savant, NY) for 30 seconds at 5.5 rpm.
Samples were centrifuged at 4°C for 30 minutes at 14,000 x g.
Phenol was removed using successive chloroform extractions in 2mL Phase Lock
Gel (PLG) Heavy tubes (Eppendorf, NY). All steps were subsequently performed quickly
and at room temperature. Briefly, the aqueous (top) phase of each sample was transferred
into a prespun (13,000 x g for 2 minutes) PLG Heavy tube to which 200 µL acidic
phenol:chloroform and 200 µL chloroform:isoamyl alcohol (Amresco, OH) was added.
The tubes were inverted gently to mix and incubated on ice for 10 minutes. Tubes were
then centrifuged at 13,000 x g for 5 minutes. A further 400 µL chloroform:isoamyl
alcohol was added, the tube was inverted to mix and centrifuged at 13,000 x g for 5
minutes.
The aqueous phase was then transferred to a new RNase-free tube and finally
treated with TURBO DNase (Ambion, TX). Briefly, a 0.1 volume of 10x TURBO DNase
Buffer was added to the sample followed by the addition of 5 µL TURBO DNase.
85
Samples were mixed gently by flicking the tubes and incubated at 37°C for 20 minutes.
Activity of the enzyme was inhibited by the addition of 0.1 volumes of resuspended
DNase Inactivation Reagent (Ambion, TX). The sample was incubated at room
temperature for 2 minutes with regular, gentle mixing and finally centrifuged at 10,000 x
g for 1 ½ minutes to pellet out the DNase Inactivation Reagent. The supernatant was
transferred to a fresh RNase-free tube.
Finally the sample was cleaned up using a modified protocol of an RNeasy Cleanup Reaction (QIAGEN, MD). Briefly, aliquots of 200 µL RNA were mixed with 700 µL
RLT Buffer (QIAGEN, MD) followed by the addition of 500 µL absolute ethanol.
Volumes of 750 µL were loaded onto an RNeasy Column (QIAGEN, MD) and
centrifuged at room temperature for 15 seconds at 10,000 x g. The eluate was discarded
and subsequent volumes of RNA were loaded onto the same column until all the sample
had been run through. The columns were then washed twice with Buffer RPE (QIAGEN,
MD) and RNA was eluted in two successive 50 µL volumes of RNase-free water. Yield
was determined by spectrometry on a Nanodrop 1000 (Nanodrop Technologies, DE) and
quality was assayed by a 2100 Bioanalyzer (Agilent, CA).
DNA Microarray Transcriptional Profiling
RNA was reverse transcribed into cDNA and indirectly labeled according to
SOP#: M007 released by PFGRC, JCVI
(http://pfgrc.jcvi.org/index.php/microarray/protocols.html). Briefly, 5 µg RNA was
reverse transcribed using SuperScript III (Invitrogen, CA) with a 0.5 mM 5-(3aminoallyl)-dUTP:dTTP (Sigma, MO) for 18 hours. The optimal ratio of aa-dUTP to
86
dTTP varies depending on the GC content of the organism in question. Organisms with
high GC content, such as Pseudomonas aeruginosa PAO1 which has a GC content of
66%, generally require a lower aa-dUTP to dTTP ratio. Organisms with low GC content,
such as Streptococcus pyogenes M1 GAS and Bacillus anthracis strain Sterne which have
GC contents of 38% and 35% respectively, usually require a higher aa-dUTP to dTTP
ratio. Since Salmonella Typhimurium LT2 has a GC content of 52% (compared with the
E. coli K12 GC content of 50%), 2:1 ratio of aa-dUTP:dTTP was decided upon. This first
strand cDNA synthesis reaction was stopped and remaining RNA degraded by alkaline
hydrolysis with sodium hydroxide and neutralization with TRIS.
Removal of unincorporated aa-dUTP and free amines was achieved using a
modified protocol from the QIAGEN MinElute PCR purification kit (QIAGEN, MD).
These modifications included the substitution of a 5 mM phosphate wash buffer pH
8.5/80% ethanol for the kit wash buffer and nuclease-free water for the elution buffer.
These substitutions were made to avoid contamination with free amines which compete
with the aa-dUTP in the subsequent Cy-dye coupling reaction.
The clean-up step was followed by drying for 30 minutes at 60°C in a CentriVap
DNA Vacuum Concentrator (Labconco, MO). Dried probes were then indirectly labeled
with Cy3 or Cy5 (Amersham, NJ). Briefly, aminoallyl-labeled cDNA was resuspended in
4.5 µL 0.1 M sodium carbonate buffer, pH 9.3. This was followed by the addition of the
appropriate DMSO-resuspended Cy dye and an incubation of between 1 and 2 hours at
room temperature in the dark. After coupling was complete, 20 µL 4.5 M sodium acetate
pH 5.2 (Ambion, TX) was added. Two important aspects of this step to note include the
87
thorough resuspension of the dried probe before the addition of the Cy dye as well as
adhering to the prescribed pH 9.3 of the sodium carbonate buffer to ensure optimum
coupling of the aminoallyl-labeled cDNA to the Cy dye ester.
Labeled cDNA was purified using the MinElute PCR Purification kit (QIAGEN,
MD) according to manufacturer’s instructions. Analysis was performed to ensure
optimum yield and labeling efficiency using the “Microarray” function of a Nanodrop
1000 (Nanodrop, DE). For each sample, the total picomoles of cDNA synthesized was
determined using the following formula:
μ
324.5
37
/
/μ
1000
/
For each sample the total picomoles of dye incorporation (Cy3 or Cy5) was
determined using the following formula:
3
5
μ
0.15
μ
0.25
And finally, the incorporation ratio of cDNA to dye was determined using the
formula:
#
88
Theoretically required limits were set at > 800 pmol of dye incorporation per
sample and a dye incorporation ratio of < 20 in order to obtain optimal microarray
hybridizations.
Following analysis, the two differentially labeled cDNA’s (Cy3 and Cy5) were
mixed and dried for 30 minutes at 60°C in a CentriVap DNA Vacuum Concentrator
(Labconco, MO). Dried probes were stored at -80°C.
Hybridization was performed according to SOP#: M008
(http://pfgrc.jcvi.org/index.php/microarray/protocols.html) using 70-mer spotted
Salmonella Typhimurium/Typhi Version 5 arrays from the PFGRC, JCVI. These
microarrays were designed on Salmonella enterica serotype Typhimurium LT2,
Salmonella enterica serotype Typhi CT18 and Ty2. Oligonucleotides (single stranded 70mers) were designed based on open reading frame sequences across all three genomes of
the microarray and did not necessarily represent a single oligo from one particular strain.
The oligonucleotides were designed to provide coverage across all the organisms used in
the creation of the microarray. The number of open reading frames used in the design of
the microarray were 4553, 4395 and 4323 and the number of oligonucleotide sequences
designed were 4504, 926 and 32 for LT2, CT18 and Ty2 respectively. This yielded a total
number of oligonucleotide sequences of 5462. Each oligo was replicated four times on
the slides. Additionally, each slide contained 10 Arabidopsis thaliana amplicons and 500
A. thaliana 70-mers as controls. The total number of elements on the array (minus empty
spots) was 23888. The PFGRC Universal Microarray Standard Set was used as an
internal control. These standards consisted of a mix of 1000 Cy-dye end labeled 40-mer
89
probes (500 Cy3 and 500 Cy5) complementary to the 500 A. thaliana 70-mer control
spots. The control probe mix was routinely spiked into the experimental probe mix
immediately before hybridization to the microarray. Spots associated with the PFGRC
Universal Microarray Standard Set have the designation “Atg1” on the annotation sheets
used during data analysis. Hybridized slides were incubated at 42°C overnight, washed in
increasing stringency buffers and finally scanned using a GenePix 4000B microarray
scanner (Molecular Devices, CA) to generate 2-color 16-bit TIFF images. If slides could
not be scanned immediately, they were stored in the dark in the final high stringency
wash buffer with 10 mM DTT (to act as an ozone scavenger), however it was observed
that storage in this manner only yielded acceptable results for up to 3 hours before
washout of the dye occurred. Five hybridizations were performed for each of the
Salmonella strains. Three hybridizations were biological replicate planktonic/biofilm
pairs and two hybridizations (technical replicates) were dye swaps (flip dyes), performed
as part of overall quality assurance.
Data Analysis
Processing of the 16-bit TIFF images from hybridized arrays was performed with
the TIGR TM4 package (Saeed et al., 2003). Intensity values for Cy3 and Cy5 channels
were obtained using TIGR Spotfinder software. Normalization was performed with the
LOWESS algorithm available in TIGR MIDAS, using the global mode and a smoothing
parameter of 0.33. All intensity values less than two times greater than background were
removed from subsequent analysis, and quadruplicate in-slide replicate intensities on
90
each slide (considered a further one technical replicate) were reduced to a single value by
computing the geometric mean.
To determine genes whose expression was significantly different from zero,
significance analysis of microarrays (SAM) software (incorporated within the TIGR TM4
package) was employed using the one-class response with 8 unique permutations. This
analysis was performed separately for each of the two individual strains. While the three
biological replicates were used for final analysis, two additional flip dye technical
replicates were also compared to observe any irregularities. None were observed.
Significant genes were determined by setting the number of median falsely called genes
to less than one and choosing similar false discovery percentage medians for each
biological replicate. At these levels, the q-values (a measure of significance in terms of
the false discovery rate) for all biological replicates were less than 0.1%. In order to
determine subsets of shared or different genes between the two strains (Salmonella
Missouri and Salmonella Typhimurium LT2) and in the two conditions (biofilm and
planktonic), the intersection function was used on significantly expressed clusters in
TMEV (Saeed et al., 2003) and generated Venn Diagrams using Venny (Oliveros, 2007).
Each SAM plotsheet contains all the genes plotted by their observed scores and
expected scores. The observed score is the relative difference in gene expression. It is
calculated by dividing the difference between gene relative abundances in the biofilm and
planktonic samples by the pooled standard error of repeated measurements of that gene in
the two samples. The expected score is calculated using the large set of permutations of
91
gene relative abundance data of the biological replicates from the biofilm and planktonic
samples.
The observed score provides a control over random fluctuation, while the
expected score allows assignment of statistical significance. The correlation of these two
scores is used for identifying genes with potentially significant differential expression. If
a gene has absolutely no differential expression, the observed relative difference would
be the same as the random fluctuation that is represented by the expected score. The data
point of such a gene in the SAM plotsheet would fall on the 45° line through the origin.
Data points representing differentially expressed genes will deviate from this 45° line.
The point displacement of a gene from the 45° line through the origin is quantitatively
measured by a delta (Δ) value in SAM. Genes with Δ values beyond a certain threshold
are called significant. The 45° upper and lower Δ lines indicate the boundary defined by a
selected Δ value.
A fold change limit of 1.5 was also applied to significant genes (subsequent to
SAM-applied Δ values) in order to further gauge the magnitude of change. However,
since fold change is somewhat arbitrary, especially when attempting to ascertain
significant biological roles, imposing a typical 2-fold criterion which removes from
consideration a gene with a 1.9 fold change that is really key to a biological mechanism,
could alter the interpretation of a study. Therefore data before fold change limits were
applied is primarily reported.
Expression Analysis Systematic Explorer (EASE) (incorporated within the TIGR
TM4 package) was used on subsets of genes determined to have significant changes in
92
expression as identified by the SAM analysis. EASE uses a modified Fisher exact test
(EASE score) to estimate the significance of classes of biological function present in a
subset of significant genes relative to the total as represented on the array. TIGR role
categories (http://cmr.jcvi.org) determined as part of the whole-genome annotations of
Salmonella enterica serotype Typhimurium LT2, Salmonella enterica Typhi CT18 and
Ty2 were used as the biological classes examined for over-representation in the lists of
significant genes and for all annotation referred to in this study. Although only biological
classes with EASE scores of ≤ 10-3 are considered significant, all results are reported for
completeness.
Results and Discussion
The ATCC type strain Salmonella enterica serotype Typhimurium LT2 was first
isolated in Sweden by Lilleengen (1948). Since then, it has been kept in culture at the
American Type Culture Collection (VA, USA).
Figure 16. Photographs of overnight planktonic cultures of Salmonella Missouri (left) and
Salmonella Typhimurium LT2 (right). Notice the flocculation ring in the flask with the
Missouri isolate.
93
Soon after first receiving the Salmonella Missouri isolate and culturing it in the
lab during various experiments, it was noticed that it behaved with a marked difference
from the ATCC type strain, Salmonella Typhimurium LT2, that this lab and most other
researchers use in their work. Primarily, an increased growth rate was noticed (Fig. 17) at
various temperatures and on different media (data not shown), and the flocculation
behavior of the bacteria in liquid culture. Routinely during overnight growth in broth, a
distinct “scum” ring (Fig. 16) around the inside of the flask in which the bacteria were
being cultured was observed. This phenomenon was never observed with Salmonella
Typhimurium LT2.
0.8
0.7
0.6
Absorbance
0.5
0.4
0.3
0.2
0.1
0
0
5
10
15
20
25
Time (hours)
OD600nm Salmonella Missouri
OD600nm Salmonella Typhimurium LT2
Figure 17. Growth curves of Salmonella Typhimurium LT2 and Salmonella Missouri
based on absorbance at an optical density of 600nm.
94
This flocculation effect was observed in liquid cultures grown in tryptic soy broth,
Luria broth, Rappaport Vassiliadis broth and M9 minimal media. Since this same effect
had been observed previously with dynamic biofilm-forming bacteria (such as
Pseudomonas aeruginosa PAO1 and Staphylococcus aureus), side by side comparisons
of Salmonella Typhimurium LT2 and Salmonella Missouri in CDC biofilm reactors were
set up. The results, revealing a thick biofilm formed by the Missouri isolate versus only a
thin film by the type strain, prompted the remainder of this study.
Despite the fact that the CDC had initially typed the Missouri isolate via PFGE as
Salmonella typhimurium, preliminary observations suggested distinct differences between
this isolate and the ATCC type strain Salmonella Typhimurium LT2 with which this lab
had worked previously. Subsequently, analysis of 16S rDNA sequence data from the two
strains suggested that the Missouri isolate was more closely related to Salmonella Typhi
and Paratyphi serotypes (Table 4). Through whole genome transcriptomics, it was shown
that in fact when the two organisms were cultured under the same conditions (either
biofilm or planktonic), there were distinct differences in gene regulation. In fact, fewer
than half the genes significantly up-regulated in either the biofilm (39% and 33%
respectively) or planktonic (42% and 29% respectively) phenotypes were shared between
Salmonella Missouri and Salmonella Typhimurium LT2 (Fig. 18).
Of the significantly up-regulated genes in each of the strains under each growth
condition, 55 were diametrically expressed in the planktonic Salmonella Typhimurium
LT2 and biofilm Salmonella Missouri cultures while 41 were diametrically expressed in
the juxtaposed position (Fig. 18).
95
Unique populations of up-regulated genes were also observed: 161 and 170 genes
in the planktonic and biofilm growth phenotypes respectively for Salmonella Missouri;
and 307 and 249 genes in the planktonic and biofilm growth phenotypes respectively for
Salmonella Typhimurium LT2 (Fig. 18).
Figure 18. Venn diagram showing significantly up-regulated genes in Salmonella
Missouri during planktonic growth (blue) and biofilm growth (green) and in Salmonella
Typhimurium LT2 during planktonic growth (yellow) and biofilm growth (red). Total upregulated Salmonella Missouri genes: Biofilm = 368, Planktonic = 347. Total Upregulated Salmonella Typhimurium LT2 genes: Biofilm = 433, Planktonic = 507.
In order to ascertain whether there were any significantly different biological
themes associated with the uniquely expressed genes for each of the strains in each
96
growth condition, the EASE algorithm was used (Table 5). “Mobile and chromosomal
element functions” emerged as a significant role category for biofilm-oriented Salmonella
Typhimurium LT2 cells while “Protein synthesis” emerged as significant for the
planktonic equivalents. “Energy metabolism” was shown to be significant in the biofilm
phenotype of Salmonella Missouri while “Transport and binding proteins” were
significant for the planktonic equivalents.
Table 5. The Institute for Genomic Research functional categories for the entire
annotated genome and uniquely expressed genes of the observed transcriptomes for the
planktonic and biofilm phenotypes. Shaded cells represent the most significant functional
category for each strain and under each growth condition. Since not all genes on the
genome have been allocated a specific functional category (not even “Unclassified” or
“Unknown function”), the Size columns may not match the values indicated in the Venn
diagram in Fig. 17.
TIGR Cellular Main Role
Category
a
Unique LT2 Biofilm
Unique MO Biofilm
Unique LT2 Planktonic
Unique MO Planktonic
Annotated
Population Population
List Size EASE
List Size EASE
List Size EASE
List Size EASE
Genes on
a
Hits
List Hits
List Hits
List Hits
List Hits
Size
b
c
d
e
Genome
Score
Score
Score
Score
Amino acid biosynthesis
132
64
1503
3
156
9.9E-01
9
121
1.3E-01
5
238
9.9E-01
7
106
Biosynthesis of cofactors,
prosthetic groups, and carriers
165
76
1503
4
156
9.9E-01
5
121
8.7E-01
20
238
2.2E-02
6
106
6.3E-01
Cell envelope
489
136
1503
12
156
8.5E-01
11
121
6.6E-01
14
238
9.9E-01
18
106
1.0E-02
Cellular processes
293
100
1503
13
156
3.3E-01
6
121
9.2E-01
20
238
2.2E-01
6
106
8.4E-01
Central intermediary metabolism
169
60
1503
5
156
8.8E-01
8
121
2.0E-01
5
238
9.9E-01
4
106
8.0E-01
DNA metabolism
162
54
1503
7
156
4.9E-01
1
121
1.0E+00
4
238
9.9E-01
3
106
9.0E-01
Energy metabolism
558
184
1503
21
156
4.4E-01
26
121
3.7E-03
23
238
9.5E-01
7
106
9.9E-01
Fatty acid and phospholipid
metabolism
75
20
1503
2
156
8.9E-01
1
121
1.0E+00
6
238
2.0E-01
0
106
1.0E+00
Hypothetical proteins
1209
28
1503
5
156
3.3E-01
2
121
9.0E-01
4
238
8.4E-01
2
106
8.7E-01
Mobile and extrachromosomal
element functions
243
45
1503
17
156
3.5E-06
3
121
8.9E-01
1
238
1.0E+00
0
106
1.0E+00
Protein fate
192
69
1503
5
156
9.4E-01
2
121
1.0E+00
16
238
1.1E-01
3
106
9.6E-01
Protein synthesis
378
138
1503
6
156
1.0E+00
9
121
8.8E-01
43
238
3.8E-06
4
106
1.0E+00
Purines, pyrimidines, nucleosides,
and nucleotides
81
42
1503
3
156
9.4E-01
3
121
8.6E-01
5
238
9.2E-01
3
106
8.1E-01
Regulatory functions
310
84
1503
11
156
3.6E-01
8
121
5.1E-01
13
238
7.0E-01
2
106
1.0E+00
Signal transduction
26
7
1503
1
156
1.0E+00
0
121
1.0E+00
0
238
1.0E+00
0
106
1.0E+00
Transcription
52
26
1503
3
156
7.7E-01
2
121
8.9E-01
10
238
1.4E-02
0
106
1.0E+00
Transport and binding proteins
527
177
1503
14
156
9.4E-01
14
121
6.8E-01
24
238
8.8E-01
23
106
3.7E-03
Unclassified
347
91
1503
13
156
2.2E-01
7
121
7.5E-01
14
238
7.0E-01
8
106
4.5E-01
Unknown function
682
213
1503
24
156
4.4E-01
15
121
8.3E-01
25
238
9.8E-01
14
106
7.5E-01
Viral functions
94
2
1503
1
156
1.0E+00
0
121
1.0E+00
0
238
1.0E+00
1
106
1.0E+00
actual number of significantly expressed genes was 1655.
actual number of significantly expressed unique LT2 biofilm genes was 249.
c
actual number of significantly expressed unique MO biofilm genes was 170.
d
actual number of significantly expressed unique LT2 planktonic genes was 307.
e
actual number of significantly expressed unique MO planktonic genes was 161.
b
2.9E-01
97
On closer inspection of the uniquely expressed genes within these functional
categories, it was found that the majority of the “Transport and binding” category for the
Salmonella Missouri planktonic phenotype consisted of genes involved in a novel outer
membrane siderophore receptor (iroN) and iron uptake (fhu). Genes included on the iro
operon (STM2773 – 2777) have been demonstrated to mediate utilization of structurally
related catecholate siderophores, including N-(2,3-dihydroxybenzoyl)-L-serine,
myxochelin A, benzaldehyde-2,3-dihydroxybenzhydrazone, 2-N,6-N-bis(2,3dihydroxybenzoyl)-L-lysine, 2-N,6-N-bis(2,3-dihydroxybenzoyl)-L-lysine amide, and
enterochelin (Baumler et al., 1998). The fhu operon is thought to code for an ABC
superfamily transporter involved in hydroxymate-dependent iron transport and uptake.
In the biofilm phenotype of Salmonella Missouri, the majority of uniquely
expressed genes were associated with “Energy metabolism” and included hydrogenase 3
(hypc/hyc), NADH dehydrogenase (nuo), 1,2-propanediol utilization (pdu), a glycine
cleavage complex (gcv) and maltodextrin-associated (mal) genes.
Genes that appeared to be unique to the Salmonella Typhimurium planktonic
phenotype were primarily assigned to the functional category of “Protein synthesis” and
were almost exclusively rps and rpl genes known to be 30S and 50S ribosomal subunit
proteins. The regulation of the biosynthesis of ribosomes, which constitute the catalytic
organelles for the translation reaction, is central for the adaptation of bacteria to different
growth conditions. The synthesis of the different ribosomal RNA and ribosomal protein
components is controlled and coordinated by a complex network of regulatory
mechanisms to adjust the translational capacity to the required cell demands (Wagner,
98
2001). Recently it has been shown that the global regulator Hfq is responsible for the
expression of many ribosomal structural protein genes (refer to Table 2) and repression of
this regulon down-regulates the rpl and rps genes (Wilson et al., 2007). It is shown here
that hfq was positively expressed in the Salmonella Typhimurium LT2 planktonic
phenotype.
An interesting observation was made with regards to the Salmonella
Typhimurium biofilm phenotype. The uniquely expressed genes fell into the “Mobile and
chromosomal elements” functional category and were primarily the three lambda-like
Gifsy-1, Gifsy-2 and Fels-1 prophage genes (Figueroa-Bossi et al., 2001) and the F
plasmid conjugative transfer (tra) genes located on the PSLT virulence plasmid. Once
again, Hfq has been demonstrated to negatively regulate the tra operon (Wilson et al.,
2007) a down-regulation of hfq in the biofilm phenotype of this strain was observed.
Significantly expressed genes shared between the strains in the biofilm phenotype
included the well-studied csg genes involved in the control of curli and cellulose
synthesis and which have also been implicated in the indirect control of c-di-GMP levels
in Salmonella through the expression of the GGDEF-domain-containing AdrA protein
(Da Re and Ghigo, 2006; Kader et al., 2006). Also in this shared group were ssa/sse
genes located on SPI-2 involved in TTSS and fep genes associated with the assimilation
of iron from enterochelin (Hall and Foster, 1996; Yancey et al., 1979). It appeared that
although the type culture LT2 strain did express some of the cob-cbi-pdu genes in
common with the environmental isolate, Salmonella Missouri expressed this operon more
completely. This same observation was made with the hydrogenase 3 (hyp/hyc) genes in
99
the biofilm phenotype and the NADH dehydrogenase (nuo) genes shared between the
more strongly expressing Missouri biofilm phenotype and the LT2 planktonic phenotype.
Interestingly, overlapping genes between the Salmonella Missouri planktonic
phenotype and the Salmonella Typhimurium biofilm phenotype were primarily located
on the PSLT virulence plasmid as conjugative transfer (tra) genes or on the SPI-1 as the
putative iron transport operon sitBCD (Zhou et al., 1999).
Conclusions
Current literature suggests that there is distinct attenuation in virulence of
repeatedly passaged microorganisms in microbiology laboratories (Fux et al., 2005). In
addition, observations have revealed that frequently cultured organisms tend to alter
physiological behavior over time, losing the ability to form biofilms, becoming less
resistant to physical and biological stress, and requiring more strictly controlled nutrient
regimes (data not shown). A case in point is the Salmonella Typhimurium LT2 ATCC
type strain, a culture which has been maintained in aseptic conditions for over half a
century (Lilleengen, 1948). This organism has been the strain of choice for hundreds of in
vitro and even in vivo experiments to study the physiology of this important human
pathogen. However, previous observations and this current study suggest that there may
be diminshed similarity between this repeatedly passaged strain and a recent
environmental isolate responsible for serious community impact.
Strikingly, over 50% of the transcriptomes of each of the biofilm and planktonic
phenotypes for the two strains were different, indicating that substantial physiological
differences exist between these two strains. On closer inspection of the differences, it was
100
evident that there were certain pathways which had become preferred by each of the
strains under specific growth conditions. This is the rationale underlying the process of
natural selection in the theory of evolution, that the exposure of highly related organisms
to different environmental conditions and pressures results in the gain and loss of genes
and the alteration of physiology to maintain optimum energy economy and ensured
survival within the lifecycle of the organism.
It should be pointed out that even the choice of a nomenclature scheme can
drastically affect the severity or importance with which an organism is regarded. Most
clinicians would regard a patient diagnosed with Salmonella Typhi as a more serious case
than a patient diagnosed with Salmonella Typhimurium. That the Missouri outbreak was
initially described using their former, non-standardized nomenclature scheme as
Salmonella typhimurium when the results here show that the strain was more closely
related to Salmonella Typhi or Paratyphi, illustrates the potential underestimation of the
severity of an outbreak depending on nomenclature and typing techniques used. The
corrected classification of the pathogen to Salmonella Missouri at least offers the
clinician the choice of urgency with which to regard the situation.
But it is not only the clinician that may be influenced by nomenclature. State and
federal health agencies may choose to down-grade their emergency response if the
causative agent carries the stigma of being only mildly virulent. Therefore, basing clinical
and physiology studies on an attenuated strain of a pathogen may not serve the public’s
best interests. Ansong et al. (2008) carried out a proteomic study in which they compared
Salmonella Typhi with Salmonella Typhimurium in an infection model to gain insights
101
into the molecular determinants that contribute to the narrow host range and
pathogenicity traits in the typhoid infection. Their results were striking in that they were
able to demonstrate a subset of proteins which were unique in the typhoid model,
suggesting that this difference in the protein complement between two genetically related
organisms can significantly alter pathogenicity and environmental response.
These findings corroborated the Ansong et al. (2008) results in that it was
demonstrated that expression of SPI-2 virulence genes ssa/sse were shared between the
two strains under biofilm growth conditions. It was also demonstrated that expression of
the apparent “universal” biofilm-related genes in Salmonella, those in the csg operon,
were also shared between the strains, indicating that perhaps genes in this operon might
serve as qualitative targets for detecting Salmonella in the biofilm phenotype in industrial
settings. Furthermore, it was also shown that expression of the iron-deficiency genes
located in the fep operon were also shared and that this ferrienterochelin may be
important in sequestering iron during limiting nutrient conditions in biofilms where
competition for micronutrients may be fierce. This might also explain why it was found
that several genes of the cob-cbi-pdu operon were expressed in both strains exhibiting the
biofilm phenotype. That said however, it must also be pointed out that the environmental
isolate appeared to exhibit greater coverage and expression of the cobalamin-dependent
1,2-propanediol utilization pathway and that this might be indicative of an environmental
adaptation that Salmonella Missouri has grown to be reliant upon whereas Salmonella
Typhimurium LT2 has had less need to compete for this particular carbon source and
therefore has an attenuated behavior in this regard. It was previously demonstrated
102
(Chapter 3) that hydrogenase 3 (hpc/hyc) and NADH dehydrogenase I (nuo) may also be
intimately (though not necessarily exclusively) involved in the biofilm phenotype, but
with the same attenuated differences as the cob-cbi-pdu operon in the two strains.
It was curious to that one of the major subsets of genes that appeared to be
uniquely up-regulated in the planktonic phenotype of Salmonella Typhimurium LT2
should be genes involved in the regulation of ribosomal biosynthesis (rps and rpl), a
central mechanism for the adaptation of bacteria to changing growth conditions. This can
possibly be explained by the infrequency with which this domesticated strain is faced
with stressful or challenging conditions and the subsequent need for the organism to
expend valuable energy in synthesizing these ribosomal protein components to elevate
the translational capacity of the cell.
The presence of multiple phage genes uniquely expressed in the Salmonella
Typhimurium LT2 phenotype may be explained by their volatile nature within the
pathogen’s genome. These genes were apparently obtained via horizontal gene transfer
(Porwollik and McClelland, 2003) and have a tendency to migrate within natural
populations, being promiscuous in nature. Since Salmonella Typhimurium LT2 has been
maintained in relative isolation concerning the availability of lateral gene transfer target
or donor groups, whereas Salmonella Missouri has presumably been in regular contact
with other microbial species harboring these phage traits, it may be that the phage genes
have been lost or significantly altered on the genome of the environmental isolate,
rendering the microarray inefficient at detecting such genes. This is supportive of the
rationale behind using the genetically stable 16S rDNA regions of the chromosome for
103
phylogenetic purposes, with the assumption that little to no change occurs within these
ribosomal genes over time, making them suitable epoch markers in the prokaryotic
community.
In conclusion, the marked differences observed between the Salmonella
Typhimurium LT2 and Salmonella Missouri biofilm and planktonic phenotype
transcriptomes is further evidence of the importance in using environmentally relevant
strains for experimental studies. The differences between the two strains overall is
evidence that so-called laboratory strains may not be the most representative strains in
elucidating real-world scenarios. However, despite the numerous transcriptional
differences, the similarities exhibited by the two strains particularly in the biofilm
phenotype confirms the notion that the environmentally relevant pathways are often
conserved in pathogens.
104
CHAPTER 5
CONCLUSIONS
This dissertation highlighted some of the major differences between the
planktonic and biofilm phenotypes of the ATCC type strain, Salmonella enterica serotype
Typhimurium LT2, and an environmental isolate, Salmonella enterica serotype Missouri.
The goal of the study was to elucidate important phenotypic differences between the
planktonic and biofilm growth phases in the enteric pathogen Salmonella at the
transcriptional level. This goal was addressed in two separate chapters by first examining
the transcriptional behavior of the robust biofilm-forming Salmonella Missouri in the two
modes of growth (Chapter 3) and subsequently studying the differences in expression
patterns between a less virulent, repeatedly cultured ATCC type strain, Salmonella
Typhimurium LT2 and a more virulent recently isolated environmental strain, Salmonella
Missouri (Chapter 4). This final chapter summarizes the key findings of each of these
chapters and discusses future directions for this work.
Salmonella Missouri had been isolated and identified as the causative agent
involved in a waterborne outbreak of salmonellosis in Gideon, MO, USA during the
Christmas of 1993. This virulent enteric pathogen had been responsible for infecting over
40% of the community, hospitalizing over 15 patients and causing mortality in a further
seven. After obtaining a culture of this organism, it was observed that it was a persistent
biofilm former and was able to survive for lengthy periods under low nutrient, suboptimal conditions. It was decided to undertake a transcriptional study of this organism in
order to delineate the major pathways active in the biofilm and planktonic phenotypes.
105
In agreement with existing literature, it was demonstrated that the global control
unit, csgD, was centrally involved in establishing the biofilm phenotype by activating
curli biosynthesis and possibly contributing to elevated levels of cyclic-di-GMP within
the cell through the activity of the GGDEF domain protein AdrA. Furthermore, it was
demonstrated that the so-called virulence plasmid and pathogenicity islands may play a
more universal role in the lifecycle of Salmonella than simply during host infection.
Although these pathogenicity islands have been primarily studied in the clinical context
of disease establishment and progression in the host, it was suggested that SPI-2 may be
intimately linked with the biofilm phenotype and involved in establishing persistence in
the non-host environment where Salmonella may spend significant time. It was further
suggested that SPI-1 may contribute to the pathogen’s ability to locate a suitable contact
surface and initial adhesion in the switch from the planktonic to biofilm phenotype.
It appears that Salmonella has acquired several major sets of genes through
horizontal gene transfer through evolutionary processes, affording the pathogen the
ability to outcompete closely related bacteria and persist in the environment as a biofilm.
One such set of gene encodes for the cobalamin-dependent 1,2-propanediol utilization
pathway (cob-cbi-pdu). This operon was observed to be consistently up-regulated in the
biofilm phenotype of both Salmonella Typhimurium LT2 and Salmonella Missouri. This
lead to the conclusion that the ability to convert several sugar compounds (including
glucose, fucose and rhamnose) to 1,2-propanediol, and subsequently utilize 1,2propanediol in a cobalamin-dependent manner under anaerobic conditions as a sole
106
carbon and energy source, may be a further reason for Salmonella to persist and thrive in
the host and non-host environments.
It was also evident, not only from visual observations of the differences in
physiological behavior of the two strains but also from transcriptomic analysis, that
Salmonella Missouri exhibits a greater degree of adaptation to survival and persistence in
the non-host environment. This result is not at all surprising, considering the length of
time for which the ATCC type strain has been maintained in culture and the repeated
passaging of this organism. The transcriptional profile of the biofilm phenotype of
Salmonella Missouri illustrated how this organism has developed strategic pathways to
overcome the stressful living conditions in which it may find itself both as a human
pathogen and as an environmental inhabitant.
Future Work
This present study represents the culmination of several years of gathering
fundamental information on the behavior of Salmonella as a biofilm in low nutrient
conditions and onto which can be built a more complete picture of how this enteric
pathogen survives and persists in a variety of niches.
One of the initial motivating factors in this research was the potential of
Salmonella to become a biothreat to the health and safety of human populations through
the drinking water distribution system. Since it has been demonstrated that Salmonella is
capable of establishing itself in biofilms on distribution pipes, filter media and premise
plumbing, it would be helpful to understand the environmental factors and physiological
responses involved in the biofilm phenotype of this pathogen. This study made use of
107
artificial media and standardized biofilm reactors in which to culture the organism for
study. However, as demonstrated with the ATCC type strain, Salmonella Typhimurium
LT2, that the use of an attenuated, lesser virulent strain of a pathogen may not effectively
demonstrate the risks of a true version of the pathogen in lab studies, so the use of
artificial environments and nutrients limits the reality of a pathogen’s potential to cause
disease. This has been the rationale behind using progressive models, from in vitro to in
vivo studies and finally to clinical trials to test the efficacy of pharmaceuticals. Therefore,
the next stage of this research may be to repeat the planktonic and biofilm experiments
using the environmental isolate, Salmonella Missouri, in small-scale, closed distribution
system studies in order to determine the effects of surface material, residence time and
shear on the survivability of the organism.
A current shortcoming of transcriptomic studies is an inherent limitation in the
technology to effectively separate out the starting mRNA from the organism of interest
from other organisms. While this may be possible in separating out mRNA from a
eukaryotic organism in a microbial community because of the presence of useful polyA
overhangs present on eukaryotic mRNA, currently there technology is not yet advanced
enough to separate out sufficient quantities of mRNA from bacteria in mixed
communities. A possible solution to this problem may be the combined use of
cryosectioning and laser dissection microscopy where it might be possible to selectively
obtain single cell isolates of bacteria from mixed communities. However, this technique
has several shortcomings in and of itself. First, the rapid half life of mRNA in bacterial
cells would require that the biofilm or other form of cell culture be harvested and fixed
108
rapidly so as to preserve the transcriptional expression pattern at a particular time point.
Second, the current requirement for mRNA starting material necessitates the harvesting
of large quantities of cells in order to obtain sufficient template for the cDNA reverse
transcription reaction. This may be addressed by using direct RNA hybridization to
cDNA microarrays, but again, this technology is severe limited by the rapid degradation
of mRNA. Should the technology become sufficiently advanced that it is possible to
obtain sufficient mRNA from discrete cells in mixed cultures, this would significantly
enhance understanding of the behavior of this and hundreds of other pathogens, the
majority of which are seldom found in pure cultures in the natural environment.
Finally, recent studies undertaken at the Center for Biofilm Engineering focusing
on the behavior of Staphylococcus aureus grown as a biofilm on mammalian cell cultures
have demonstrated the potential of a novel system in which to observe pathogen
interaction with host cells in vivo. Preliminary attempts to manipulate this system for use
with Salmonella demonstrated that in its current form, which inherently separates the
bacterial pathogen from the mammalian cell culture by a porous membrane, Salmonella
does not appear to cause cell damage. This can be understood within the context of
Salmonella pathogenicity, which is known to require direct contact with epithelial cells in
order for the TTSSs to inject effector proteins responsible for actin rearrangement and
penetration of the pathogen into the host cells. However, it may be possible to substitute
the nanopore membranes currently employed in this assay with larger pore membranes to
allow for occasional direct pathogen-host contact.
109
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126
APPENDICES
127
APPENDIX A
SIGNIFICANT GENES DATA SET FOR CHAPTER 3
128
Locus
PSLT006
PSLT014
PSLT023
PSLT024
PSLT036
PSLT039
PSLT040
PSLT041
PSLT042
PSLT043
PSLT044
PSLT046
PSLT047
PSLT052
PSLT053
PSLT060
PSLT072
PSLT075
PSLT094
PSLT095
PSLT096
PSLT103
PSLT104
STM0003
STM0004
STM0007
STM0012
STM0027
STM0031
STM0032
STM0041
STM0054
STM0056
STM0064
STM0066
STM0067
STM0073
STM0074
STM0096
STM0106
STM0110
STM0111
STM0112
STM0113
STM0150
STM0154
STM0157
STM0169
STM0170
STM0171
STM0172
STM0181
STM0183
STM0191
STM0192
STM0211
STM0216
STM0219
STM0223
STM0224
STM0225
STM0228
STM0234
STM0245
STM0248
STM0259
STM0262
STM0263
STM0266
STM0267
STM0268
STM0311
STM0316
STM0319
STM0322
STM0324
STM0343
STM0350
STM0351
STM0352
STM0354
STM0358
STM0363
STM0366
STM0369
STM0371
STM0383
STM0385
STM0388
STM0389
STM0396
STM0401
STM0428
STM0431
STM0432
STM0435
STM0436A
STM0446
STM0447
STM0452
STM0460
STM0461
STM0462
STM0463
STM0464
STM0469
STM0470
STM0471
STM0476
STM0485
STM0488
Significant Genes from Salmonella MO with q‐values < 0.1%, Number False Sig Genes (Median) = 0.73978 and FDR 0.08572% (410 Biofilm Genes, 447 Planktonic Genes)
Gene Expected Observed Denominator Gene Name
Numerator(r)
q‐value (%)
107808
Symbol score (dExp)
score(d)
(s+s0)
DNA replication
putative outer membrane protein
DNA replication
hypothetical protein
putative transposase, IS200‐like
Salmonella plasmid virulence: hydrophilic protein
Salmonella plasmid virulence: outer membrane protein
Salmonella plasmid virulence: regulation of spv operon
putative integrase protein
putative phosphoribulokinase / uridine kinase family
putative integrase protein
putative carbonic anhydrase
putative cytoplasmic protein
plasmid partition protein A
plasmid partition protein B
putative cytoplasmic protein
putative transglycosylase
conjugative transfer: regulation
conjugative transfer: assembly
conjugative transfer: aggregate stability
conjugative transfer
conjugative transfer: surface exclusion
conjugative transfer: DNA transport
homoserine kinase
threonine synthase
transaldolase B
chaperone Hsp70 in DNA biosynthesis/cell division
fimbrial chaparone
putative transcription regulator
putative arylsulfatase
putative glycosyl hydrolase
putative oxalacetate decarboxylase, subunit beta
putative oxalacetate decarboxylase, subunit gamma
dihydrodipicolinate reductase
carbamoyl‐phosphate synthetase, glutamine‐hydrolysing small subunit
carbamoyl‐phosphate synthase, large subunit
putative acyl‐CoA dehydrogenase, carnitine metabolism
putative BCCT family, betaine/carnitine/choline transport protein
RNA polymerase associated protein, putative SNF2 family
putative ABC‐transport protein
3‐isopropylmalate isomerase (dehydratase), subunit with LeuC
3‐isopropylmalate isomerase (dehydratase), subunit with LeuD
3‐isopropylmalate dehydrogenase
2‐isopropylmalate synthase
APC family, aromatic amino acid transporter
lipoamide dehydrogenase (NADH) component of 2‐oxodehydrogenase and
putative outer membrane protein
glucose dehydrogenase
hypoxanthine phosphoribosyltransferase
putative carbonic anhydrase
putative ABC‐type multidrug transport system, ATPase component
pantothenate synthetase
7,8‐dihydro‐6‐hydroxymethylpterin‐pyrophosphokinase, PPPK
outer membrane protein receptor / transporter for
ABC superfamily (atp_bind), hydroxymate‐dependent iron transport
putative cytoplasmic protein
30S ribosomal subunit protein S2
ribosome releasing factor
putative membrane‐associated Zn‐dependent protease
putative outer membrane antigen
histone‐like protein, located in outer membrane
UDP‐N‐acetylglucosamine acetyltransferase
lysine decarboxylase 2, constitutive
putative outer membrane lipoprotein
putative dehydratase
putative methyltransferase in menaquinone/biotin biosynthesis
putative SAM‐dependent methyltransferase
RNase HI, degrades RNA of DNA‐RNA hybrids
putative cytoplasmic protein
putative cytoplasmic protein
putative cytoplasmic protein
putative glutamine amidotransferase
aminoacyl‐histidine dipeptidase (peptidase D)
transcriptional regulator of cryptic csgA gene for
gamma‐glutamylphosphate reductase
putative inner membrane protein
putative Diguanylate cyclase/phosphodiesterase domain 1
homology to outer membrane efflux protein
putative cation efflux system protein
putative cation efflux pump
putative transcriptional regulator
DNA restriction (DNA helicase
putative transcription regulator, AraC family
putative periplasmic protein
putative citrate synthase
putative acetyl‐CoA synthetase, propionate catabolism operon
putative cytoplasmic protein
putative diguanylate cyclase/phosphodiesterase domain 1
shikimate kinase II
putative cytoplasmic protein
ATP‐dependent dsDNA exonuclease
maltodextrin glucosidase
2‐aminoethylphosphonate transporter,ATPase component
2‐aminoethylphosphonate transport
2‐aminoethylphosphonate transport
putative cytoplasmic protein
IS903 transposase
morphogene putative regulator of murein genes (BolA
peptidyl‐prolyl cis/trans isomerase, trigger factor a molecular
peptidyl prolyl isomerase
putative ABC superfamily (atp) transporter
putative ABC superfamily (atp&membrane) transporter
regulatory protein, P‐II 2, for nitrogen assimilation
putative Amt family, ammonium transport protein
acyl‐CoA thioesterase II
putative 50S ribosomal protein L31 (second copy)
putative 50S ribosomal protein L36 (second copy)
putative inner membrane protein
acridine efflux pump
putative cytoplasmic protein
adenylate kinase
repA
orf6
repA2
spvB
spvA
spvR
rlgA
parA
parB
finP
traJ
trbC
traN
trbE
traT
traD
thrB
thrC
talB
dnaK
bcfG
dapB
carA
carB
caiA
caiT
hepA
yabJ
leuD
leuC
leuB
leuA
aroP
lpdA
yacH
gcd
hpt
yadF
yadG
panC
folK
fhuA
fhuC
yaeH
rpsB
frr
yaeL
yaeT
hlpA
lpxA
ldcC
yaeC
yaeD
yafE
yafS
rnhA
yafJ
pepD
crl
proA
res
yahO
prpC
prpE
yaiB
yaiC
aroL
yaiA
sbcD
malZ
phnT
phnW
phnX
yajQ
bolA
tig
cypD
mdlA
mdlB
glnK
amtB
tesB
rpmE2
rpmJ2
ylaC
acrA
ybaB
adk
0.104944296
‐0.2717591
0.02902207
0.015338479
0.6619383
0.3451125
0.12597384
0.5280604
1.0153017
‐0.076198705
‐0.35482937
0.43125764
‐0.36528504
0.22071066
0.9242672
‐0.503064
0.33128756
‐0.75755405
‐0.74059606
0.072409235
0.011326586
‐0.05340151
0.32163835
0.3731943
‐0.23842911
0.022878118
‐0.24008778
0.39438474
0.25770834
‐0.31135422
‐0.29370916
‐0.12743631
0.7631232
‐0.061718486
0.45898014
0.05301397
0.08282884
‐0.31307504
‐0.46144098
‐0.4388538
0.095710576
1.2813643
0.9146848
0.54918724
‐0.90354496
0.17271183
0.56994534
‐1.7519572
0.31792352
0.28780282
0.48575526
0.26421428
0.25296074
‐0.9581498
‐0.21520603
0.5736256
0.10987641
0.4616791
0.05938715
‐0.47657797
‐1.0063118
‐0.48575526
‐0.3799009
‐0.11784761
‐0.18181716
‐0.32467642
‐0.19503678
0.45729053
0.03633827
0.55740213
0.24975686
‐0.3123075
0.29522222
‐0.23575908
0.1268639
‐0.45898014
‐0.21675953
1.1832253
‐0.4337433
1.214031
0.19398473
0.28092447
‐0.4730723
‐0.12833788
1.6554445
0.54299587
‐0.46944648
0.59701335
‐0.05993005
‐0.30700204
0.60831934
0.237694
‐0.16867991
‐0.06288169
0.8484593
0.18962856
0.46944648
0.15034653
0.620536
‐1.301176
1.2157859
‐0.18625572
‐0.42231038
0.5317064
‐0.17169346
‐0.001346741
‐2.1953468
0.33938333
0.5709482
‐0.596286
0.18878233
1.9600818
1.9315368
2.0378094
2.1821437
1.9249718
3.730863
3.0069344
1.7494527
2.4233482
2.6377935
3.0464878
1.6800685
2.0366328
1.5905259
2.0767963
‐1.5957878
1.6001691
1.575407
2.1151586
1.9366502
1.6559206
2.1905904
2.0872748
‐2.865248
‐1.6807305
3.1774638
‐2.589143
‐2.4562256
1.6790329
2.076453
1.5048043
‐2.4273508
‐2.139305
‐6.913448
‐5.0335317
‐4.6263185
1.8060813
1.5931356
‐1.824222
‐1.6991203
6.583725
8.166836
8.07625
10.239214
1.7143809
2.2910266
‐2.0895703
1.5694543
1.8715332
4.9549255
1.5527482
‐1.6072483
‐1.9135267
2.0976856
1.6930404
3.3923361
‐1.98902
1.5258104
1.6136407
1.6624389
3.0332167
1.6226844
1.6932362
3.122391
2.56547
2.5306163
2.269245
1.5386066
‐2.347133
‐2.31671
‐2.5039003
1.9502835
2.1541834
1.9872247
‐2.2395682
‐1.7054257
2.677911
‐1.5723702
‐1.801101
‐2.7127073
‐2.0123951
1.6455429
1.917425
3.479826
‐2.6600907
‐1.8005381
‐3.9394166
‐4.324508
2.91053
2.3532898
‐1.8980027
‐1.9701208
‐1.8471417
‐1.5379883
‐2.229105
1.6703997
‐1.6752232
2.329697
2.3983042
1.7160473
‐2.1817987
‐2.4928818
‐10.616214
‐11.134695
‐2.3282132
5.337574
6.5218506
1.9444011
1.5192364
2.1674752
‐2.1039302
0.50870204
0.380888
0.4901857
0.45487335
0.4800788
0.8478979
0.9168429
0.57788384
0.50700295
0.5201619
0.63300794
0.4287064
0.4778348
0.41512597
0.42101747
‐0.34180608
0.4574093
0.3857001
0.45043716
0.45661223
0.3692458
0.48780736
0.4257448
‐0.97947013
‐0.3645335
0.7765127
‐0.6160514
‐0.78674674
0.36837336
0.60086226
0.29460108
‐0.62845695
‐0.45572165
‐1.5090705
‐1.1686505
‐1.1902834
0.37246543
0.3547541
‐0.44441262
‐0.47691223
1.6092142
1.9181032
1.8719113
2.1105087
0.37897933
0.5616982
‐0.44268334
0.3682456
0.49547055
1.2961013
0.35061258
‐0.36514792
‐0.38334984
0.5305229
0.43968567
0.7839944
‐0.552573
0.4298571
0.30970484
0.4184704
0.6145841
0.3795888
0.3664753
0.7852388
0.49893078
0.52342516
0.6194391
0.35818568
‐0.55782306
‐0.6252847
‐0.5029192
0.485739
0.54524845
0.43583065
‐0.45645252
‐0.33347082
0.78673744
‐0.5248595
‐0.49487287
‐0.63740706
‐0.597014
0.3113941
0.3840036
1.082961
‐0.82515436
‐0.5133654
‐0.9674523
‐1.1396213
0.6445213
0.50275105
‐0.39250594
‐0.5027518
‐0.42524725
‐0.33342257
‐0.6137898
0.37248254
‐0.38447344
0.5824739
0.6421274
0.4151523
‐0.52821445
‐0.6117885
‐2.2544765
‐2.5194488
‐0.65982836
1.5835129
1.562265
0.50941765
0.3550747
0.5880913
‐0.5463128
0.25953102
0.19719426
0.24054542
0.20845252
0.24939522
0.22726588
0.3049095
0.33032265
0.2092159
0.19719584
0.20778286
0.25517198
0.23462
0.2609992
0.20272449
0.2141927
0.2858506
0.24482569
0.21295668
0.23577425
0.22298521
0.22268306
0.20397161
0.3418448
0.21688993
0.24438128
0.2379364
0.3203072
0.21939616
0.28936955
0.19577369
0.2589065
0.21302322
0.21828045
0.23217307
0.25728524
0.2062285
0.22267665
0.24361762
0.28068185
0.24442306
0.23486492
0.23177975
0.2061202
0.22105901
0.24517314
0.21185377
0.2346329
0.26474047
0.26157838
0.22580132
0.22718824
0.20033681
0.25290868
0.25970182
0.23110752
0.2778117
0.2817238
0.19192925
0.2517208
0.20261793
0.23392646
0.21643484
0.2514864
0.19447929
0.20683703
0.27297148
0.23279874
0.23766147
0.269902
0.20085432
0.2490607
0.25311142
0.21931624
0.20381273
0.19553523
0.29378775
0.33380148
0.27476132
0.23497082
0.29666838
0.18923487
0.20027047
0.31121123
0.31019783
0.28511778
0.24558263
0.2635262
0.22144464
0.21363755
0.20679946
0.25518832
0.23021907
0.21679136
0.27535257
0.22299007
0.22950579
0.2500213
0.26774225
0.24192359
0.24210045
0.24541417
0.21236163
0.22627012
0.28340548
0.2966728
0.23954321
0.26199207
0.23371918
0.2713255
0.259663
0.03676819
0.035703473
0
0
0.035160456
0
0
0.058067188
0
0
0
0.052916735
0
0.04736082
0
0.04670303
0.048099868
0.04670303
0
0.035703473
0.052023627
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0.052916735
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0
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0.052916735
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0.08572143
0
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0.061239734
0.048099868
0.061239734
0.055124886
0
0
0
0
0.055790044
0
0
0.04670303
0.0654669
0
0.046063263
0.04736082
0.033565152
0
0.05455575
0
0.03676819
0.066927865
0.04958284
0.052023627
0
0.04958284
0.05455575
0
0
0
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0.068245016
0
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0.036121875
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0.055790044
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0.068245016
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0.050878678
0.034698687
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0
0.06083684
0
0
0
0
0.0654669
0.036121875
0.063013285
0.08572143
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0.052916735
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0.055790044
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0
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0
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0.036121875
0.06573839
0
0
0.5171119
0.3638063
0.59046596
0.4361952
0.42819518
0.8129133
1.0600393
0.7151635
0.5352007
0.52404296
0.6716581
0.29661897
0.39670837
0.37233824
0.44112355
‐0.39337102
0.27459073
0.34387413
0.46203178
0.5083317
0.30819207
0.5539146
0.40272415
‐0.69281363
‐0.314873
0.7974293
‐0.5170135
‐0.5230399
0.4192517
0.39936844
0.2974965
‐0.5026722
‐0.45647347
‐1.4498417
‐1.1434257
‐1.053431
0.4080665
0.42188185
‐0.35401532
‐0.38421997
1.5279573
1.8703383
1.9474282
2.0958962
0.33038053
0.640753
‐0.40804002
0.2772285
0.4162164
1.1643332
0.29700285
‐0.43498638
‐0.39269713
0.6176664
0.4876314
0.70088106
‐0.4021984
0.2711675
0.3049555
0.43271163
0.5923797
0.46926323
0.4041073
0.7503361
0.5059839
0.5335188
0.49389648
0.31111524
‐0.51841563
‐0.46269473
‐0.49753565
0.57043815
0.4249264
0.38255042
‐0.42575482
‐0.34722316
0.65208244
‐0.234343
‐0.37917757
‐0.5922731
‐0.4025938
0.310187
0.3706963
0.91624224
‐0.60706687
‐0.701977
‐1.0665052
‐1.035921
0.6025709
0.5258289
‐0.38914096
‐0.3888723
‐0.3416402
‐0.32715797
‐0.44300044
0.33008066
‐0.37019327
0.46069
0.77709967
0.5217175
‐0.4450372
‐0.4977934
‐2.2110238
‐2.5150805
‐0.69778085
1.3985962
1.5099168
0.38107553
0.3923507
0.42250806
‐0.55290645
107809
0.62749356
0.3857596
0.46488547
0.49495822
0.41039482
0.9255149
1.004456
0.29407802
0.51944155
0.5330904
0.61639065
0.5118478
0.48000222
0.5566913
0.42865178
‐0.3175781
0.60735095
0.49739492
0.40329906
0.49951515
0.4279481
0.47054815
0.4190764
‐1.2177294
‐0.36514962
0.86131924
‐0.66296506
‐0.91175896
0.31224498
0.71335566
0.3056859
‐0.746571
‐0.41269276
‐1.5317243
‐1.2538745
‐1.2448778
0.35277745
0.33328038
‐0.5445657
‐0.6614861
1.7166674
2.0110316
1.8711624
2.0898426
0.36546996
0.5927695
‐0.4874071
0.39958212
0.6481248
1.417171
0.42260903
‐0.3594995
‐0.39771083
0.56935674
0.5320316
0.80845404
‐0.54393405
0.42408898
0.31661424
0.52033836
0.6102872
0.32102868
0.38366818
0.9077048
0.5039926
0.54910225
0.7803889
0.3165024
‐0.49931577
‐0.69639415
‐0.4845398
0.36815205
0.6467224
0.48966178
‐0.47432962
‐0.32326004
0.9945076
‐0.68150187
‐0.66379964
‐0.7305447
‐0.77680856
0.3130102
0.37361923
1.010098
‐1.0282005
‐0.4562795
‐0.96745145
‐1.2856466
0.70973486
0.45232546
‐0.3624438
‐0.62017125
‐0.4693416
‐0.28767043
‐0.7276151
0.44103426
‐0.461738
0.62693226
0.50235707
0.37075484
‐0.51094645
‐0.66604364
‐2.2586772
‐2.587126
‐0.4796042
1.5783657
1.5123256
0.511171
0.40799665
0.66256225
‐0.41970772
107810
0.3815007
0.39309806
0.41520572
0.43346664
0.60164636
0.8052654
0.68603337
0.72441
0.46636653
0.5033524
0.610975
0.47765243
0.5567938
0.31634837
0.39327705
‐0.31446916
0.4902862
0.3158313
0.4859806
0.3619898
0.3715972
0.43895933
0.45543385
‐1.0278673
‐0.41357788
0.67078954
‐0.6681755
‐0.9254414
0.37362337
0.6898628
0.28062084
‐0.63612765
‐0.49799874
‐1.5456456
‐1.1086514
‐1.2725413
0.3565523
0.30910006
‐0.43465686
‐0.38503063
1.583018
1.8729396
1.7971433
2.145787
0.44108745
0.4515722
‐0.43260288
0.4279262
0.4220704
1.3067999
0.3322259
‐0.3009579
‐0.35964152
0.4045455
0.29939404
0.84264797
‐0.7115866
0.5943148
0.3075448
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‐2.2937286
‐2.4561398
‐0.8021
1.7735767
1.6645528
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‐0.6663243
129
STM0498
STM0499
STM0500
STM0510
STM0511
STM0529
STM0530
STM0533
STM0534
STM0536
STM0562
STM0570
STM0576
STM0585
STM0587
STM0589
STM0603
STM0605
STM0607
STM0608
STM0621
STM0629
STM0632
STM0635
STM0639
STM0659
STM0661
STM0662
STM0663
STM0664
STM0665
STM0669
STM0671
STM0680
STM0690
STM0693
STM0703
STM0705
STM0720
STM0722
STM0730
STM0740
STM0741
STM0742
STM0749
STM0756
STM0759
STM0760
STM0762
STM0764
STM0766
STM0768
STM0771
STM0772
STM0782
STM0792
STM0793
STM0802
STM0803
STM0826
STM0828
STM0829
STM0830
STM0831
STM0833
STM0834
STM0846
STM0852
STM0853
STM0863
STM0887
STM0891
STM0933
STM0934
STM0947
STM0959
STM0965
STM0972
STM0973
STM0974
STM0988
STM0989
STM0999
STM1066
STM1068
STM1070
STM1076
STM1077
STM1079
STM1091
STM1102
STM1106
STM1112
STM1113
STM1121
STM1122
STM1124
STM1128
STM1139
STM1140
STM1141
STM1142
STM1145
STM1146
STM1147
STM1150
STM1152
STM1177
STM1178
STM1179
STM1204
STM1210
STM1214
STM1218
putative copper‐transporting ATPase
copA
putative heavy metal transcriptional repressor (MerR family)
cueR
putative Membrane protein implicated in regulation of
ybbJ
putative ABC‐type transport system ATPase component/cell division
sfbA
putative ABC‐type transport system ATPase component/cell division
sfbB
fdrA
putative acyl‐CoA synthetase, involved in protein transport
putative cytoplasmic protein
ylbE
phosphoribosylaminoimidazole carboxylase
purK
phosphoribosylaminoimidazole carboxylase
purE
peptidyl‐prolyl cis‐trans isomerase B (rotamase B)
ppiB
putative transport protein
apeE
outer membrane N‐acetyl phenylalanine beta‐naphthyl ester‐cleaving esterase
putative transport protein, PTS system
outer membrane porin, receptor for ferric enterobactin
fepA
putative cytoplasmic protein
ybdZ
ferric enterobactin (enterochelin) transporter
fepE
putative aminotransferase
ybdL
putative 3‐phosphoadenosine 5‐phosphosulfate sulfotransferase (PAPS reductase)/FAD synthybdN
periplasmic disulfide isomerase, thiol‐disulphide oxidase
dsbG
alkyl hydroperoxide reductase, C22 subunit detoxification of
ahpC
bifunctional citrate lyase alpha chain/citrate‐ACP transferase
citF
RNA chaperone, negative regulator of cspA transcription
cspE
putative Sec‐independent protein secretion pathway component
ybeC
lipB
putative ligase in lipoate biosynthesis
rod shape‐determining membrane protein cell elongation in
mrdB
putative heatshock protein, homolog of hsp70 in
hscC
putative purine nucleoside hydrolase
ybeK
ABC superfamily (atp_bind), glutamate/aspartate transporter
gltL
ABC superfamily (membrane), glutamate/aspartate transporter
gltK
gltJ
ABC superfamily (membrane), glutamate/aspartate transporter
ABC superfamily (bind_prot), glutamate/aspartate transporter
gltI
putative phosphate starvation‐inducible protein, ATP‐binding
phoL
putative monooxygenase
ubiF
asparagine synthetase B
asnB
citrate utilization protein b
citB
transcriptional repressor of iron‐responsive genes (Fur family)
fur
sensory kinase in two‐component regulatory system wtih
kdpD
P‐type ATPase, high‐affinity potassium transport system, B
kdpB
putative glycosyl transferase
putative ABC transporter permease protein
citrate synthase
gltA
cydA
cytochrome d terminal oxidase, polypeptide subunit I
cytochrome d terminal oxidase polypeptide subunit II
cydB
putative outer membrane lipoprotein
ybgT
tol protein required for outer membrane integrity
pal
quinolinate synthetase, A protein
nadA
putative homeobox protein
ybgS
3‐deoxy‐D‐arabinoheptulosonate‐7‐phosphate synthase (DAHP synthetase, phenylalanine re aroG
fumarate hydratase, alpha subunit
transcriptional regulator, lysR family
Oxalacetate decarboxylase: gamma chain
dcoC
Oxalacetate decarboxylase: beta chain
dcoB
putative ABC‐type cobalamin/Fe3 ‐siderophores transport system, ATPase component
phosphoglyceromutase 1
gpmA
modB
ABC superfamily (membrane), molybdate transporter
putative Phospholipid‐binding protein
ybhB
7,8‐diaminopelargonic acid synthetase
bioA
molybdopterin biosynthesis, protein A
moaA
molybdopterin biosynthesis, protein B
moaB
putative SAM‐dependent methyltransferase
ybiN
ABC superfamily (atp_bind), glutamine high‐affinity transporter
glnQ
ABC superfamily (membrane), glutamine high‐affinity transporter
glnP
glnH
ABC superfamily (bind_prot), glutamine high‐affinity transporter
stress response DNA‐binding protein starvation induced resistance
dps
outer membrane protease, receptor for phage OX2
ompX
putative Integral membrane protein
ybiP
molybdopterin biosynthesis protein
moeA
putative Fe‐S oxidoreductases family 1
yliG
putative cytoplasmic protein
yliH
D‐alanyl‐D‐alanine carboxypeptidase penicillin‐binding protein 6a
dacC
ABC superfamily (bind_prot), arginine 3rd transport system
artJ
ABC superfamily (atp&memb), arginine transport system
artP
putative nucleoside‐diphosphate‐sugar epimerase
ybjT
ltaA
L‐allo‐threonine aldolase
putative integrase protein
regulator for lrp regulon and high‐affinity branched‐chain
lrp
anaerobic dimethyl sulfoxide reductase, subunit B
dmsB
homologous to secreted protein sopD
pflB
pyruvate formate lyase I, induced anaerobically
putative FNT family, formate transporter (formate channel
focA
CTP:CMP‐3‐deoxy‐D‐manno‐octulosonate transferase
kdsB
mukF protein (killing factor KicB)
outer membrane protein 1a (iab
ompF
rmf
ribosome modulation factor (involved in dimerization of
putative protease
lonH
putative hydrogenase, membrane component
ompA
methylglyoxal synthase
mgsA
putative periplasmic protein
yccT
putative inner membrane protein
yccV
Salmonella outer protein: homologous to ipgD of
sopB
4‐hydroxyphenylacetate catabolism
hpaE
hpaI
4‐hydroxyphenylacetate catabolism
curved DNA‐binding protein
cbpA
Suppression of copper sensitivity: putative copper binding
scsA
putative cytoplasmic protein
ymdF
putative transcriptional repressor (TetR/AcrR family)
ycdC
putA
bifunctional in plasma membrane proline dehydrogenase and
putative sodium/glucose cotransporter
putative transcriptional regulator in curly assembly/transport, 2nd
csgG
curli production assembly/transport component, 2nd curli operon
csgF
curli production assembly/transport component, 2nd curli operon
csgE
csgD
putative transcriptional regulator (LuxR/UhpA family)
putative curli production protein
csgC
putative periplasmic protein
ymdA
putative ACR related to the C‐terminal domain
periplasmic glucans biosynthesis protein
mdoG
putative outer membrane lipoprotein
yceK
flgE
flagellar biosynthesis, hook protein
flagellar biosynthesis, cell‐proximal portion of basal‐body rod
flgF
flagellar biosynthesis, cell‐distal portion of basal‐body rod
flgG
outer membrane receptor for Fe(III)‐coprogen, Fe(III)‐ferrioxamine B
fhuE
putative esterase
ycfP
putative outer membrane protein
ycfR
ABC transporter, ATP‐binding protein
ycfV
1.7955384
0.19276725
0.11949775
0.1668846
‐0.08784842
0.41612765
‐0.5576427
‐0.112411916
0.46376753
‐0.33535585
‐0.0918953
1.1376332
0.7095931
‐0.26110312
0.49835232
0.008713709
0.20608158
‐0.560405
‐0.26241556
‐0.4185652
1.7519572
0.08445541
0.67103475
0.03481237
‐0.85597587
0.4057137
0.696366
0.77890545
‐0.53539973
‐0.04397718
‐0.32732183
‐0.60831934
0.8493065
0.9266177
0.7244088
0.3812666
‐0.27883244
‐0.34951028
‐0.41182843
0.42316884
0.70858985
‐0.23059107
‐1.3062085
‐0.22767934
0.27062392
‐0.23515905
‐0.3967707
‐0.43927655
0.60460293
0.4040136
0.15832898
0.37165958
1.193833
‐0.8419666
0.35583586
‐0.44278896
0.27155972
‐0.5271988
0.44850615
0.15711944
0.61755073
0.04622489
‐0.027825346
0.38856125
‐0.894851
‐0.5037716
0.98027563
0.79355973
0.59155977
‐1.7955384
‐0.6243266
0.35814568
0.28247392
‐0.4631164
‐0.5565279
‐0.09547095
0.32926166
‐0.036557928
‐1.2157859
0.07664908
0.22008257
‐0.19417097
‐0.62731314
1.3327785
‐0.7728079
‐0.18909171
0.17430596
0.6117423
‐0.37682334
‐0.6070124
‐0.41014105
‐0.23352773
0.8542845
0.21702328
‐0.6821211
0.4337433
0.34658915
0.42190516
0.77964735
‐0.75900143
‐0.86330074
0.098342165
0.16054967
0.40154338
0.39656392
‐0.5807144
1.4436659
0.55069715
‐0.1828094
‐0.047583573
‐0.8087064
0.4722967
0.25943294
0.024447255
‐3.210016
‐1.7597262
‐1.8477458
6.0525165
1.9568615
‐1.719746
‐2.1532056
‐1.6155987
‐2.1505558
1.6453243
‐1.8481066
‐1.9821059
‐1.7835367
4.4908957
7.501955
2.366718
1.6621474
1.9868742
2.3344712
1.8831567
‐2.16279
‐3.0244715
‐4.526405
1.676569
2.961502
‐1.94025
‐2.7483447
‐2.9508567
‐2.2514381
‐2.770816
‐3.290779
1.7770917
‐1.9149624
‐7.1684628
‐1.6129488
2.7272217
‐1.7146358
‐1.5678964
2.2202878
1.9776976
2.6080453
‐1.851417
‐1.6244359
‐2.6640706
1.8569702
‐1.6049786
2.4259317
2.1301208
1.8738213
1.6474941
‐2.394381
‐1.9073848
1.5206591
2.968651
‐1.8115685
2.1622388
3.8552244
3.1834714
1.597035
‐2.2844927
‐2.3183796
‐2.4646764
‐7.2183504
3.2509615
1.5788158
2.4400842
‐1.9357418
‐2.0096643
‐5.9793787
1.6642708
‐5.0072575
‐2.1235948
‐1.5760477
‐1.7137818
1.5861906
‐1.7718674
‐2.2748322
‐9.174371
‐7.2015295
‐5.7152643
‐1.7235955
‐2.5064335
2.7414734
‐2.848908
2.1189413
3.1507075
‐2.1019766
‐2.5462399
1.7550408
2.089835
‐2.3558972
‐2.476858
‐1.7353709
‐2.967234
‐5.8344264
‐2.2432156
‐2.6396484
1.7923956
‐3.1918595
‐3.496217
‐2.6320384
‐4.3753157
‐7.121766
‐4.225173
‐3.2161393
2.3874726
‐1.9095751
‐1.7683151
‐2.5236685
‐2.0759044
1.758844
‐1.6445006
‐1.8843414
‐1.9173665
‐0.6610619
‐0.4299958
‐0.52701235
1.477358
0.40788195
‐0.35023797
‐0.46535012
‐0.41601005
‐0.44838896
0.43101352
‐0.39792618
‐0.5462902
‐0.35082793
0.99126065
1.6706742
0.57368934
0.46642593
0.4318384
0.58452135
0.42993405
‐0.6100003
‐0.77316743
‐1.0366611
0.47140098
0.65604544
‐0.39612734
‐0.58041734
‐0.9205653
‐0.59583706
‐0.5858979
‐0.731802
0.43248376
‐0.53705525
‐1.5837377
‐0.39187354
0.7778041
‐0.42435774
‐0.34875596
0.5481772
0.6089239
0.7048525
‐0.5488461
‐0.3364993
‐0.51926285
0.52224356
‐0.32340333
0.6378029
0.49966294
0.4617117
0.4500975
‐0.49949095
‐0.7278099
0.36208725
0.6427208
‐0.38428447
0.51662874
0.89793646
0.66588086
0.39585403
‐0.62163687
‐0.6608881
‐0.518
‐1.6085253
0.7384427
0.40480867
0.69245136
‐0.4597353
‐0.5237102
‐1.538247
0.45627418
‐1.3314965
‐0.56166404
‐0.44895193
‐0.4338928
0.3204029
‐0.3830747
‐0.5344706
‐1.8337104
‐1.4780028
‐1.2789366
‐0.38696107
‐0.7407295
0.6724593
‐0.9029276
0.42138618
0.97630244
‐0.46763796
‐0.5262113
0.39683345
0.5049752
‐0.56243765
‐0.6124471
‐0.44503054
‐0.76023734
‐1.5654155
‐0.5075514
‐0.6631503
0.34941962
‐1.0043005
‐0.8307732
‐0.8747101
‐1.3654959
‐1.4728444
‐1.2272855
‐0.88336945
0.59783334
‐0.41174266
‐0.49171424
‐0.6080689
‐0.42729485
0.4042112
‐0.4648065
‐0.42561358
‐0.4429794
0.20593725
0.24435382
0.28521907
0.24408987
0.2084368
0.2036568
0.21611968
0.2574959
0.2084991
0.26196265
0.2153156
0.275611
0.19670351
0.22072671
0.22269851
0.24239868
0.28061646
0.21734561
0.25038704
0.22830498
0.28204325
0.2556372
0.22902527
0.28117004
0.22152455
0.20416304
0.21118797
0.31196544
0.2646473
0.2114532
0.22237955
0.24336603
0.2804521
0.22093129
0.24295473
0.28520015
0.24749146
0.2224356
0.24689466
0.30789536
0.27026084
0.29644653
0.2071484
0.19491333
0.2812342
0.20150009
0.2629105
0.23457024
0.24640115
0.2732013
0.20860963
0.38157478
0.23811205
0.21650265
0.21212803
0.23893233
0.2329142
0.20916815
0.24786809
0.27211156
0.28506464
0.21016958
0.22283834
0.22714594
0.2564002
0.28378174
0.23749825
0.26059586
0.25725865
0.27415863
0.26591334
0.2644874
0.28485936
0.25317854
0.20199521
0.2161983
0.23494947
0.19987315
0.20523457
0.22377558
0.22450806
0.29553127
0.2452912
0.31693813
0.19886638
0.30986768
0.22247534
0.20666212
0.22611067
0.24163401
0.23873608
0.24726775
0.25644693
0.25621077
0.26830667
0.22626063
0.25122675
0.19494559
0.31464434
0.23762059
0.3323318
0.31209084
0.20680887
0.29046988
0.27466765
0.25040427
0.21562004
0.27806935
0.24094641
0.20583552
0.22981639
0.28264293
0.22586861
0.23103532
0
0.05861933
0.063013285
0
0.03676819
0.056731287
0
0.048099868
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0.050878678
0.063013285
0.03676819
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0.055790044
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0.063013285
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0.06489263
0.04736082
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0.0654669
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0.033565152
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0.05861933
0.05046221
0.06489263
0.03424889
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‐0.5260582
‐0.33343032
1.4184393
0.44251212
‐0.37706634
‐0.42593813
‐0.30675235
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0.28459483
‐0.42998475
‐0.37236246
‐0.3486708
0.9580155
1.6586463
0.6729647
0.42625427
0.3849634
0.5100641
0.35502318
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‐0.7889897
‐1.1095876
0.3011361
0.6760607
‐0.42572558
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‐0.673679
‐0.5092478
‐0.5555748
‐0.66387933
0.50777453
‐0.3663575
‐1.5608506
‐0.2981579
0.58997774
‐0.33127868
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0.63560265
0.37024572
0.6266423
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0.4004878
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0.5829259
0.54628253
0.36975694
0.2849219
‐0.50166947
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0.4087879
0.6452878
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0.49917254
0.80960715
0.65986574
0.29125378
‐0.4781753
‐0.8392573
‐0.4746565
‐1.635288
0.66140884
0.4758158
0.6281674
‐0.4043882
‐0.4049356
‐1.6434526
0.31407633
‐1.4173365
‐0.71155953
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0.3429845
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‐1.8201692
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0.559427
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0.40872064
1.1558242
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0.3499813
0.41726974
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1.0559162
1.7351841
0.4872057
0.64241004
0.48471278
0.70760614
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0.6332867
0.49719876
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0.7175984
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0.44216406
1.0283022
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1.4249496
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1.6181923
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‐0.4751201
130
STM1224
STM1237
STM1238
STM1255
STM1261
STM1263
STM1264
STM1267
STM1274
STM1279
STM1280
STM1284
STM1285
STM1291
STM1295
STM1304
STM1310
STM1315
STM1335
STM1336
STM1338
STM1341
STM1345
STM1367
STM1370
STM1372
STM1373
STM1374
STM1378
STM1384
STM1393
STM1396
STM1397
STM1398
STM1399
STM1400
STM1401
STM1402
STM1406
STM1407
STM1408
STM1409
STM1410
STM1411
STM1412
STM1413
STM1419
STM1420
STM1427
STM1431
STM1440
STM1445
STM1451
STM1478
STM1489
STM1496
STM1497
STM1509
STM1512
STM1513
STM1525
STM1552
STM1554
STM1567
STM1586
STM1591
STM1592
STM1593
STM1594
STM1595
STM1601
STM1612
STM1613
STM1614
STM1616
STM1623
STM1644
STM1645
STM1651
STM1660
STM1661
STM1662
STM1682
STM1698
STM1708
STM1713
STM1716
STM1724
STM1725
STM1726
STM1728
STM1732
STM1749
STM1751
STM1753
STM1754
STM1764
STM1770
STM1774
STM1781
STM1782
STM1786
STM1788
STM1790
STM1801
STM1812
STM1815
STM1823
STM1825
STM1836
STM1837
STM1838
STM1839
STM1840
lysosomal glycoprotein (lgp)‐containing structures replication in macrophages
sifA
putative ribosomal large subunit pseudouridine synthase
ymfC
isocitrate dehydrogenase in e14 prophage, specific for
icdA
putative ABC transporter periplasmic binding protein
putative cytoplasmic protein
putative periplasmic protein
Aminoglycoside adenyltransferase
aadA
putative cytoplasmic protein
yeaQ
putative inner membrane protein
putative regulator (AraC/XylS family)
yeaM
putative inner membrane protein
yeaL
putative cytoplasmic protein
yeaH
putative Ser protein kinase
yeaG
putative domain frequently associated with peptide methionine
yeaA
protease IV, a signal peptide peptidase
sppA
arginine succinyltransferase
astA
NAD synthetase, prefers NH3 over glutamine
nadE
transcriptional repressor of cel operon (AraC/XylS family)
celD
50S ribosomal subunit protein L35
rpmI
50S ribosomal subunit protein L20
rplT
phenylalanine tRNA synthetase, beta‐subunit
pheT
btuE
ABC superfamily (binding protein), vitamin B12 transport
putative cytoplasmic protein
ydiU
putative cytoplasmic protein
ydiH
putative ABC transporter
sufB
required for stability of iron‐sulfur component of
sufD
selenocysteine lyase
sufS
putative SufE protein probably involved in Fe‐S
ynhA
pyruvate kinase I (formerly F), fructose stimulated
pykF
Tetrathionate reductase complex, subunit C
ttrC
ssaB
Secretion system apparatus
Secretion system effector
ssaE
Secretion system effector
sseA
Secretion system effector
sseB
Secretion system chaparone
sscA
Secretion system effector
sseC
Secretion system effector
sseD
Secretion system effector
sseE
Secretion system apparatus
ssaG
Secretion system apparatus
ssaH
Secretion system apparatus
ssaI
Secretion system apparatus: homology with the yscJ/mxiJ/prgK
ssaJ
putative cytoplasmic protein
Secretion system apparatus
ssaK
Secretion system apparatus
ssaL
Secretion system apparatus
ssaM
Secretion system apparatus: homology with YscR of
ssaR
Secretion system apparatus: homology with YscS of
ssaS
cyclopropane fatty acyl phospholipid synthase
cfa
superoxide dismutase, iron
sodB
copper/zinc superoxide dismutase
sodC
putative outer membrane lipoprotein
slyB
glutathionine S‐transferase
gst
putative periplasmic protein
ydgH
putative dethiobiotin synthase
ynfK
putative dimethylsulfoxide reductase
putative dimethyl sulphoxide reductase
putative cytoplasmic protein
ydfZ
dipeptidyl carboxypeptidase II
dcp
putative cytoplasmic protein
putative glutaminase
yneH
putative cytoplasmic protein
putative coiled‐coil protein
alcohol dehydrogenase, propanol preferring
adhP
putative periplasmic protein
putative inner membrane protein
ydcZ
putative cytoplasmic protein
ydcY
ssrAB activated gene
srfA
ssrAB activated gene
srfB
ssrAB activated gene: predicted coiled‐coil structure
srfC
putative membrane protein: homology with chitinase from
ugtL
putative cellulase protein
putative PTS system, enzymeIIB component
putative PTS system enzyme IIC component
putative Sugar Specific PTS Enzyme II
putative carboxylesterase
putative periplasmic protein
ydbL
ynbE
putative outer membrane lipoprotein
putative pyruvate‐flavodoxin oxidoreductase
nifJ
transcriptional regulation of aerobic, anaerobic respiration, osmotic
fnr
putative universal stress protein
ydaA
putative inner membrane protein
ynaJ
thiol peroxidase
tpx
putative inner membrane protein
putative N‐acetylglucosaminyl transferase
yciM
cysB
transcriptional regulator for cysteine regulon (LysR familiy)
putative peptidase
sohB
anthranilate synthase, component II, bifunctional: glutamine amidotransferase
trpD
bifunctional: N‐(5‐phosphoribosyl)anthranilate isomerase indole‐3‐glycerolphosphate synthe trpC
tryptophan synthase, beta protein
trpB
putative cytoplasmic protein
yciG
outer membrane protein W colicin S4 receptor
ompW
iron‐dependent alcohol dehydrogenase of the multifunctional alcohol
adhE
DNA‐binding protein HLP‐II (HU, BH2, HD, NS)
hns
hnr
Response regulator in protein turnover: mouse virulence
putative phosphoesterase
ychK
nitrate reductase 1, alpha subunit
narG
cation transport regulator
chaB
Regulation of invasion genes
sirC
putative SulP family transport protein
ychM
putative inner membrane protein
ychH
hydrogenase‐1 small subunit
putative Ni/Fe‐hydrogenase 1 b‐type cytochrome subunit
putative thiol‐disulfide isomerase and thioredoxins
putative CPA1 family, Na:H transport protein
ycgO
putative Fumarylacetoacetate (FAA) hydrolase family
ycgM
minD
cell division inhibitor, a membrane ATPase, activates
putative cytoplasmic protein
yoaH
putative NTP pyrophosphohydrolase
yeaB
putative penicillin‐binding protein‐3
cold shock protein, multicopy suppresses mukB mutants
cspC
putative cytoplasmic protein
yobF
putative periplasmic or exported protein
putative inner membrane protein
yobG
‐0.6748907
0.67902565
0.3889185
‐0.85976905
0.4246444
‐0.3720983
‐0.4489355
‐1.6276593
‐0.5106567
0.596286
0.41556072
‐1.0195017
0.5807144
0.2485467
0.009176371
0.17579252
‐0.043558788
‐0.22973107
‐0.3579326
‐5.18E‐04
0.589356
‐0.72050655
0.54063034
‐0.77816063
0.5088498
0.31884903
1.4544895
0.09703424
‐0.72706467
0.3823088
‐3.5863433
1.0441267
0.97233033
0.41536158
‐0.018371316
‐0.92264754
‐0.29012236
0.35549143
‐0.52065974
‐0.39101136
‐0.24232072
0.28364876
‐0.06895825
0.21816084
0.9547462
‐0.716915
‐0.13103093
0.01898982
0.4185652
0.17044921
0.2806547
‐0.338812
‐0.5933706
‐1.193833
‐0.6498044
0.6945419
0.6914045
‐3.926644
0.18678641
0.10918752
0.41990083
‐0.52230024
0.07525889
‐0.3468314
‐0.915721
0.13037644
0.7944661
0.20990089
0.59881985
0.36089244
‐0.25149482
0.088906236
‐0.10828866
0.49615058
0.047583573
0.17831652
0.43623662
0.44094396
0.6186724
‐0.85749865
‐0.15250711
‐0.43658268
0.3756022
0.045942247
‐0.7503825
‐0.12179912
‐0.23099546
0.27366877
0.34277532
‐0.79187536
0.36959308
‐0.12717927
0.37748227
‐0.72885436
‐0.35583586
‐0.009772128
‐0.16630559
0.48628333
0.33346766
0.30978233
‐0.006837662
0.72050655
0.42897072
‐0.5935595
‐0.06272232
‐0.8043529
‐0.31884903
0.4166632
‐0.2603662
0.10412655
0.338812
‐0.4868646
0.9481789
‐0.22598222
‐2.6178644
‐1.8545784
1.7481579
1.6431319
1.5545261
11.453309
1.5995172
‐2.0003424
2.818252
‐1.8185207
‐1.8218545
1.5069036
3.1448574
2.4102736
‐1.6234945
‐2.2579145
1.6405406
2.3955271
‐5.4844904
‐4.481987
1.7982643
1.9587833
4.359923
‐4.127592
8.448214
6.0610247
3.9399076
3.3610842
4.527835
‐1.8441163
‐3.321381
‐3.704352
‐4.8352513
‐6.4116616
‐5.2020483
‐2.8720765
‐2.187747
‐2.1521764
‐5.901822
‐11.970955
‐7.416066
‐5.6432705
‐5.8044457
‐3.228976
‐4.32037
‐3.9147432
‐7.5789514
‐2.9427886
2.7529767
‐4.0022006
2.893049
2.7311957
2.0478852
1.9415034
‐4.431105
‐1.5442942
‐1.8863444
‐3.2346575
1.5201771
‐1.6188295
‐1.6722969
1.8279696
2.1909156
1.9271544
4.32344
‐2.0564837
‐1.793019
‐1.6977005
‐2.2193012
‐1.7212176
‐4.7809167
‐2.5167675
‐1.85785
‐1.7630444
‐2.7225544
‐2.429326
‐1.7277565
‐1.9450592
‐1.5383135
1.5622748
1.6208183
2.4383981
2.793964
‐2.3116808
1.6700544
1.7845266
1.8918875
3.805509
3.0510228
2.9440353
‐3.1783125
‐1.6688439
‐4.5034084
1.5504103
1.5627533
1.736842
‐1.5444626
2.3577487
‐1.602213
‐1.6164109
‐1.7690433
‐1.8940483
‐2.9473095
‐1.6620376
‐1.5632942
1.9445734
2.2938716
‐2.046521
‐1.9616361
1.7451955
‐2.1933084
‐1.6014076
‐3.0785325
‐2.68555
‐0.7439603
‐0.35797212
0.3568656
0.34467316
0.4261478
2.2708313
0.3191596
‐0.5169653
0.73309934
‐0.47315857
‐0.3674988
0.33913857
0.6973707
0.6207158
‐0.38114733
‐0.5842572
0.35218927
0.5065527
‐1.617162
‐1.1953037
0.36011034
0.4892975
1.3019979
‐1.1103107
1.8081558
1.4977404
0.92516994
0.77273583
1.0338037
‐0.48361963
‐0.94357896
‐0.78974617
‐1.2037889
‐1.57193
‐1.1248634
‐0.8302631
‐0.48835576
‐0.58988625
‐1.5728054
‐2.4865324
‐1.7376173
‐1.5680448
‐1.2747184
‐0.98158574
‐1.4888674
‐0.8005478
‐2.0216393
‐0.67480695
0.55761516
‐1.0226153
0.6454468
0.6346749
0.46913302
0.36741075
‐1.0965344
‐0.33959153
‐0.4750416
‐1.1263951
0.33116612
‐0.6046071
‐0.4214768
0.3799975
0.45562753
0.42115048
1.1393574
‐0.55696636
‐0.46596527
‐0.5505139
‐0.5292037
‐0.46938416
‐1.178434
‐0.6693413
‐0.37949064
‐0.48960954
‐0.6297695
‐0.6851491
‐0.33559528
‐0.41516778
‐0.41540343
0.38641268
0.31413227
0.5442187
0.6592289
‐0.6160934
0.37725565
0.4553582
0.4465226
0.752909
0.6466134
0.7161858
‐0.9411072
‐0.42574275
‐1.0059755
0.4070008
0.33332562
0.39835596
‐0.3304342
0.534197
‐0.4214592
‐0.3744907
‐0.37773493
‐0.4484414
‐0.6711616
‐0.39791244
‐0.31932694
0.5223995
0.550004
‐0.42742923
‐0.4049636
0.34207723
‐0.46800873
‐0.36553746
‐0.74039847
‐0.56033957
0.28418598
0.19302075
0.2041381
0.20976597
0.27413356
0.19826858
0.19953495
0.25843844
0.26012555
0.26018873
0.20171687
0.22505657
0.22174954
0.2575292
0.2347697
0.25875965
0.2146788
0.21145771
0.29486093
0.26669058
0.20025441
0.24979666
0.29862866
0.2689972
0.21402818
0.2471101
0.23482022
0.22990672
0.22832187
0.26225007
0.28409234
0.21319415
0.24896097
0.24516734
0.2162347
0.28908113
0.22322313
0.27408823
0.2664949
0.2077138
0.23430444
0.277861
0.2196107
0.3039929
0.3446157
0.20449561
0.26674393
0.22930868
0.2025499
0.25551325
0.22310261
0.23237987
0.2290817
0.18924034
0.24746296
0.2199008
0.25183186
0.348227
0.21784706
0.3734841
0.2520347
0.20787956
0.20796216
0.21853489
0.26353028
0.27083433
0.25987747
0.32427034
0.2384551
0.27270472
0.24648704
0.2659528
0.20426334
0.27770686
0.23131567
0.28203258
0.1942376
0.21344738
0.27003822
0.24733976
0.19381091
0.22318698
0.23594755
0.26651317
0.22589423
0.25517032
0.23601963
0.19784711
0.21193333
0.24326672
0.2961028
0.25511238
0.22338091
0.26251167
0.21329382
0.22935647
0.2139477
0.22657079
0.26304817
0.2316804
0.21352497
0.23676343
0.2277201
0.23941241
0.20426542
0.26864478
0.23977105
0.20885651
0.20644176
0.19601083
0.21338026
0.2282601
0.24050371
0.20864984
0
0.06410537
0.058067188
0.050878678
0.046063263
0
0.048099868
0
0
0.061239734
0.061239734
0.08572143
0
0
0.048099868
0
0.050878678
0
0
0
0.06083684
0.03676819
0
0
0
0
0
0
0
0.063013285
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0.036121875
0
0.06573839
0.0654669
0
0.06573839
0.048099868
0.052916735
0.063013285
0
0.035160456
0
0
0.060340617
0.055124886
0
0.056731287
0
0
0.06410537
0.05861933
0
0
0.056731287
0.035160456
0.08572143
0.046063263
0.04958284
0
0
0
0.052916735
0.060340617
0.033565152
0
0
0
0
0.052023627
0
0.046063263
0.046063263
0.057885446
0.06573839
0
0.04736082
0.048099868
0.05861933
0.0654669
0
0.052023627
0.066927865
0.036121875
0
0
0.035703473
0.058067188
0
0.04736082
0
0
‐0.9267093
‐0.3603536
0.33846152
0.37114596
0.27194655
2.2810953
0.3403232
‐0.5855323
0.65378964
‐0.32984093
‐0.3692966
0.2744936
0.68933046
0.5449279
‐0.2943676
‐0.44366714
0.29985374
0.5395745
‐1.4608428
‐1.0606834
0.3735125
0.5887696
1.1109093
‐1.1607132
1.8288628
1.4969852
1.0143319
0.6949266
1.0706054
‐0.3832782
‐1.0297388
‐0.81178594
‐1.091089
‐1.6741128
‐1.1751125
‐0.89993477
‐0.45797774
‐0.7404304
‐1.7223208
‐2.5226486
‐1.7125388
‐1.745902
‐1.2823895
‐1.212782
‐1.1971893
‐0.77967024
‐2.10759
‐0.6231562
0.53838634
‐1.1040957
0.63274634
0.54758734
0.41312236
0.36855495
‐1.1623932
‐0.3685398
‐0.3500527
‐1.3511477
0.27252302
‐0.7871764
‐0.31196776
0.35886806
0.43193775
0.4718006
1.0042905
‐0.41115236
‐0.38371983
‐0.6197868
‐0.44180423
‐0.6356835
‐1.0815575
‐0.52231705
‐0.3519927
‐0.33452767
‐0.5471751
‐0.6286272
‐0.33070552
‐0.4214404
‐0.5660243
0.2812335
0.30495355
0.532323
0.6041635
‐0.7111045
0.30234858
0.3855786
0.5411348
0.7407707
0.68937397
0.6247902
‐0.90716577
‐0.3329894
‐0.94126964
0.28761715
0.30030814
0.47854376
‐0.28035256
0.564737
‐0.47131088
‐0.43034276
‐0.42107615
‐0.35838655
‐0.7412754
‐0.31401733
‐0.30309612
0.6757513
0.64360964
‐0.40831774
‐0.38418204
0.339694
‐0.41805288
‐0.30826873
‐0.64205503
‐0.582477
‐0.7023861
‐0.3645241
0.38819313
0.3023748
0.56820977
2.2803102
0.3025448
‐0.5884757
0.6692242
‐0.53718746
‐0.34357765
0.40142876
0.7587421
0.75876415
‐0.45289037
‐0.64911693
0.38263682
0.46215114
‐1.5701078
‐1.1933404
0.37035775
0.37719476
1.4927708
‐1.217718
1.8384182
1.599814
0.8581476
0.8367215
1.076777
‐0.43991503
‐1.0485076
‐0.8172066
‐1.2985953
‐1.4779617
‐1.1205108
‐0.95905095
‐0.44925886
‐0.5855545
‐1.4588965
‐2.480366
‐1.8266512
‐1.4621507
‐1.324541
‐0.865683
‐1.7317013
‐0.8322191
‐2.092133
‐0.64566845
0.5852242
‐1.0742626
0.5926958
0.6674519
0.4460167
0.3679174
‐1.1485412
‐0.37358811
‐0.55640876
‐1.210879
0.3652916
‐0.79220533
‐0.5324096
0.4189197
0.44049537
0.42413142
1.1498488
‐0.5632204
‐0.6083607
‐0.28830865
‐0.5306051
‐0.41037938
‐1.1713259
‐0.7856752
‐0.3795157
‐0.6439114
‐0.6508115
‐0.8680327
‐0.32884836
‐0.4550827
‐0.39470112
0.39288732
0.31373945
0.49079153
0.75391585
‐0.4611765
0.41149044
0.58886385
0.38968608
0.77152985
0.60817844
0.7092721
‐1.1423037
‐0.555194
‐1.0152637
0.39059618
0.38211897
0.34373415
‐0.3466574
0.45832387
‐0.27464998
‐0.2892813
‐0.33402443
‐0.5240665
‐0.6669674
‐0.38956434
‐0.3038189
0.4047032
0.539904
‐0.405646
‐0.38979676
0.35629803
‐0.49406308
‐0.44221333
‐0.8194449
‐0.57865244
‐0.60278565
‐0.34903866
0.34394217
0.3604987
0.43828702
2.2510886
0.31461075
‐0.376888
0.8762841
‐0.5524473
‐0.38962212
0.3414933
0.6440396
0.5584553
‐0.39618397
‐0.6599875
0.37407726
0.5179325
‐1.8205353
‐1.3318871
0.3364608
0.50192815
1.3023136
‐0.95250094
1.7571864
1.3964219
0.9030303
0.78655946
0.9540288
‐0.62766564
‐0.7524905
‐0.74024594
‐1.2216823
‐1.5637157
‐1.0789667
‐0.6318036
‐0.55783063
‐0.44367382
‐1.5371989
‐2.4565828
‐1.6736618
‐1.4960818
‐1.2172247
‐0.86629224
‐1.5377116
‐0.78975403
‐1.865195
‐0.7555962
0.549235
‐0.8894877
0.7108983
0.6889855
0.54826
0.36575988
‐0.97866875
‐0.27664664
‐0.51866335
‐0.81715876
0.35568377
‐0.23443952
‐0.4200531
0.3622047
0.4944495
0.3675194
1.263933
‐0.69652635
‐0.4058153
‐0.74344635
‐0.6152019
‐0.36208963
‐1.2824186
‐0.7000317
‐0.40696353
‐0.49038953
‐0.69132197
‐0.5587874
‐0.34723192
‐0.3689802
‐0.28548488
0.4851172
0.3237038
0.6095416
0.6196073
‐0.67599916
0.41792795
0.3916322
0.40874696
0.74642646
0.64228785
0.81449515
‐0.77385217
‐0.3890448
‐1.0613933
0.5427891
0.3175498
0.37279
‐0.36429262
0.5795301
‐0.5184167
‐0.40384802
‐0.37810418
‐0.46287107
‐0.6052419
‐0.49015567
‐0.3510658
0.48674396
0.46649835
‐0.46832395
‐0.440912
0.33023962
‐0.49191025
‐0.34613034
‐0.7596955
‐0.51988935
131
STM1854
STM1867
STM1888
STM1890
STM1891
STM1902
STM1907
STM1915
STM1916
STM1945
STM1946
STM1947
STM1959
STM1972
STM1978
STM1990
STM2017
STM2022
STM2024
STM2025
STM2027
STM2028
STM2029
STM2033
STM2039
STM2041
STM2043
STM2045
STM2046
STM2048
STM2049
STM2050
STM2052
STM2053
STM2054
STM2056
STM2058
STM2059
STM2071
STM2072
STM2073
STM2083
STM2087
STM2088
STM2089
STM2090
STM2091
STM2105
STM2106
STM2107
STM2108
STM2115
STM2137
STM2138
STM2139
STM2141
STM2146
STM2147
STM2148
STM2165
STM2177
STM2182
STM2199
STM2215
STM2220
STM2228
STM2232
STM2238
STM2263
STM2267
STM2277
STM2278
STM2281
STM2284
STM2285
STM2287
STM2288
STM2302
STM2303
STM2305
STM2309
STM2316
STM2317
STM2318
STM2319
STM2320
STM2321
STM2323
STM2324
STM2326
STM2327
STM2328
STM2336
STM2337
STM2338
STM2352
STM2354
STM2355
STM2356
STM2361
STM2362
STM2378
STM2379
STM2381
STM2387
STM2389
STM2390
STM2398
STM2402
STM2405
STM2408
STM2409
STM2430
STM2432
putative inner membrane protein
PhoPQ‐activated gene
pagK
pyruvate kinase II, glucose stimulated
pykA
putative Peptidase
yebA
ABC superfamily (bind_prot) high affinity Zn transport
znuA
putative isochorismatase
yecD
copper homeostasis protein
cutC
cheZ
chemotactic response CheY protein phophatase
chemotaxis regulator, transmits chemoreceptor signals to flagelllar
cheY
phosphatidylglycerophosphate synthetase (CDP‐1,2‐diacyl‐sn‐glycero‐3‐phosphate phosphat pgsA
UvrC with UvrAB is a DNA excision
uvrC
putative response regulator (LuxR/UhpA familiy)
uvrY
flagellar biosynthesis flagellin, filament structural protein
fliC
fliI
flagellum‐specific ATP synthase
flagellar biosynthesis
fliO
putative permease
yedA
cobalamin 5‐phosphate synthase
cobS
synthesis of vitamin B12 adenosyl cobalamide precursor
cbiN
synthesis of vitamin B12 adenosyl cobalamide precursor
cbiL
cbiK
synthesis of vitamin B12 adenosyl cobalamide precursor
synthesis of vitamin B12 adenosyl cobalamide precursor
cbiH
synthesis of vitamin B12 adenosyl cobalamide precursor
cbiG
synthesis of vitamin B12 adenosyl cobalamide precursor
cbiF
cbiC
synthesis of vitamin B12 adenosyl cobalamide precursor
Propanediol utilization: polyhedral bodies
pudB
Propanediol utilization: dehydratase, medium subunit
pduD
Propanediol utilization: diol dehydratase reactivation
pduG
Propanediol utilization: polyhedral bodies
pduJ
pduK
Propanediol utilization: polyhedral bodies
Propanediol utilization
pduM
Propanediol utilization: polyhedral bodies
pduN
Propanediol utilization: B12 related
pduO
Propanediol utilization: propanol dehydrogenase
pduQ
Propanediol utilization: polyhedral bodies
pduS
pduT
Propanediol utilization: polyhedral bodies
Propanediol utilization
pduV
Propanediol utilization
pduX
putative cytoplasmic protein
yeeX
ATP phosphoribosyltransferase
hisG
histidinal dehydrogenase (also histidinol dehydrogenase activity)
hisD
histidinol phosphate aminotransferase
hisC
LPS side chain defect: phosphomannomutase
rfbK
LPS side chain defect: abequosyltransferase
rfbV
LPS side chain defect: putative O‐antigen transferase
rfbX
rfbJ
LPS side chain defect: CDP‐abequose synthase
LPS side chain defect: CDP‐6deoxy‐D‐xylo‐4‐hexulose‐3‐dehydrase
rfbH
LPS side chain defect: CDP glucose 4,6‐dehydratase
rfbG
mannose‐1‐phosphate in colanic acid gene cluster
manC
putative glycosyl transferase in colanic acid biosynthesis
wcaI
wcaH
GDP‐mannose mannosyl hydrolase in colanic acid biosynthesis
bifunctional GDP fucose synthetase in colanic acid
wcaG
putative glycosyl transferase in colanic acid biosynthesis
wcaA
putative cytoplasmic protein
putative cytoplasmic protein
putative inner membrane protein
fbaB
3‐oxoacyl‐[acyl‐carrier‐protein] synthase I
bifunctional enzyme: hydroxy‐phosphomethylpyrimidine kinase (HMP‐P kinase) hydroxy‐met thiD
hydoxyethylthiazole kinase (THZ kinase)
thiM
putative periplasmic protein
putative ABC superfamily (bind_prot) transport protein (possibly
yehZ
putative flutathione S‐transferase
putative transmembrane protein
yohK
outer membrane porin, receptor for colicin I
cirA
putative membrane protein involved in resistance to
rtn
putative cytoplasmic protein
yejG
yejM
putative hydrolase of alkaline phosphatase superfamily
O‐antigen five: acetylation of the O‐antigen (LPS)
oafA
putative phage protein
putative ABC‐type multidrug/protein/lipid transport system, ATPase component
yojI
outer membrane protein 1b (ibc), porin
ompC
ribonucleoside diphosphate reductase 1, alpha subunit
nrdA
ribonucleoside‐diphosphate reductase 1, beta subunit
nrdB
putative transcriptional regulator, LysR family
sn‐glycerol‐3‐phosphate dehydrogenase (anaerobic), large subunit
glpA
sn‐glycerol‐3‐phosphate dehydrogenase (anaerobic), membrane anchor subunit
glpB
putative cytoplasmic protein
putative cytoplasmic protein
putative inner membrane protein
putative inner membrane protein
o‐succinylbenzoate‐CoA ligase
menE
bifunctional: 2‐oxoglutarate decarboxylase SHCHC synthase
menD
NADH dehydrogenase I chain N
nuoN
NADH dehydrogenase I chain M
nuoM
NADH dehydrogenase I chain L
nuoL
NADH dehydrogenase I chain K
nuoK
NADH dehydrogenase I chain J
nuoJ
NADH dehydrogenase I chain I
nuoI
NADH dehydrogenase I chain G
nuoG
NADH dehydrogenase I chain F
nuoF
NADH dehydrogenase I chain C,D
nuoC
NADH dehydrogenase I chain B
nuoB
NADH dehydrogenase I chain A
nuoA
putative cytoplasmic protein
ackA
acetate kinase A (propionate kinase 2)
phosphotransacetylase
pta
ABC superfamily (membrane),histidine and lysine/arginine/ornithine transport protein
hisM
ABC superfamily (bind_prot), histidine transport protein
hisJ
ABC superfamily (bind_prot), lysine/arginine/ornithine transport protein
argT
ubiX
3‐octaprenyl‐4‐hydroxybenzoate carboxy‐lyase
putative regulatory protein
amidophosphoribosyltransferase (PRPP amidotransferase)
purF
3‐oxoacyl‐[acyl‐carrier‐protein] synthase I
fabB
putative peptidase
putative cytoplasmic protein
yfcM
phosphohistidine phosphatase
sixA
yfcY
paral putative acetyl‐CoA acetyltransferase
putative cytoplasmic protein
yfcZ
Phosphoglycerate transport: protein for signal transmission
pgtC
putative aminotransferase
yfdZ
putative thiamine pyrophosphate enzymes
Nramp family, manganese/divalent cation transport prortein
mntH
NUP family, nucleoside transport
nupC
cysK
subunit of cysteine synthase A and O‐acetylserine
General PTS family (Enzyme I) PEP‐protein phosphotransferase
ptsI
‐0.14225803
0.23225684
‐0.8872296
0.48606992
0.27830613
0.65049744
0.04163464
0.46254298
0.6972522
0.17695531
‐0.5243877
0.08631868
‐0.4239646
0.5728258
0.10780544
‐0.03008651
0.012055409
0.1329408
0.6821211
‐0.17740087
‐0.34015727
‐1.1164812
0.18976788
‐0.23452298
0.2779956
0.49715197
‐0.25450563
0.78167754
0.242989
0.7955477
‐0.6600288
0.134613
0.06272232
0.55507284
‐0.7478967
0.20473526
0.70679843
0.07272805
0.010775363
0.7553158
0.124783926
‐1.1639477
0.5941703
‐0.48211044
0.2607379
3.926644
0.3878993
‐0.43147963
‐0.06639378
‐0.08616231
0.3645222
0.25384754
0.0023499
0.74059606
0.32774305
0.29865554
0.08117722
‐0.15110785
‐0.95610934
‐0.13962671
0.5935595
0.41579372
‐0.12922949
‐0.29431117
‐0.19318686
‐0.14666101
0.32732183
0.36262566
‐0.96113396
‐0.7809095
‐0.48932013
‐2.1630812
0.17133029
0.6802861
‐0.2790565
0.23472808
0.2042397
0.68675524
0.3675542
0.52284837
‐0.6644143
‐0.3913837
‐0.070373535
0.5106567
0.5521063
‐0.13995406
‐0.64088565
‐0.7296543
0.3997259
0.61789894
‐1.7359381
‐0.4166632
‐0.66304207
0.5191252
0.75595593
‐0.48606992
1.7563617
‐0.63420165
0.7143338
0.8369787
0.16881002
0.2437359
‐0.031086246
0.44535005
‐0.1834248
0.13399245
‐0.28506687
‐0.15515926
‐0.08337924
‐0.5341613
‐0.57709175
‐0.8325245
‐0.54243934
1.0520763
‐1.8908732
‐1.7750379
‐1.7508423
3.0416074
6.4869614
‐1.8461673
‐2.8789215
‐1.6862135
‐1.9842178
1.5019146
2.2524245
2.1065667
2.0544918
‐1.9406577
‐2.7776895
‐1.617108
‐1.613745
‐2.8734584
‐1.9011219
‐1.9498528
‐1.622655
‐1.7631509
‐2.417208
‐1.536577
‐2.9346273
‐2.9236968
‐2.400453
‐3.0361834
‐2.8958943
‐2.5935204
‐3.3329809
‐4.498622
‐2.2732737
‐2.4895022
‐1.7570235
‐2.086925
2.0807743
1.5468447
4.8080096
2.816082
1.7110859
2.0992186
4.508169
1.9578187
2.8666573
2.1308615
1.5706683
‐2.6516657
‐1.5617541
‐2.3840563
‐1.8586746
‐1.6581541
1.7516836
‐2.107548
‐6.303984
5.2366257
4.1462216
3.2664611
2.5296724
1.7878022
‐2.0857024
‐1.7213658
1.5710416
1.6561495
2.620795
1.6415534
1.6109928
1.6090502
2.2059066
‐1.9021436
2.1312099
2.0535486
1.546044
‐1.773006
‐2.5175543
‐6.2657723
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‐1.6581715
‐2.62942
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‐3.9200768
‐3.036932
‐1.7319527
‐2.0668354
‐2.155235
‐3.00943
‐3.8015668
‐1.9314836
‐2.5627573
‐1.6542156
‐2.05375
‐2.351337
‐1.5773194
‐2.774061
‐6.5478616
‐1.7028176
1.6060458
2.1691628
‐2.6296556
‐2.1643114
‐1.8295588
‐2.1401942
‐2.0348394
‐4.8828397
1.5940671
2.7230554
‐1.5316386
2.3724792
2.2364955
2.981871
1.9883046
‐0.57870054
‐0.546496
‐0.46418396
0.7799957
1.3998303
‐0.38982597
‐0.64926696
‐0.34680057
‐0.40368968
0.40419325
0.46098557
0.44886565
0.53775656
‐0.3873637
‐0.6053593
‐0.42059827
‐0.37900436
‐0.6194955
‐0.48326436
‐0.54513216
‐0.32925114
‐0.41459784
‐0.53393686
‐0.4781363
‐0.6442693
‐0.66400766
‐0.7069993
‐0.8561333
‐0.7494269
‐0.5469762
‐0.7046891
‐1.186744
‐0.5017642
‐0.59797454
‐0.48667103
‐0.44307682
0.42267004
0.37417004
1.3240678
0.59487605
0.4798721
0.5090754
0.95922565
0.5429813
0.6779768
0.4609501
0.30383807
‐0.66243654
‐0.35225782
‐0.5075489
‐0.46265164
‐0.4503259
0.37919724
‐0.4649673
‐1.4011434
1.0823237
0.8702698
0.79367554
0.63332325
0.36244223
‐0.56562793
‐0.4044415
0.3538934
0.42364764
0.6993397
0.3987934
0.43825793
0.465682
0.562082
‐0.53480476
0.5401507
0.43424866
0.43788272
‐0.39965507
‐0.5193986
‐1.7654071
‐0.5073072
‐0.340133
‐0.39424852
‐0.41073996
‐0.56831187
‐0.5714599
‐0.6920966
‐0.94015235
‐0.7651977
‐0.5037587
‐0.50264955
‐0.49767953
‐1.1499493
‐0.8547408
‐0.3917852
‐0.5517462
‐0.3539837
‐0.45850068
‐0.49103177
‐0.382113
‐0.66503084
‐1.3726482
‐0.4425513
0.34779134
0.62381923
‐0.63853145
‐0.4638559
‐0.42270818
‐0.46132487
‐0.56511503
‐1.0083835
0.34968966
0.5595862
‐0.33553457
0.52456117
0.4327145
0.6296421
0.48012874
0.30604938
0.3078785
0.26512036
0.25644192
0.21579137
0.2111542
0.22552437
0.20566824
0.20345029
0.26911867
0.20466195
0.21307926
0.26174676
0.19960433
0.21793628
0.26009288
0.23486014
0.21559231
0.25419956
0.27957606
0.20290889
0.23514597
0.22088991
0.31116977
0.21954042
0.22711235
0.29452744
0.28197682
0.25878945
0.21090107
0.21142909
0.26380166
0.22072317
0.24019843
0.27698606
0.21231085
0.20313112
0.24189243
0.27538794
0.21124245
0.28044885
0.2425071
0.21277499
0.27733994
0.2365043
0.216321
0.19344509
0.24981903
0.22555268
0.21289301
0.24891481
0.27158266
0.21647587
0.22062004
0.22226316
0.20668341
0.20989466
0.24297719
0.2503578
0.20273061
0.27119303
0.23495384
0.22526036
0.25580278
0.26684257
0.2429366
0.27204216
0.28941423
0.2548077
0.28115898
0.25344792
0.21146257
0.28322786
0.22541101
0.2063108
0.2817541
0.22958905
0.21719901
0.25625712
0.24770656
0.21613583
0.28881946
0.3006458
0.23983008
0.25196406
0.29086173
0.24319766
0.23091659
0.38211533
0.22483908
0.20284158
0.21529397
0.21398886
0.22325048
0.20883088
0.24225469
0.23973188
0.20963305
0.25989357
0.21655132
0.28758526
0.24281941
0.21432032
0.23104377
0.2155528
0.27771974
0.20651579
0.21936947
0.2054994
0.21906902
0.22110254
0.19347881
0.21115674
0.24147645
0.0654669
0.05861933
0.058067188
0
0
0.063013285
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0.05455575
0.03676819
0.08572143
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0.035160456
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‐0.8055051
‐0.72634923
‐0.45786908
0.7314299
1.3631965
‐0.3656827
‐0.6602084
‐0.377238
‐0.38359508
0.55077624
0.4476193
0.4637784
0.39477825
‐0.3656029
‐0.57403517
‐0.28627598
‐0.35943896
‐0.5787262
‐0.36653033
‐0.5268891
‐0.30465424
‐0.35900822
‐0.57792366
‐0.6331885
‐0.60162073
‐0.6417456
‐0.83050066
‐0.6813047
‐0.8887621
‐0.5684741
‐0.7128168
‐1.039871
‐0.44857442
‐0.49494177
‐0.43534124
‐0.4730784
0.39321396
0.32313725
1.4977757
0.62781864
0.6341258
0.4056601
0.98017097
0.64507776
0.5925547
0.51607764
0.29437086
‐0.59368026
‐0.42459244
‐0.5529024
‐0.5649272
‐0.61527276
0.3653426
‐0.5279302
‐1.4245783
1.0503691
0.8380818
0.8900621
0.7350009
0.33395103
‐0.43391448
‐0.49740475
0.42267513
0.38642746
0.545852
0.30365953
0.3239555
0.27185622
0.6755607
‐0.3649795
0.64364344
0.45811883
0.48504767
‐0.4733156
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‐1.9183186
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0.54774284
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0.4415167
0.6733387
0.5854015
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0.6941771
1.3828597
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0.49335694
0.48216712
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‐0.73989624
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‐0.6592007
‐0.3958133
0.43653312
0.3182445
1.2457414
0.60583025
0.4897871
0.53315276
0.9868867
0.3657743
0.6823352
0.44115597
0.305522
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0.43325955
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1.0828861
0.9110559
0.7898668
0.5211285
0.37947157
‐0.7184064
‐0.35330626
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0.55447435
0.8042508
0.49258414
0.38961717
0.51321316
0.4455595
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0.4201201
0.38812217
0.5733965
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0.53790146
0.4327222
0.6188528
0.41560653
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0.91438
1.453435
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0.3895036
0.4419805
0.40065145
0.6376977
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0.7590404
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0.3116214
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0.3389896
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0.86167157
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0.37390408
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0.59673494
0.43937817
132
STM2433
STM2434
STM2467
STM2473
STM2474
STM2479
STM2494
STM2498
STM2502
STM2511
STM2517
STM2519
STM2522
STM2542
STM2544
STM2549
STM2551
STM2553
STM2555
STM2565
STM2579
STM2589
STM2590
STM2591
STM2592
STM2595
STM2596
STM2602
STM2604
STM2605
STM2606
STM2607
STM2610
STM2639
STM2640
STM2646
STM2663
STM2667
STM2668
STM2669
STM2670
STM2671
STM2674
STM2677
STM2679
STM2746
STM2749
STM2751
STM2771
STM2773
STM2774
STM2775
STM2776
STM2777
STM2779
STM2780
STM2782
STM2787
STM2788
STM2795
STM2799
STM2800
STM2805
STM2806
STM2807
STM2808
STM2814
STM2829
STM2839
STM2842
STM2843
STM2844
STM2845
STM2846
STM2847
STM2848
STM2849
STM2850
STM2851
STM2852
STM2853
STM2854
STM2855
STM2856
STM2857
STM2858
STM2860
STM2861
STM2862
STM2863
STM2864
STM2865
STM2866
STM2869
STM2870
STM2874
STM2876
STM2884
STM2886
STM2901
STM2911
STM2912
STM2913
STM2915
STM2916
STM2917
STM2924
STM2935
STM2951
STM2953
STM2963
STM2971
STM2976
STM2992
PTS family, glucose‐specific IIA component
crr
putative cytoplasmic protein
putative cobalamin adenosyltransferase, ethanolamine utilization
eutT
transaldolase A
talA
transketolase 2, isozyme
tktB
putative oxidoreductase
aegA
putative inner membrane or exported
uracil phosphoribosyltransferase
upp
exopolyphosphatase
ppx
guaB
IMP dehydrogenase
Similar to E. coli intimin and Y.
sinH
putative GTP‐binding protein
engA
histidine tRNA synthetase
hisS
NifU homologs involved in Fe‐S cluster formation
nifU
believed to be involved in assembly of
yfhP
anaerobic sulfide reductase
asrB
putative inner membrane protein
stationary phase inducible protein
csiE
serine hydroxymethyltransferase
glyA
phosphoribosylformylglycinamidine synthetase
purG
gap repair gene
recO
Gifsy‐1 prophage: similar to host specificity protein‐J
Gifsy‐1 prophage: similar to tail assembly protein
Gifsy‐1 prophage: similar to tail assembly protein
Gifsy‐1 prophage: similar to phage tail component
Gifsy‐1 prophage: similar to minor tail protein
Gifsy‐1 prophage: similar to minor tail protein
Gifsy‐1 prophage: similar to DNA packaging protein
Gifsy‐1 prophage: similar to head protein gpshp
Gifsy‐1 prophage: similar to head‐tail preconnector gp5
Gifsy‐1 prophage: similar to head‐tail preconnector gp4
Gifsy‐1 prophage: similar to head to tail
Gifsy‐1 prophage
anti sigma E (sigma 24) factor, negative
rseA
sigma E (sigma 24 ) factor of
rpoE
putative formate acetyltransferase
yfiD
yfiO
putative lipoprotein
bifuctional: chorismate mutase P prephenate dehydratase
pheA
putative cytoplasmic protein
bifunctional: chorismate mutase T prephenate dehydrogenase
tyrA
3‐deoxy‐D‐arabinoheptulosonate‐7‐phosphate synthase (DAHP synthetase), tyrosine repress aroF
putative periplasmic protein
yfiR
tRNA (guanine‐7‐)‐methyltransferase
trmD
4.5S‐RNP protein, GTP binding export factor, part
ffh
putative membrane protein
yfjD
putative Excinuclease ATPase subunit
putative cytoplasmic protein
putative PTS enzyme III glucitol
Flagellar synthesis: phase 2 flagellin (filament structural
fljB
putative glycosyl transferase, related to UDP‐glucuronosyltransferase
iroB
putative ATP binding cassette (ABC) transporter
iroC
Similar to enterochelin esterase of E. coli
iroD
putative hydrolase of the alpha/beta superfamily
iroE
iroN
TonB‐dependent siderophore receptor protein
putative inner membrane protein
Homolog of pipB, putative pentapeptide repeats (8
putative transcription activator
mig14
tricarboxylic transport
tricarboxylic transport
putative LysM domain
ygaU
stpA
DNA‐binding protein with chaperone activity
putative inner membrane protein
glutaredoxin‐like protein hydrogen donor
nrdH
stimulates ribonucleotide reduction
nrdI
ribonucleoside diphosphate reductase 2, alpha subunit
nrdE
ribonucleoside‐diphosphate reductase 2, beta subunit
nrdF
multidrug resistance secretion protein
emrA
DNA strand exchange and recombination protein with
recA
putative regulator (EBP family)
ygaA
hydrogenase maturation protein
hypF
electron transport protein (FeS senter) from formate
hydN
putative periplasmic or exported protein
protease involved in processing C‐terminal end of
hycI
hycH
processing of HycE (part of the FHL
hydrogenase activity
hycG
hydrogenase 3, putative quinone oxidoreductase
hycF
hydrogenase 3, large subunit (part of FHL
hycE
hydrogenase 3, membrane subunit (part of FHL
hycD
hycC
hydrogenase 3, membrane subunit (part of FHL
hydrogenase‐3, iron‐sulfur subunit (part of FHL complex)
hycB
transcriptional repressor of hyc and hyp operons
hycA
guanine‐nucleotide binding protein in formate‐hydrogenlyase system, functions
hypA
hypB
hydrogenase‐3 accessory protein, assembly of metallocenter
putative hydrogenase expression/formation protein
hypC
putative hydrogenase expression/formation protein
hypD
putative hydrogenase expression/formation protein
hypE
putative cytoplasmic protein
ygbA
Salmonella iron transporter: fur regulated
sitA
sitB
Salmonella iron transporter: fur regulated
Salmonella iron transporter: fur regulated
sitC
Salmonella iron transporter: fur regulated
sitD
putative inner membrane protein
avrA
transcriptional regulator
sprB
putative flagellar biosynthesis/type III secretory pathway protein
orgA
putative inner membrane protein
cell invasion protein
prgH
invasion genes transcription activator
hilA
cell invasion protein
sipC
surface presentation of antigens secretory proteins
sicA
putative cytoplasmic protein
putative permease
putative transcriptional regulators, LysR family
putative permease
putative endonuclease
ygbM
putative fuculose phosphate aldolase
ygbL
paral putative tRNA synthase
ygbK
sigma S (sigma 38) factor of RNA
rpoS
ATP‐sulfurylase, subunit 1 (ATP:sulfate adenylyltransferase)
cysD
putative Organic radical activating enzymes
ygcF
CTP synthetase
pyrG
putative MFS superfamily, D‐glucarate permease
L‐serine dehydratase (L‐threonine deaminase 2)
sdaB
L‐fucose isomerase
fucI
argA
N‐alpha‐acetylglutamate synthase (amino‐acid acetyltransferase)
‐0.65337825
‐0.38856125
‐0.013171276
‐0.16054967
‐0.5674203
‐0.30372322
0.26768297
0.6009477
0.43058366
0.33034065
0.2865135
‐0.17327718
0.26110312
0.08616231
‐0.37775114
0.15547217
0.23599179
0.09262392
‐0.7095931
‐0.021467928
0.17475298
0.64088565
0.38600674
‐0.7314146
‐0.1254499
0.31760445
0.05993005
0.9521248
0.32908002
0.95610934
‐0.007332975
‐0.029520666
0.21790259
‐0.08816588
0.23431368
‐0.18066832
‐0.6043905
2.0980732
0.5136386
0.081469074
0.11829828
‐0.4149684
0.16898407
0.3341258
‐0.28888452
0.28186047
0.47202364
‐0.67629176
0.40745282
‐1.0346557
‐0.011871857
0.7353798
‐0.19924144
‐0.4069506
0.47630718
‐0.46633133
‐0.25296074
0.57586616
0.9376291
‐0.03481237
0.49670693
0.21383426
‐0.36406824
0.47769812
‐0.39838722
‐0.07272805
0.18665256
0.29619932
0.892488
0.0680781
‐0.09703424
‐0.30537802
‐0.008713709
1.952237
0.43555936
‐0.32774305
‐0.10447852
0.8157917
‐0.1668846
‐0.7970295
‐0.6972522
‐0.527547
‐0.59802824
0.29370916
‐0.43555936
‐0.064038225
0.040863574
0.7550373
‐0.33848143
‐0.5332558
‐0.46562156
‐0.2670785
0.308206
2.3926606
‐0.3761747
‐0.696366
‐0.33177054
0.21098736
‐0.7702837
0.49063027
‐0.18137346
0.045784447
‐0.6802861
0.13783324
‐0.049529877
0.52850026
‐0.48767444
‐0.03192459
‐1.4100732
‐0.42557448
2.5459478
‐1.0841919
0.0894275
‐0.6009477
1.8192166
1.6121976
‐2.8735518
2.561785
4.666097
‐1.926026
‐1.5628579
‐1.7749461
3.177252
1.684308
2.1056473
3.3033478
1.5559567
2.1722233
9.5240965
‐2.385942
‐2.5028055
‐2.0437748
2.7489436
‐1.5699105
‐1.9708909
‐2.3857079
‐3.466351
‐1.6680993
‐1.8686115
‐1.7917174
‐1.582121
‐1.7196335
‐2.585872
‐2.3411322
‐1.9253645
‐1.7281822
3.8077862
‐3.3410387
‐2.2173152
‐11.103164
1.5775374
3.5734046
2.3783302
5.419729
5.744588
1.6690217
1.8849525
1.5047429
1.8464377
2.202804
‐2.092767
‐1.6093239
2.5403817
6.189298
6.68708
4.474524
4.0543313
7.56298
‐5.8051662
‐3.59977
4.1857886
‐2.0372272
‐1.5308144
2.9865005
2.5214539
‐4.598871
6.1426373
6.8323383
4.6810384
6.8673444
‐3.0507817
1.87776
‐1.9058558
‐3.583148
‐9.977834
‐6.415396
‐8.437943
‐8.423226
‐7.27101
‐6.8854866
‐7.199212
‐7.5005045
‐7.3001404
‐5.7668977
‐11.173628
‐5.8847423
‐6.240275
‐5.545602
‐5.526359
‐6.1224804
2.5183148
7.4020724
9.684762
5.7489934
3.4989843
2.6908598
2.6650038
1.6843232
2.4290555
2.0439458
2.5835035
1.5504521
2.5279467
1.685345
‐1.5582019
‐1.5383174
‐1.6398499
‐1.5541407
‐2.2552972
‐2.4557018
2.25904
1.6190747
1.8315825
2.2851748
2.8567734
‐1.5614433
‐2.0800235
‐7.1791983
0.3542742
0.33624816
‐0.625198
0.59729755
1.0819167
‐0.46602872
‐0.38142538
‐0.38160723
0.6388487
0.4266534
0.56546915
0.8809325
0.33507386
0.45517138
1.9619348
‐0.53982776
‐0.5609435
‐0.52561206
0.59083503
‐0.31634206
‐0.48655787
‐0.57298076
‐0.76763445
‐0.32971835
‐0.37236515
‐0.41204378
‐0.33095923
‐0.48144004
‐0.6103121
‐0.61972415
‐0.4464568
‐0.35720184
1.1969088
‐0.7606921
‐0.46861127
‐2.4723043
0.35398266
0.79526293
0.6116032
1.3014176
1.4662604
0.40024126
0.46972016
0.3685255
0.3972695
0.6331306
‐0.42148352
‐0.46324494
0.69475317
1.4180722
1.4215128
0.8989909
0.9122978
2.0399888
‐1.5396948
‐0.9542383
1.0240896
‐0.44473085
‐0.4246101
0.7203916
0.6293155
‐1.012539
1.52848
1.6026502
1.2849627
1.417359
‐0.6271336
0.4893526
‐0.4110887
‐0.99806815
‐2.1389928
‐1.2712086
‐1.9920542
‐2.118257
‐1.8727365
‐1.366492
‐1.6625693
‐1.6631119
‐1.5842414
‐1.6479834
‐2.2596273
‐1.4088316
‐1.6178005
‐1.4704473
‐1.4411981
‐1.2040635
0.5333035
1.6802702
1.9805951
1.4459906
0.9153204
0.5966483
0.8635065
0.3551381
0.5277148
0.49309307
0.5453996
0.40571925
0.51347303
0.5332098
‐0.35548824
‐0.3232793
‐0.36311668
‐0.3682516
‐0.62285304
‐0.6114726
0.76321775
0.33162707
0.55930185
0.54230773
0.59356046
‐0.35461727
‐0.6155243
‐1.8984652
0.19473998
0.2085651
0.21756977
0.23315679
0.23186758
0.24196388
0.24405634
0.21499652
0.20106958
0.25331077
0.26854885
0.2666787
0.2153491
0.20954171
0.20599695
0.22625351
0.22412588
0.25717708
0.21493167
0.20150323
0.24687205
0.24017222
0.22145317
0.1976611
0.19927372
0.22997141
0.20918705
0.27996665
0.23601791
0.26471132
0.2318817
0.20669223
0.31433195
0.22768132
0.21134175
0.22266665
0.22438939
0.2225505
0.25715655
0.24012594
0.25524205
0.23980589
0.24919468
0.24490929
0.21515456
0.2874203
0.20140012
0.28785068
0.27348378
0.22911681
0.21257602
0.20091319
0.22501807
0.26973346
0.26522836
0.26508313
0.2446587
0.21830204
0.2773753
0.24121596
0.24958438
0.22017121
0.24883124
0.23456833
0.27450377
0.20639114
0.20556489
0.26060444
0.2156977
0.27854505
0.21437447
0.19814967
0.23608291
0.2514781
0.25756207
0.19845976
0.23093767
0.22173335
0.21701519
0.28576604
0.20222862
0.23940413
0.25925148
0.26515558
0.26078618
0.1966627
0.21176998
0.22699997
0.20450632
0.25152066
0.26159602
0.22173147
0.324017
0.21084914
0.21725103
0.24124567
0.21110852
0.26167804
0.2031186
0.3163802
0.22814004
0.21015123
0.22143288
0.23694868
0.27617338
0.24900116
0.33785045
0.20482506
0.30536535
0.23731564
0.20777303
0.22710864
0.2959218
0.2644397
0.062375717
0.04958284
0
0
0
0.03424889
0.066927865
0.05861933
0
0.052916735
0
0
0.046063263
0
0
0
0
0
0
0.068245016
0.036121875
0
0
0.052023627
0.064440414
0.060340617
0.046063263
0.056731287
0
0
0.03424889
0.056731287
0
0
0
0
0.04670303
0
0
0
0
0.052916735
0.033565152
0.08572143
0.064440414
0
0
0.04736082
0
0
0
0
0
0
0
0
0
0
0.08572143
0
0
0
0
0
0
0
0
0.0654669
0.033565152
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0.052916735
0
0
0
0.046063263
0
0.052916735
0.066927865
0.08572143
0.05046221
0.06573839
0
0
0
0.04958284
0.063013285
0
0
0.066927865
0
0
0.35445872
0.2990498
‐0.5692435
0.5624847
1.0057616
‐0.3615075
‐0.49168766
‐0.34565735
0.61512345
0.5478117
0.47166616
0.7479109
0.3655798
0.49533635
1.9767494
‐0.46834084
‐0.50833637
‐0.40518212
0.64363766
‐0.34233952
‐0.371346
‐0.4698734
‐0.7199838
‐0.33095503
‐0.393688
‐0.4272208
‐0.30662757
‐0.3195953
‐0.51528144
‐0.46762577
‐0.4409544
‐0.3932887
0.95621353
‐0.72710884
‐0.47248483
‐2.409216
0.42493463
0.8552046
0.6434514
1.3667911
1.4136881
0.489211
0.4924994
0.3377278
0.41756362
0.59398854
‐0.4076845
‐0.26452866
0.59391034
1.4615705
1.4685358
0.88882965
0.8541298
1.9108407
‐1.6570932
‐1.0780922
0.9791757
‐0.386124
‐0.24668622
0.6232691
0.51035285
‐1.0397096
1.4108615
1.5859082
1.3610189
1.3861983
‐0.6603798
0.36601838
‐0.37556294
‐1.0317818
‐2.111915
‐1.2787188
‐2.0330992
‐1.9982865
‐1.9896524
‐1.3526257
‐1.5778861
‐1.721211
‐1.5309073
‐1.7143096
‐2.2677011
‐1.380965
‐1.510201
‐1.6043607
‐1.3017131
‐1.2006162
0.48882106
1.7026858
2.0106812
1.479524
1.0156461
0.6580734
0.59358567
0.36044982
0.58417714
0.42180738
0.5715682
0.43151522
0.48522937
0.28170028
‐0.36350116
‐0.3450248
‐0.41174516
‐0.3617602
‐0.4605548
‐0.5294304
1.0578645
0.3542767
0.62965447
0.46347573
0.6211641
‐0.32765755
‐0.40149662
‐1.8826816
0.3651713
0.34132865
‐0.638844
0.68613225
1.0836624
‐0.49790597
‐0.31301418
‐0.43354815
0.6584442
0.32566613
0.72495323
1.0189564
0.28132844
0.44656402
1.9268703
‐0.59718376
‐0.62913424
‐0.6434078
0.55979085
‐0.30040976
‐0.561585
‐0.6328658
‐0.7517651
‐0.34511426
‐0.36545414
‐0.3336518
‐0.31391972
‐0.6365987
‐0.6633785
‐0.6847157
‐0.37403706
‐0.34442255
1.3815212
‐0.83900166
‐0.4270707
‐2.5270565
0.3290534
0.7936667
0.7115405
1.3381793
1.5990025
0.31111732
0.561775
0.47810686
0.34423426
0.48456725
‐0.40928802
‐0.57024425
0.86389077
1.4559537
1.3882108
0.9238883
0.9028306
2.1902285
‐1.5668646
‐0.8139626
1.1358998
‐0.48439232
‐0.5167338
0.73295707
0.7136659
‐1.0487089
1.5631614
1.6896712
1.1131215
1.4173386
‐0.61795837
0.616091
‐0.3929376
‐0.8278202
‐2.1141264
‐1.2830478
‐1.896973
‐2.2120636
‐1.878313
‐1.386063
‐1.6977483
‐1.6057289
‐1.5929081
‐1.7733897
‐2.278509
‐1.3377738
‐1.5917325
‐1.3384742
‐1.5445496
‐1.1917812
0.54308647
1.6050758
1.9755465
1.534634
0.77281904
0.54348016
0.9752863
0.31386286
0.5098313
0.46114555
0.5001568
0.5177704
0.5348135
0.617756
‐0.28299135
‐0.27976608
‐0.37754562
‐0.28758729
‐0.64603853
‐0.7297677
0.65946704
0.29968372
0.71734643
0.63191265
0.5561981
‐0.43095577
‐0.7043617
‐2.0373597
0.34319264
0.36836603
‐0.6675065
0.54327565
1.156326
‐0.5386727
‐0.33957434
‐0.36561623
0.64297855
0.4064823
0.499788
0.87593013
0.3583133
0.42361376
1.9821848
‐0.55395865
‐0.54535985
‐0.52824616
0.5690766
‐0.30627686
‐0.52674264
‐0.6162032
‐0.8311544
‐0.31308576
‐0.35795328
‐0.47525877
‐0.37233043
‐0.48812613
‐0.65227646
‐0.7068311
‐0.5243789
‐0.33389425
1.2529918
‐0.7159658
‐0.5062783
‐2.4806406
0.30795994
0.7369175
0.47981763
1.1992822
1.3860908
0.40039545
0.354886
0.28974184
0.43001056
0.820836
‐0.44747806
‐0.5549619
0.62645835
1.3366925
1.4077921
0.88425475
0.97993296
2.018897
‐1.3951266
‐0.97066003
0.95719343
‐0.46367618
‐0.51041025
0.8049486
0.6639277
‐0.9491986
1.6114173
1.5323713
1.3807477
1.44854
‐0.6030626
0.48594844
‐0.46476558
‐1.1346024
‐2.1909368
‐1.2518593
‐2.0460904
‐2.144421
‐1.750244
‐1.3607873
‐1.7120734
‐1.6623961
‐1.6289089
‐1.4562511
‐2.2326722
‐1.5077561
‐1.7514678
‐1.4685069
‐1.4773316
‐1.2197933
0.56800294
1.7330488
1.9555578
1.3238136
0.95749605
0.5883913
1.0216476
0.39110157
0.48913586
0.5963263
0.56447375
0.2678721
0.52037615
0.7001731
‐0.4199722
‐0.34504697
‐0.3000593
‐0.4554073
‐0.7619659
‐0.57521975
0.5723216
0.3409208
0.33090457
0.53153473
0.6033192
‐0.30523852
‐0.7407146
‐1.7753541
133
STM3003
STM3033
STM3034
STM3036
STM3038
STM3039
STM3040
STM3048
STM3053
STM3054
STM3055
STM3060
STM3062
STM3063
STM3067
STM3068
STM3073
STM3074
STM3075
STM3076
STM3084
STM3086
STM3111
STM3118
STM3123
STM3134
STM3141
STM3160
STM3161
STM3163
STM3175
STM3176
STM3214
STM3217
STM3218
STM3229
STM3230
STM3231
STM3233
STM3234
STM3237
STM3253
STM3255
STM3269
STM3283
STM3287
STM3290
STM3298
STM3301
STM3307
STM3310
STM3319
STM3321
STM3322
STM3323
STM3330
STM3331
STM3336
STM3344
STM3345
STM3346
STM3347
STM3348
STM3351
STM3352
STM3353
STM3356
STM3359
STM3376
STM3399
STM3400
STM3404
STM3406
STM3408
STM3409
STM3410
STM3411
STM3444
STM3455
STM3468
STM3494
STM3505
STM3506
STM3507
STM3510
STM3528
STM3541
STM3547
STM3549
STM3550
STM3551
STM3552
STM3559
STM3562
STM3585
STM3608
STM3617
STM3622
STM3630
STM3641
STM3648
STM3666
STM3679
STM3682
STM3684
STM3686
STM3689
STM3695
STM3713
STM3715
STM3717
STM3719
STM3721
STM3722
General PTS system, enzyme I, transcriptional regulator
putative nucleic acid‐binding protein, contains PIN domain
putative cytoplasmic protein
putative inner membrane protein
putative metalloendopeptidase
isopentenyldiphosphate isomerase
lysine tRNA synthetase, constitutive
putative aminomethyltransferase
glycine cleavage complex protein P, glycine decarboxylase
glycine cleavage complex protein H, carrier of
glycine cleavage complex protein T, aminomethyltransferase, tetrahydrofolate‐dependent
putative cytoplasmic protein
D‐3‐phosphoglycerate dehydrogenase
ribosephosphate isomerase, constitutive
putative membrane protein, involved in stability of
fructose‐bisphosphate aldolase
putative ABC‐type cobalt transport system, permease component
putative ABC‐type cobalt transport system, ATPase component
putative ABC‐type cobalt transport system, ATPase component
transketolase 1 isozyme
putative regulatory protein, gntR family
arginine decarboxylase
putative cytoplasmic protein
putative acetyl‐CoA hydrolase
putative arylsulfatase regulator
putative permease
molybdenum‐binding periplasmic protein
putative inner membrane protein
cystathionine beta‐lyase (beta‐cystathionase)
putative transcriptional regulator (AraC/XylS family)
putative bacterial regulatory helix‐turn‐helix proteins, araC family
putative outer membrane protein
putative transporter
aerotaxis sensor receptor, senses cellular redox state
putative acetylornithine aminotransferase
putative inner membrane protein
putative inner membrane protein
putative inner membrane protein
putative glutathione S‐transferase
putative inner membrane protein
putative cytoplasmic protein
putative fructose/tagatose biphosphate aldolase
putative phosphotransferase system fructose‐specific component IIB
putative intracellular proteinase
30S ribosomal subunit protein S15
transcription pausing L factor
argininosuccinate synthetase
putative RNA‐binding protein containing KH domain
putative GTP‐binding protein
UDP‐N‐acetylglucosamine 1‐carboxyvinyltransferase
putative ABC superfamily (atp&memb), transport protein
putative ABC superfamily (atp_bind) transport protein
putative sigma N modulation factor
sugar specific PTS family, enzyme IIA, also
putative P‐loop‐containing kinase
glutamate synthase, large subunit
glutamate synthase, small subunit
putative ManNAc kinase
30S ribosomal subunit protein S9
50S ribosomal subunit protein L13
putative ATPase
putative periplasmic protein
serine endoprotease
putative sodium ion pump oxaloacetate decarboxylase beta
putative sodium ion pump oxaloacetate decarboxylase alpha
putative sodium ion pump oxaloacetate decarboxylase gamma
putative cation transporter
malate dehydrogenase
putative oxidoreductase
putative ferripyochelin binding protein
putative periplasmic protein
putative cytoplasmic protein
peptide deformylase
putative rRNA methylase
Trk system transport of potassium
mechanosensitive channel
putative cytoplasmic protein
regulatory or redox component complexing with Bfr
FKBP‐type peptidyl prolyl cis‐trans isomerase (rotamase)
acetylornithine transaminase (NAcOATase and DapATase)
putative NTP pyrophosphohydrolase
ferrous iron transport protein A
FeoB family, ferrous iron transport protein B
putative cytoplasmic protein
putative amidophosphoribosyltransferase
putative periplasmic phosphate‐binding protein
low affinity gluconate permease
putative transcriptional regulator of sugar metabolism
putative inner membrane protein
putative phosphotriesterase
gamma‐glutamyltranspeptidase
putative outer membrane protein
putative cytoplasmic protein
ABC superfamily (membrane), branched‐chain amino acid transporter
putative ABC superfamily (atp_bind/membrane) transport protein
putative tRNA‐processing ribonuclease
endo‐1,4‐D‐glucanase
putative cytoplasmic protein
ABC superfamily (peri_perm), dipeptide transport protein
putative lipase
putative transcriptional regulator
paral putative oxidoreductase
putative cytoplasmic protein
selenocysteinyl‐tRNA‐specific translation factor
putative glutathione S‐transferase
mannitol‐1‐phosphate dehydrogenase
putative cytoplasmic protein
putative tRNA/rRNA methyltransferase
O‐antigen ligase
lipopolysaccharide core biosynthesis
UDP‐D‐glucose:(galactosyl)lipopolysaccharide glucosyltransferase
UDP‐D‐galactose:(glucosyl)lipopolysaccharide‐1,6‐D‐galactosyltransferase
lipopolysaccharide core biosynthesis phosphorylation of core heptose
glucosyltransferase I
ptsP
idi
lysS
ygfZ
gcvP
gcvH
gcvT
ygfE
serA
rpiA
yggB
fba
tktA
speA
yggX
metC
yqhC
ygiW
yqjH
aer
oat
yqjD
yqjE
yqjK
yqjG
yhaH
yhaL
yhbO
rpsO
nusA
argG
yhbY
yhbZ
murA
yrbC
yhbG
yhbH
ptsN
yhbJ
gltB
gltD
nanK
rpsI
rplM
yhcM
yhcB
degQ
oadB
oadA
oadG
mdh
yhdH
yrdA
yrdB
smg
def
sun
trkA
mscL
bfd
slyD
argD
yrfE
feoA
feoB
yhgG
yhgH
gntU
ggt
yhhA
yhhV
livM
yhhJ
yhjD
bcsC
yhjS
dppA
yhjY
yiaG
ysaA
selB
yibF
mtlD
yibL
yibK
rfaL
rfaZ
rfaJ
rfaB
rfaP
rfaG
0.6755954
0.23257047
‐0.06721762
‐0.25521052
0.043558788
0.4110363
0.43422556
‐0.666905
‐0.1678553
‐0.4529079
0.1369937
0.48813185
‐0.31056175
‐0.950021
‐0.26195955
‐0.34157068
0.008064115
0.5741068
‐0.8996354
0.11028937
0.70009315
0.20643686
‐0.098475926
0.14759047
0.4846312
‐0.5832454
‐0.23403399
0.28888452
‐0.21098736
‐0.29278332
‐0.12315611
0.32277566
1.0479784
‐0.56348324
0.2318009
‐0.98730326
0.5157611
‐0.22929639
‐0.49204087
‐0.31471863
0.35671255
‐0.44171777
‐0.32163835
‐0.16838183
0.30372322
‐0.33590025
‐0.65049744
‐0.63119006
0.46059808
‐0.045942247
0.20944834
0.14287926
0.18611106
‐0.2806547
‐0.19040503
‐1.1462337
0.40435228
0.13808168
0.6781181
0.5394953
‐0.19449352
0.18202876
‐0.47515002
0.47321808
‐0.15068413
0.63738245
‐0.84726703
0.06865428
0.37864769
0.75414443
‐0.19530067
‐1.1222371
0.15068413
0.51471597
‐0.9533757
0.107027
0.6403776
‐0.080864854
0.45096314
‐0.57937014
‐0.27923536
0.17860433
0.34184274
‐0.7353798
0.47819886
‐0.20990089
0.12382674
‐0.80572575
0.21333815
‐0.58120793
‐0.37864769
‐0.29703346
0.44830734
0.72732615
0.29278332
‐0.33938333
‐0.20685117
‐0.4742528
‐0.19732961
‐0.25549942
‐0.27465343
0.011871857
0.49298185
‐1.1542956
‐0.4000066
‐0.29463667
0.4466139
0.5674203
‐0.40543115
0.17513816
‐0.7238866
0.14179465
0.34437576
‐1.6554445
2.1136682
1.6121213
2.057447
1.8093271
1.503213
1.9553742
2.0721443
1.6791351
‐1.548765
‐1.9693778
‐1.8163794
‐4.994263
2.8053248
2.1047325
2.2456944
1.7177707
‐3.549998
‐2.210317
‐1.6162373
‐1.7007806
2.792682
1.5791565
1.5307235
2.4272947
2.399998
1.956313
‐2.2366416
‐2.4107106
1.6816583
1.6084288
‐1.6195523
‐1.8365009
2.268089
1.6768337
6.66837
1.5292214
2.1823924
1.8793113
1.9746901
1.9638025
‐2.331444
1.6612177
1.6488768
4.024114
‐1.9455602
1.5562496
‐3.6524975
1.6343018
1.8668038
1.6632278
1.8080856
1.5383027
4.0351615
1.6364739
2.044123
‐4.5282335
‐5.754339
‐1.7145517
‐1.5522492
‐1.5666604
2.2489936
1.6118252
1.6138811
‐1.8969579
‐1.7228147
‐2.3605113
1.6132051
5.349108
‐1.9252613
1.5964084
1.5368217
1.970463
2.2570117
1.5143003
2.1018822
7.7003984
2.6114893
1.6972271
1.5787463
‐4.9745827
1.6730511
‐3.7791817
‐4.084264
‐2.926362
‐1.9534088
1.8143873
‐1.8159596
1.7613442
2.6149595
1.8890399
3.7877216
1.5481534
‐1.6243072
‐1.7891289
‐1.549129
2.5381799
1.6005901
2.3276753
3.3539507
2.5380428
2.8019512
‐1.7150571
‐1.6969042
‐1.6817443
1.5722961
2.3630202
1.6536298
‐1.8137153
1.9103702
2.534816
1.9889339
1.5872976
1.7386192
2.0911803
0.45365244
0.3775923
0.49821556
0.49499306
0.33276376
0.5108181
0.55931985
0.34947154
‐0.30206802
‐0.45057556
‐0.4176878
‐1.1262976
0.724494
0.47034854
0.4502834
0.3701238
‐0.95269996
‐0.5113617
‐0.4140885
‐0.53263664
0.72715414
0.4206928
0.3294322
0.64203227
0.53296655
0.39576995
‐0.4870507
‐0.5822555
0.4773572
0.3853789
‐0.33203724
‐0.36205012
0.4899775
0.33439645
1.8616135
0.4232078
0.43675342
0.43695128
0.40787387
0.3988789
‐0.46848142
0.37201008
0.4417901
0.8957086
‐0.47298902
0.42970932
‐0.80491114
0.39191687
0.40519696
0.34663767
0.49032056
0.4402938
1.1183393
0.37110034
0.45387977
‐1.144475
‐1.1972159
‐0.3675056
‐0.32076043
‐0.36633584
0.47426036
0.41901252
0.4109477
‐0.59574056
‐0.42028627
‐0.6863903
0.34528437
1.0320538
‐0.38043925
0.33414793
0.38499892
0.4710404
0.47581294
0.3354247
0.42573324
1.6406862
0.56206405
0.44617307
0.33144507
‐1.0719284
0.39433223
‐0.83861786
‐0.798303
‐0.6313221
‐0.39899692
0.4996787
‐0.38044965
0.37545747
0.5218723
0.4274388
0.8074597
0.38999406
‐0.3995211
‐0.39328074
‐0.33445248
0.51426595
0.40892595
0.48388755
0.6884257
0.6006069
0.776201
‐0.39172906
‐0.5012656
‐0.45353958
0.3495993
0.51300955
0.4465721
‐0.39065447
0.4311251
0.5261738
0.5328845
0.56814337
0.4682747
0.5393938
0.21462803
0.23422077
0.24215232
0.27357852
0.22136833
0.26123804
0.2699232
0.20812592
0.195038
0.22879082
0.22995625
0.22551827
0.25825673
0.22347188
0.20050965
0.21546753
0.26836634
0.23135222
0.25620526
0.31317186
0.26037842
0.2664035
0.21521339
0.26450527
0.22206959
0.202304
0.21775983
0.24152857
0.283861
0.2395996
0.20501792
0.19714127
0.21603099
0.19942135
0.27917072
0.27674723
0.20012599
0.23250607
0.20655082
0.2031156
0.20094046
0.2239382
0.26793396
0.22258529
0.243112
0.27611852
0.22037281
0.23980692
0.21705386
0.20841262
0.27118218
0.28622052
0.27714857
0.22676826
0.22204132
0.25274205
0.20805445
0.21434502
0.20664236
0.23383231
0.2108767
0.25996152
0.2546332
0.3140505
0.24395327
0.29078034
0.21403626
0.19293942
0.19760396
0.20931232
0.25051633
0.23905061
0.21081546
0.22150473
0.20254856
0.2130651
0.2152274
0.26288354
0.20994194
0.21548107
0.23569646
0.22190462
0.19545823
0.21573615
0.20425674
0.27539805
0.20950337
0.2131653
0.19957185
0.22627304
0.2131782
0.25190917
0.24596402
0.2198169
0.21589711
0.2026121
0.2554845
0.20788448
0.20525815
0.23664176
0.27702162
0.22840583
0.29540005
0.26968402
0.22234952
0.2170991
0.27005568
0.21538907
0.22567621
0.20757869
0.26792467
0.35793123
0.26933715
0.2579375
0
0.04958284
0
0.061239734
0.08572143
0.03676819
0
0.052916735
0.06573839
0.036121875
0.061239734
0
0
0
0
0.055790044
0
0
0.048099868
0.055124886
0
0.04670303
0.066927865
0
0
0.03676819
0
0
0.052916735
0.04958284
0.048099868
0.062375717
0
0.052916735
0
0.066927865
0
0.0654669
0
0.03676819
0
0.052023627
0.050878678
0
0.035160456
0.046063263
0
0.05046221
0.06489263
0.052023627
0.061239734
0.068245016
0
0.050878678
0
0
0
0.055790044
0.06573839
0.066927865
0
0.04958284
0.04958284
0.0654669
0.056731287
0
0.04958284
0
0.03424889
0.048099868
0.066927865
0
0
0.06573839
0
0
0
0.05455575
0.04670303
0
0.052916735
0
0
0
0.035703473
0.062375717
0.061239734
0.05861933
0
0.033565152
0
0.068245016
0.048099868
0.060340617
0.06573839
0
0.048099868
0
0
0
0
0.055790044
0.055124886
0.052916735
0.04670303
0
0.052023627
0.061239734
0.034698687
0
0
0.04736082
0.057885446
0
0.45904133
0.2999577
0.39470655
0.40918556
0.3941764
0.3653111
0.5489557
0.37370208
‐0.28896147
‐0.44275403
‐0.4154128
‐1.2001287
0.8323728
0.5394156
0.47451338
0.3727042
‐0.7943754
‐0.493748
‐0.499996
‐0.2935491
0.6612686
0.53480905
0.28002083
0.69300693
0.48359686
0.36976013
‐0.45330793
‐0.68835145
0.65483147
0.29529727
‐0.31041464
‐0.36870337
0.53003407
0.35210353
1.691354
0.3128186
0.4432915
0.44499046
0.43303484
0.37349963
‐0.4875742
0.37932602
0.28756332
0.86880946
‐0.5601261
0.45427257
‐0.8604555
0.2899381
0.45941237
0.31915554
0.45055595
0.55796766
1.0253689
0.35407287
0.4593303
‐1.2374511
‐1.2325765
‐0.3400754
‐0.31225324
‐0.42418668
0.46733466
0.27658775
0.29680672
‐0.34602475
‐0.31769782
‐0.4816189
0.37959757
1.0391147
‐0.38041863
0.33387408
0.36810875
0.55361795
0.45074987
0.27524516
0.45403755
1.6509857
0.61358094
0.29753736
0.29044163
‐1.0901717
0.3264107
‐0.8980078
‐0.8008093
‐0.65874517
‐0.40665218
0.42640808
‐0.40383425
0.3454789
0.52324367
0.44532394
0.85632825
0.26605102
‐0.51195174
‐0.33340865
‐0.376025
0.504887
0.5395899
0.47895348
0.65638983
0.50655806
0.64083105
‐0.3849482
‐0.29648966
‐0.46270218
0.31454217
0.5595593
0.36531964
‐0.38597736
0.36301234
0.4886192
0.5205779
0.23581295
0.62995374
0.5888077
0.49615526
0.45859674
0.5751511
0.6653593
0.2812448
0.58983773
0.705428
0.3103816
‐0.31050998
‐0.3848467
‐0.34686542
‐1.0961808
0.74745554
0.44647112
0.4381121
0.415672
‐1.0122044
‐0.44734427
‐0.46201798
‐0.7141154
0.6492397
0.4557718
0.33606505
0.49232864
0.5973249
0.4173206
‐0.46229258
‐0.52397484
0.44960093
0.47260767
‐0.32097733
‐0.37273464
0.43696576
0.31415823
2.0013297
0.3589067
0.4529989
0.5090171
0.3726188
0.42449296
‐0.44483563
0.30711573
0.55266887
0.85471255
‐0.48675564
0.5678735
‐0.8045967
0.43150806
0.36197802
0.385592
0.6493985
0.51682436
1.2957793
0.44442272
0.5092408
‐1.1750478
‐1.1646444
‐0.3430637
‐0.2942787
‐0.39810398
0.51619864
0.5025476
0.52625495
‐0.6961095
‐0.43460757
‐0.7889358
0.36113432
1.0235662
‐0.36449853
0.29805514
0.50004303
0.37892056
0.5205464
0.34158424
0.41118976
1.6773255
0.5232863
0.5292295
0.3634315
‐1.1069815
0.48532274
‐0.8358187
‐0.7850094
‐0.65858203
‐0.36850718
0.67299736
‐0.39919758
0.35628942
0.54050964
0.35474345
0.79020727
0.4760673
‐0.36480522
‐0.43975687
‐0.28247398
0.5422027
0.37002033
0.5198404
0.7135767
0.66632545
0.74478775
‐0.3260673
‐0.65751076
‐0.58953184
0.31675866
0.5188325
0.36450312
‐0.43957305
0.49145386
0.5517573
0.40170062
0.79257816
0.3803654
0.62728035
0.4057607
0.37422243
0.52478904
0.41043428
0.3228701
0.5773056
0.4235758
0.36433092
‐0.30673265
‐0.52412593
‐0.4907852
‐1.0825833
0.5936536
0.42515892
0.4382247
0.32199523
‐1.05152
‐0.5929929
‐0.28025147
‐0.5902455
0.87095416
0.27149752
0.37221068
0.74076116
0.51797795
0.40022916
‐0.5455516
‐0.5344401
0.32763925
0.38823175
‐0.36471972
‐0.34471235
0.50293267
0.33692762
1.892157
0.59789807
0.4139699
0.3568463
0.41796798
0.39864415
‐0.47303447
0.42958847
0.4851381
0.9636039
‐0.37208533
0.26698193
‐0.7496812
0.45430443
0.39420047
0.33516544
0.37100726
0.24608935
1.0338696
0.31480545
0.3930682
‐1.0209262
‐1.1944269
‐0.41937774
‐0.35574937
‐0.27671683
0.4392478
0.47790214
0.40978143
‐0.74508744
‐0.5085534
‐0.78861606
0.29512122
1.0334805
‐0.3964006
0.3705146
0.28684494
0.48058265
0.45614257
0.38944465
0.4119724
1.5937471
0.549325
0.5117523
0.34046206
‐1.0186319
0.37126324
‐0.78202707
‐0.80909026
‐0.5766391
‐0.42183143
0.39963064
‐0.33831713
0.42460406
0.50186354
0.482249
0.7758436
0.42786384
‐0.3218064
‐0.4066767
‐0.34485847
0.49570817
0.3171676
0.45286873
0.6953107
0.6289372
0.9429842
‐0.4641717
‐0.54979634
‐0.3083847
0.41749704
0.46063688
0.6098935
‐0.34641305
0.43890908
0.53814477
0.676375
0.67603904
0.39450496
0.4020932
134
STM3727
STM3728
STM3735
STM3739
STM3753
STM3754
STM3756
STM3757
STM3767
STM3781
STM3784
STM3788
STM3794
STM3795
STM3796
STM3832
STM3835
STM3859
STM3860
STM3862
STM3866
STM3877
STM3879
STM3884
STM3887
STM3898
STM3901
STM3902
STM3903
STM3904
STM3905
STM3912
STM3919
STM3939
STM3941
STM3942
STM3944
STM3947
STM3957
STM3964
STM3965
STM3967
STM3970
STM3972
STM3974
STM3986
STM3994
STM3999
STM4001
STM4002
STM4006
STM4007
STM4010
STM4012
STM4015
STM4017
STM4044
STM4050
STM4051
STM4052
STM4055
STM4063
STM4068
STM4074
STM4075
STM4076
STM4096
STM4098
STM4100
STM4105
STM4108
STM4121
STM4122
STM4123
STM4159
STM4160
STM4161
STM4162
STM4163
STM4165
STM4170
STM4181
STM4182
STM4209
STM4220
STM4222
STM4223
STM4224
STM4237
STM4248
STM4254
STM4256
STM4271
STM4274
STM4280
STM4282
STM4285
STM4306
STM4329
STM4336
STM4339
STM4343
STM4362
STM4363
STM4389
STM4406
STM4414
STM4418
STM4419
STM4428
STM4442
STM4446
STM4447
STM4469
50S ribosomal subunit protein L33
rpmG
50S ribosomal subunit protein L28
rpmB
putative stress‐induced protein
yicC
putative DNA ligase
yicF
ATP binding protein
sugR
putative cytoplasmic protein
putative cytoplasmic protein
rmbA
putative autotransported protein
misL
putative cytoplasmic protein
putative sugar (pentulose and hexulose) kinase
putative phosphotransferase system mannitol/fructose‐specific IIA domain
uhpC
membrane protein, regulator of uhpT expression
putative regulatory protein, deoR family
acetolactate synthase I, small subunit
ilvN
acetolactate synthase I, large subunit, valine sensitive
ilvB
putative permease
DNA gyrase, subunit B (type II topoisomerase)
gyrB
putative shikimate / quinate 5‐dehydrogenase
putative dipeptide/oligopeptide/nickel ABC‐type transport systems, periplasmic component
N‐acetyl glucosamine‐1‐phosphate uridyltransferase and glucosamine‐1‐phosphate acetyl traglmU
membrane‐bound ATP synthase, F1 sector, gamma‐subunit
atpG
asparagine synthetase A
asnA
paral putative regulator protein
yieN
ABC superfamily (peri_perm), D‐ribose transport protein
rbsB
putative MFS family tranport protein (1st mdule)
yieO
putative LysR type transcriptional regulator with pssR
yifE
acetolactate synthase II, large subunit, fragment 1
ilvG
acetolactate synthase II, small subunit
ilvM
branched‐chain amino‐acid aminotransferase
ilvE
dihydroxyacid dehydratase
ilvD
threonine deaminase
ilvA
rep helicase, a single‐stranded DNA dependent ATPase
rep
modulator of enterobacterial common antigen (ECA) polysaccharide
wzzE
adenylate cyclase
cyaA
putative inner membrane protein
putative cytoplasmic protein
putative inner membrane protein
diaminopimelate epimerase
dapF
outer membrane phospholipase A
pldA
metR
regulator for metE and metH (LysR family)
5‐methyltetrahydropteroyltriglutamate‐homocysteine S‐methyltransferase
metE
putative dienelactone hydrolase family
dlhH
S‐adenosylmethionine : 2‐DMK methyltransferase and 2‐octaprenyl‐6‐methoxy‐1,4‐benzoqui ubiE
putative regulator in ubiquinone biosynthesis
aarF
component of Sec‐independent protein secretion pathway
tatB
Trk family, potassium transport protein, requires TrkE
trkH
putative molybdopterin‐guanine dinucleotide biosynthesis protein
mobA
DNA polymerase I, 3 ‐‐ 5 polymerase
polA
putative GTPase, involved in coordination of cell
yihA
putative cytoplasmic protein
sensory kinase (phosphatase) in two‐component regulatory system
glnL
glutamine synthetase
glnA
putative hydrolase
putative coproporphyrinogen III oxidase and related FeS
putative cytoplasmic protein
putative GPH family transport protein
yihO
putative iron‐containing alcohol dehydrogenase
DMT Superfamily, L‐rhamnose:H symporter protein
rhaT
putative outer membrane protein
putative C4‐dicarboxylate transport system
superoxide dismutase, manganese
sodA
ABC superfamily (bind_prot), sulfate transport protein
sbp
putative regulatory protein, gntR family
putative ABC‐type sugar, aldose transport system, ATPase
ego
putative ABC superfamily (membrane), sugar transport protein
ydeY
putative ABC superfamily (membrane), sugar transport protein
ydeZ
50S ribosomal subunit protein L31
rpmE
putative arylsulfate sulfotransferase
cystathionine gamma‐synthase
metB
5,10‐methylenetetrahydrofolate reductase
metF
glycerol dehydrogenase, NAD
gldA
N‐acetyl‐gamma‐glutamylphosphate reductase
argC
acetylglutamate kinase
argB
argininosuccinate lyase
argH
thiH
deoxyxylulose‐5‐P thi‐S‐COSH tyrosine
deoxyxylulose‐5‐P thi‐S‐COSH tyrosine
thiG
putative involved in thiamine biosynthesis
catalyzes the adenylation of thisS as part
thiF
thiamin phosphate synthase (thiamine phosphate pyrophosphorylase)
thiE
regulator of sigma D, has binding activity
rsd
DNA‐binding protein HU‐alpha (HU‐2)
hupA
putative acetyltransferase
yjaB
homoserine transsuccinylase
metA
putative inner membrane protein
aspartokinase III, lysine sensitive
lysC
putative outer membrane protein
yjbE
putative outer membrane lipoprotein
yjbF
putative periplasmic protein
yjbG
SOS response regulator, transcriptional repressor (LexA family)
lexA
tyrB
tyrosine aminotransferase, tyrosine repressible
UvrA with UvrBC is a DNA excision
uvrA
ssDNA‐binding protein controls activity of RecBCD nuclease
ssb
putative inner membrane protein
putative inner membrane protein
yjcH
putative nitrate reductase, formate dependent
nrfD
nrfG
part of formate‐dependent nitrite reductase complex involved
formate dehydrogenase
fdhF
putative anaerobic dimethyl sulfoxide reductase, subunit B
chaperone Hsp10, affects cell division
mopB
putative entericidin B precursor
ecnB
outer membrane lipoprotein (lipocalin)
blc
fumarate reductase, anaerobic, flavoprotein subunit
frdA
putative GTP‐ase, together with HflCK possibly involved
hflX
with HflC, part of modulator for protease
hflK
putative outer membrane protein
yjfY
putative cytoplasmic protein
ytfK
inorganic pyrophosphatase
ppa
sugar (and other) transporter
sugar (and other) transporter
putative permease
putative cytoplasmic protein
putative selenocysteine synthase [L‐seryl‐tRNA(Ser) selenium transferase
putative periplasmic protein
ornithine carbamoyltransferase 1
argI
0.1301892
‐0.3780471
‐0.68675524
0.17353666
‐0.47684246
0.31969455
0.51307684
‐0.41458035
0.5678712
‐0.52694124
‐3.0451999
‐0.13783324
0.63420165
‐0.04255068
‐0.33471116
‐0.41137883
0.014867804
‐0.29522222
0.4650053
‐0.25826892
‐0.3545216
‐0.2263804
0.13103093
‐0.15711944
‐0.082485124
‐0.21383426
‐1.879907
0.68424237
0.36235517
‐0.48547572
‐0.5703434
0.09942931
‐0.21702328
‐0.28849924
0.15665773
‐0.54959726
0.0356387
‐0.6192518
‐0.6526042
‐0.21790259
0.5000016
0.42949915
‐0.47769812
0.65638953
‐0.042263385
0.27883244
‐0.12210245
‐0.34398723
0.49538356
‐0.5802446
0.24259792
‐0.092812985
‐0.5882759
0.19134629
0.2744039
‐0.6100708
0.18566619
0.18909171
‐0.6281051
0.4620052
‐0.49239075
‐0.4593492
0.931704
‐0.056709845
‐0.9815406
‐0.19276725
0.6940803
‐0.15832898
‐0.6186724
0.082485124
‐0.32403237
0.3298821
0.8724605
‐0.45369187
0.6655571
‐0.12347267
‐0.17311701
‐0.16321859
‐0.61755073
0.4868646
0.1547093
‐0.48628333
‐0.15436698
‐0.505967
‐0.86451375
0.11456228
‐1.952237
‐0.06963306
‐0.15642636
‐0.90958524
‐0.75989574
‐0.012055409
0.16376834
0.6100708
0.22428694
‐0.2318009
0.0855047
0.006172235
‐0.21186993
‐0.4503383
0.06498495
0.08171417
‐0.1558558
‐1.6163129
0.894851
0.93876207
0.23807266
‐1.0153017
0.58439744
0.19530067
0.28506687
0.30279577
‐0.21333815
‐0.43788415
1.605819
1.955886
1.6156315
1.6391077
2.1396935
1.5200504
1.7668608
1.5712994
‐1.8977661
1.9337174
2.364518
‐1.5452976
1.7026069
4.1565914
5.550189
2.0627105
1.8083141
2.1979892
1.5305167
1.9085512
1.6940398
‐7.9468703
1.9051694
1.8763212
1.585647
2.3108907
2.9675903
4.168034
3.8437219
1.9831517
2.0576208
2.1033072
1.6406711
4.398021
2.06263
2.0346022
1.8969996
1.8873991
1.8269706
2.4859245
9.195377
2.867417
2.48138
1.9997739
1.7091753
1.8580741
1.6856477
1.6466826
2.3654792
6.0609818
‐2.0877984
‐2.6353803
2.4007227
1.9572333
1.6393343
1.6875355
‐2.3585281
1.7020295
1.847927
1.8644136
4.3115897
3.6809943
‐1.9415044
1.5847982
1.6034166
2.3568122
‐2.40593
2.107291
1.9149498
4.9100404
‐1.7187896
‐7.00797
‐5.5200133
‐6.326408
1.9949859
2.7008054
2.6730256
2.0685506
2.3483047
2.2970204
3.0071814
1.5604886
3.9471924
‐1.7779773
‐3.3963428
‐10.081721
‐1.5435418
‐2.2580628
1.8176259
2.0587034
1.5824612
2.822107
‐1.8470995
‐1.6569892
‐1.5790939
‐1.6900375
‐5.2187743
‐3.1490297
‐2.0601845
2.2616508
1.9442763
‐2.0651295
2.901106
3.6108074
‐1.958884
3.1500947
2.3549054
2.0922332
2.1450062
‐1.8720412
‐2.3116417
‐2.2090225
‐1.5569214
‐5.1410637
0.44745818
0.44447473
0.34351423
0.36658975
0.48596856
0.41399205
0.3677635
0.4469973
‐0.5191424
0.46641704
0.53195083
‐0.3369816
0.3517111
1.04016
1.4274511
0.4464571
0.5025008
0.4633829
0.35714597
0.45362625
0.4262952
‐1.9373995
0.46846965
0.39542574
0.33321476
0.633534
0.6094899
0.96123534
0.76985306
0.5742589
0.49188125
0.49100342
0.36819875
0.8866541
0.46457082
0.5273971
0.44918942
0.38624415
0.38733566
0.5481714
2.0591905
0.6445667
0.6148735
0.41125435
0.36889693
0.38901678
0.3811573
0.4377981
0.46261853
1.8694432
‐0.5045588
‐0.59251535
0.48924688
0.45540714
0.40781978
0.3963741
‐0.49964577
0.410316
0.4098875
0.46624777
0.9755554
1.1947391
‐0.5420718
0.45291167
0.36356896
0.71426153
‐0.5846065
0.6554832
0.5192227
1.136547
‐0.42860514
‐1.8144642
‐1.2989787
‐1.4246911
0.43634397
0.59175986
0.6788698
0.45746613
0.48944348
0.5652766
0.65318567
0.38863373
0.88750505
‐0.42324895
‐0.9882611
‐2.1054304
‐0.42309836
‐0.4635481
0.4132672
0.52193683
0.41460815
0.59220576
‐0.41584668
‐0.33754137
‐0.44720033
‐0.42897272
‐1.3442297
‐0.80663604
‐0.48067027
0.6320353
0.4079992
‐0.5069592
0.7587986
0.7583688
‐0.4843642
1.0473622
0.51015383
0.40358648
0.43582895
‐0.5923989
‐0.5741389
‐0.5517769
‐0.3323978
‐1.3976216
0.27864796
0.22724982
0.21261919
0.22365202
0.22712064
0.27235416
0.20814514
0.28447622
0.27355447
0.24120228
0.22497222
0.21806906
0.2065721
0.25024348
0.25718963
0.21644194
0.27788356
0.21082129
0.23334992
0.23768094
0.25164413
0.24379402
0.24589397
0.21074523
0.21014436
0.27415144
0.2053821
0.2306208
0.20028844
0.28956884
0.2390534
0.23344351
0.2244196
0.20160295
0.22523227
0.25921386
0.23678942
0.2046436
0.2120098
0.22051008
0.22393757
0.22479
0.24779499
0.20565042
0.21583329
0.20936559
0.22611919
0.26586673
0.19557074
0.30843902
0.24167028
0.22483106
0.2037915
0.23267902
0.24877158
0.23488341
0.21184643
0.24107455
0.22180936
0.25007743
0.22626351
0.32456967
0.27920195
0.28578508
0.22674643
0.30306256
0.24298567
0.3110549
0.27114168
0.23147406
0.24936453
0.25891438
0.23532166
0.22519748
0.21872032
0.21910496
0.25397056
0.22115298
0.20842418
0.24609125
0.2172086
0.24904619
0.22484463
0.2380508
0.290978
0.20883639
0.27410877
0.20528574
0.22736648
0.25352696
0.26200208
0.20984524
0.22513495
0.20370765
0.2832006
0.25382438
0.25757575
0.25615382
0.23331419
0.2794575
0.2098463
0.24548542
0.26155493
0.21002749
0.24726538
0.33248594
0.21663454
0.19289747
0.20318307
0.31644544
0.24836846
0.24978328
0.21349683
0.27185458
0.048099868
0.03676819
0.04958284
0.050878678
0
0.06573839
0.05861933
0.04670303
0.0654669
0.035703473
0
0.06573839
0.055124886
0
0
0
0.061239734
0
0.066927865
0.034698687
0.05455575
0
0.034698687
0.0654669
0.04736082
0
0
0
0
0
0
0
0.050878678
0
0
0
0.03424889
0.033565152
0.063013285
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0
0
0
0
0.055124886
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0.052916735
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0
0
0
0
0
0.03676819
0.050878678
0.052916735
0
0.055124886
0.064440414
0.06489263
0
0
0.035160456
0.04736082
0.048099868
0
0
0
0.034698687
0
0.056731287
0
0
0
0
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0
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0.046063263
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0.05994943
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0
0.06573839
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0.050878678
0.068245016
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0
0
0
0
0.036121875
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0
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0.035703473
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0
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0.064440414
0
0
0.066927865
0
0.6258041
0.5031419
0.36955753
0.33638847
0.43738025
0.29049364
0.3757983
0.63744277
‐0.3511006
0.37124303
0.60478884
‐0.2906086
0.37849623
0.91801894
1.5609252
0.50030506
0.58903855
0.5036455
0.41193685
0.36955515
0.54671985
‐1.8288294
0.5740368
0.42535704
0.30532005
0.47292084
0.6425514
1.0454634
0.79254895
0.775312
0.5118394
0.40508392
0.38888365
0.91051465
0.5347797
0.42004734
0.38673782
0.37373444
0.40118644
0.496016
2.0208678
0.57621735
0.5451342
0.38699812
0.3267777
0.43091
0.34198838
0.37616727
0.46204188
1.8951077
‐0.6108326
‐0.53651893
0.46053627
0.4891817
0.28797778
0.48487806
‐0.45278054
0.36642
0.461429
0.38197103
0.89982533
0.92472845
‐0.4316753
0.33004305
0.28925765
0.51653886
‐0.52524084
0.5901314
0.3551766
1.0520654
‐0.49974674
‐1.6799085
‐1.2066184
‐1.35849
0.49387768
0.5696071
0.74364185
0.42741707
0.4782781
0.5121794
0.6041425
0.41277462
0.83211875
‐0.50856966
‐1.1065358
‐2.0814438
‐0.37885618
‐0.43143997
0.4908214
0.48781145
0.5232973
0.5871153
‐0.42716506
‐0.3073611
‐0.6087446
‐0.3483499
‐1.2277148
‐0.7360135
‐0.5202757
0.4911552
0.41673467
‐0.43022296
0.7876796
0.8000094
‐0.36662456
0.7850865
0.45368612
0.3966816
0.46449316
‐0.34634352
‐0.6668347
‐0.42905918
‐0.38117865
‐1.3485008
0.38240027
0.37100726
0.36587334
0.4368734
0.56249774
0.57427406
0.33025235
0.37397614
‐0.57912034
0.47435084
0.48963878
‐0.39224416
0.35960653
1.1181724
1.3317875
0.40592232
0.5949088
0.42613268
0.26801392
0.5402315
0.3996228
‐2.0108335
0.4551856
0.35170707
0.37606826
0.7659487
0.59973615
0.92444766
0.75233585
0.45393547
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0.4176267
0.88454133
0.4101256
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0.41951457
0.6067155
2.130202
0.6570585
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0.4565878
0.5917273
0.4504875
1.6498793
‐0.4447654
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0.49396023
0.5094267
0.454913
0.37679827
‐0.5214348
0.51521206
0.347276
0.5864078
1.0143545
1.3605927
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0.9562479
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‐1.3378628
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0.86858255
0.7273756
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1.075081
0.5373738
0.4120458
0.41518277
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‐1.5603379
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0.29511184
0.3265074
0.4580277
0.3772084
0.39723983
0.329573
‐0.62720615
0.5536573
0.5014249
‐0.32809198
0.31703052
1.0842886
1.3896406
0.43314388
0.32355496
0.46037054
0.3914871
0.4510921
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0.3761866
0.40921313
0.31825593
0.66173244
0.58618224
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0.7646743
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0.5679266
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0.29808593
0.8649062
0.4488071
0.66109145
0.41637605
0.41847432
0.34130597
0.5417827
2.026502
0.70042425
0.5664514
0.40212184
0.35949153
0.36982083
0.34489578
0.34549972
0.47532624
2.0633426
‐0.4580785
‐0.66090095
0.5132441
0.367613
0.4805686
0.327446
‐0.524722
0.3493159
0.4209575
0.4303645
1.0124865
1.2988963
‐0.47238067
0.38345605
0.41718525
0.7124973
‐0.5349336
0.48338243
0.62016344
1.1934389
‐0.47880226
‐1.8451334
‐1.3596027
‐1.4299273
0.39095336
0.5532246
0.5477212
0.4220712
0.46170875
0.68055075
0.70391434
0.4795135
0.87414855
‐0.4246055
‐0.7839398
‐2.0887516
‐0.3017875
‐0.48869783
0.3812299
0.6478722
0.2742742
0.6316421
‐0.47306418
‐0.34812275
‐0.4524054
‐0.5585485
‐1.4671113
‐0.9421135
‐0.5307021
0.8024351
0.4400085
‐0.6185513
0.6201337
0.7477214
‐0.5438123
1.2819192
0.53940153
0.40203202
0.4278109
‐0.65391564
‐0.5937166
‐0.60982305
‐0.2977271
‐1.2840261
135
STM4473
STM4486
STM4492
STM4495
STM4498
STM4505
STM4511
STM4513
STM4514
STM4519
STM4533
STM4549
STM4550
STM4552
STM4561
STM4562
STM4573
STM4593
STM4594
STM4595
STM4596
STY0287
STY0402
STY0439
STY0586
STY0861
STY0936
STY0963
STY1164
STY1284
STY1472
STY1488
STY1505
STY2099
STY2115
STY2258
STY2303
STY2535
STY2695
STY2703
STY2717
STY2751
STY2893
STY2894
STY2897
STY2966
STY3034
STY3470
STY3532
STY3533
STY3724
STY3725
STY3769
STY4091
STY4154
STY4163
STY4175
STY4202
STY4259
STY4260
t0080
t3166
putative acetyltransferase
putative alcohol dehydrogenase
putative cytoplasmic protein
putative type II restriction enzyme, methylase subunit
putative inner membrane protein
putative inner membrane or exported
putative transcriptional regulator, LysR family
putative permease
putative inner membrane protein
putative NAD‐dependent aldehyde dehydrogenase
methyl‐accepting chemotaxis protein I, serine sensor receptor
putative cytoplasmic protein
ferric hydrozamate transport, involved in reduction of
putative inner membrane protein
hyperosmotically inducible periplasmic protein, RpoS‐dependent stationary phase
putative inner membrane protein
putative fimbrial chaparone protein
putative fimbrial usher protein
putative fimbrial chaparone protein
putative fimbrial chaparone protein
putative inner membrane protein
hypothetical protein
PrpD protein
maltodextrin glucosidase
putative membrane protein
hypothetical protein
putative virK protein
anaerobic dimethyl sulfoxide reductase chain B
putative membrane transporter
putative invasin
putative virulence effector protein
respiratory nitrate reductase 2 alpha chain
putative glycogen debranching protein
high‐affinity zinc uptake system periplasmic binding protein
putative copper homeostasis protein
putative ferredoxin
putative reductase RfbI
O‐succinylbenzoic acid‐CoA ligase
ethanolamine ammonia‐lyase heavy chain
putative cobalamin adenosyltransferase
putative oxidoreductase
GMP synthase (glutamine‐hydrolyzing)
putative exported protein
TonB‐dependent outer membrane siderophore receptor protein
conserved hypothetical protein
putative exported protein
hypothetical protein
argininosuccinate synthetase
oxaloacetate decarboxylase alpha chain
oxaloacetate decarboxylase gamma chain
thiamine biosynthesis protein
thiamine biosynthesis protein
cystathionine gamma‐synthase
2,3‐bisphosphoglycerate‐independent phosphoglycerate mutase
putative DNA‐binding protein
hypothetical protein
hypothetical protein
putative phosphosugar‐binding protein
hypothetical protein
gamma‐glutamyltranspeptidase precursor
putative metabolite transport protein
hypothetical protein
yjgM
yjgB
yjiE
yjiG
yjiH
tsr
fhuF
osmY
stjC
sthB
sthA
prpD
malZ
ybcI
ybjX
dmsB
srfA
narZ
glgX
yebL
cutC
pduS
rfbI
menE
eutB
aegA
guaA
iroE
iroN
argG
oadA
oadG
thiS
thiG
metB
ggt
yaaU
‐0.71215767
‐0.11949775
‐0.5941703
0.23842911
‐0.7631232
0.12053465
3.0451999
0.38334697
‐0.5954039
‐0.024576357
0.15356995
0.39336935
0.03778016
‐0.1356715
‐0.8455967
‐0.7222619
‐0.4490622
‐0.37704462
‐0.08171417
0.21577792
0.5386312
‐0.3905154
0.59466296
0.52694124
0.4844363
‐0.18842188
‐0.2103791
‐0.17353666
‐0.01806822
0.17594515
‐0.45500827
‐0.8157917
‐0.012356399
‐0.04622489
1.0694163
0.10332791
‐0.27765492
‐0.21771874
0.6988597
‐0.43592656
‐0.3926839
‐1.5188409
1.4100732
0.077165596
‐0.45116913
‐0.56153303
0.2633421
0.9257506
0.72089875
‐0.08631868
‐0.044669397
0.3761747
‐0.31661856
0.47470537
‐0.3089121
‐0.014090952
0.23624487
‐0.8119977
0.10265508
‐0.13645609
‐0.5191252
‐0.54731643
1.593907
2.278952
2.5838516
1.5136276
1.9802327
2.2200248
‐1.7070447
‐4.7692523
‐2.1606038
1.5270014
‐1.6729057
2.7949016
3.8569243
5.468598
2.8529289
2.328125
1.6897191
2.5734284
1.8201561
1.952907
2.088449
‐2.3752172
‐2.3385806
‐1.5636102
‐1.7372906
‐1.7608556
3.5299184
‐1.9120498
1.6345549
1.6050096
‐1.6420331
‐1.8987545
‐1.7237203
6.638497
‐3.090817
‐1.5463238
2.282679
‐1.64059
‐1.5830407
‐1.9174988
‐2.1972065
2.1293032
4.2431254
4.3721895
‐7.0437884
‐5.3715653
‐2.0251381
‐4.191836
‐2.112639
‐1.8961029
1.6659126
2.8552682
3.3029058
‐4.0558205
1.7678808
‐1.6739954
‐3.4714706
2.0096915
1.7132899
2.4212725
1.5017532
‐2.2515032
0.36478534
0.5181439
0.6488349
0.39394987
0.40949884
0.578649
‐0.50016266
‐0.9544537
‐0.5022019
0.40365338
‐0.9974906
0.56562847
0.7813237
1.6186746
0.61580104
0.62252986
0.44662827
0.68401676
0.51402205
0.44954565
0.45491496
‐0.49395123
‐0.5209139
‐0.41040137
‐0.3617383
‐0.49434984
0.943098
‐0.43810558
0.35074425
0.45023513
‐0.39458135
‐0.5004718
‐0.37865144
1.8014921
‐0.74927926
‐0.49018532
0.82277745
‐0.38969326
‐0.41469145
‐0.52570236
‐0.59363675
0.55082524
0.8910266
1.6631677
‐1.5071532
‐1.262799
‐0.53842866
‐0.88805217
‐0.5543712
‐0.45030677
0.3687843
0.64458287
0.6846172
‐1.2421782
0.6529806
‐0.41327924
‐0.74050146
0.43511128
0.3831437
0.5848236
0.35812873
‐0.49981746
0.22886238
0.2273606
0.2511115
0.2602687
0.2067933
0.26064977
0.29299915
0.20012648
0.23243591
0.26434383
0.5962623
0.20237868
0.20257688
0.29599446
0.21584871
0.26739538
0.26432103
0.2657998
0.28240547
0.23019306
0.21782431
0.20796044
0.22274789
0.2624704
0.2082198
0.2807441
0.26717275
0.22912875
0.2145809
0.28051865
0.24030048
0.26357898
0.21967104
0.27137047
0.2424211
0.31700045
0.36044377
0.23753239
0.2619588
0.27416044
0.27017796
0.25868803
0.20999299
0.380397
0.21396911
0.23508957
0.26587257
0.2118528
0.26240698
0.23749068
0.22137074
0.22575213
0.20727725
0.3062705
0.36935782
0.24688195
0.2133106
0.21650651
0.2236304
0.24153563
0.23847376
0.22199278
0.048099868
0
0
0.06573839
0
0
0.055790044
0
0
0.066927865
0.052916735
0
0
0
0
0
0.05455575
0
0.062375717
0.03676819
0
0
0
0.066927865
0.056731287
0.05861933
0
0.033565152
0.05046221
0.048099868
0.05046221
0.0654669
0.056731287
0
0
0.06573839
0
0.05046221
0.046063263
0.03424889
0
0
0
0
0
0
0
0
0
0.0654669
0.052023627
0
0
0
0.05994943
0.052916735
0
0
0.055790044
0
0.08572143
0
0.28985777
0.5597197
0.5707446
0.25195864
0.38002673
0.4717325
‐0.29897767
‐0.96606237
‐0.4175689
0.55251664
‐0.9134698
0.54050124
0.77914
1.443204
0.58273304
0.69533205
0.3577469
0.83054364
0.3393081
0.47992814
0.453717
‐0.5284297
‐0.49298972
‐0.26598063
‐0.39932278
‐0.39604163
0.8266219
‐0.45513213
0.35195166
0.6207646
‐0.29640138
‐0.5651388
‐0.31610373
1.6600322
‐0.83848965
‐0.36159647
0.6925853
‐0.3119127
‐0.2979307
‐0.38120845
‐0.4300859
0.67157376
0.93417346
1.2964964
‐1.4992087
‐1.3324382
‐0.68828505
‐0.8413535
‐0.40848166
‐0.54803133
0.34690958
0.6056575
0.7182417
‐1.0078194
0.51049954
‐0.29650614
‐0.70266485
0.49000984
0.39459327
0.68399864
0.34281677
‐0.47960433
0.4287503
0.5544405
0.7728898
0.4843493
0.44331577
0.7163038
‐0.650452
‐0.9663083
‐0.52337974
0.35538727
‐1.7421912
0.567556
0.80690694
1.5985178
0.5943737
0.46468645
0.59769696
0.6540209
0.6615488
0.36690807
0.50647706
‐0.46068415
‐0.5892416
‐0.5112237
‐0.33200687
‐0.67891777
1.0932217
‐0.3605968
0.39548445
0.30455282
‐0.41446215
‐0.5857039
‐0.41061938
1.9473672
‐0.75747293
‐0.36156255
1.1637181
‐0.37656242
‐0.39554596
‐0.6780023
‐0.67344296
0.55280757
0.86765563
1.9452901
‐1.4673667
‐1.1740903
‐0.42935696
‐0.9153108
‐0.60562116
‐0.39315587
0.4336048
0.7192756
0.68269473
‐1.3371959
0.43609375
‐0.4657217
‐0.7875038
0.4181711
0.43763816
0.5683288
0.45150468
‐0.56542253
0.37574795
0.44027153
0.60287035
0.44554168
0.40515405
0.54791063
‐0.55105835
‐0.9309904
‐0.5656572
0.3030562
‐0.33681077
0.5888282
0.757924
1.8143021
0.6702963
0.707571
0.38444096
0.5674857
0.5412092
0.5018008
0.4045508
‐0.49273983
‐0.48051035
‐0.4539998
‐0.3538852
‐0.4080901
0.9094505
‐0.49858785
0.30479664
0.42538792
‐0.4728805
‐0.35057256
‐0.40923125
1.7970768
‐0.65187526
‐0.74739695
0.61202896
‐0.48060465
‐0.55059767
‐0.5178964
‐0.6773814
0.42809445
0.87125075
1.7477167
‐1.5548842
‐1.2818687
‐0.49764392
‐0.9074922
‐0.6490108
‐0.40973312
0.3258385
0.60881543
0.6529152
‐1.3815194
1.0123487
‐0.4776099
‐0.7313358
0.39715287
0.31719965
0.5021433
0.28006473
‐0.45442554
136
APPENDIX B
DATASET FOR FIGURE 12
137
Expected score (dExp)
‐0.16097945
0.52972996
0.7314146
0.26868537
Observed score (d)
0.32585317
Observed score (d)
sdh
STM0732
STM0733
STM0734
STM0735
fba
STM3068 fructose‐bisphosphate aldolase
fba
‐0.34157068
1.7177707
0.3701238
0.21546753
0.055790044
STM4221 glucosephosphate isomerase
STM0698 phosphoglucomutase
pgi
pgm
‐0.41912338
‐0.17831652
0.5373871
0.5294637
0.121118516
0.13027412
0.22538413
0.2460492
2.981996
2.981996
gmd
STM2109 GDP‐D‐mannose dehydratase in colanic acid gene cluster
gmd
‐0.15905677
‐0.34493408
0.2675742
0.115076266
wca
STM2098
STM2099
STM2100
STM2101
STM2102
STM2103
STM2104
STM2105
STM2106
STM2107
STM2108
STM2109
STM2110
STM2111
STM2112
STM2113
STM2114
STM2115
STM2116
STM2117
STM2118
putative glucose‐1‐phosphate uridylyltransferase (UDP‐glucose pyrophosphorylase), non‐catgalF
putative colanic acid biosynthesis protein
wcaM
putative glycosyl transferase in colanic acid gene
wcaL
putative galactokinase in colanic acid gene cluster
wcaK
putative export protein in colanic acid gene
wzxC
putative UDP‐glucose lipid carrier transferase/glucose‐1‐phosphate transferase in
wcaJ
phosphomannomutase in colanic acid gene cluster
cpsG
mannose‐1‐phosphate in colanic acid gene cluster
manC
putative glycosyl transferase in colanic acid biosynthesis
wcaI
GDP‐mannose mannosyl hydrolase in colanic acid biosynthesis
wcaH
bifunctional GDP fucose synthetase in colanic acid
wcaG
GDP‐D‐mannose dehydratase in colanic acid gene cluster
gmd
putative acyltransferase in colanic acid biosynthesis
wcaF
wcaE
putative transferase in colanic acid biosynthesis
wcaD
putative colanic acid polymerase
putative glycosyl transferase in colanic acid biosynthesis
wcaC
putative acyl transferase in colanic acid biosynthesis
wcaB
putative glycosyl transferase in colanic acid biosynthesis
wcaA
putative tyrosine‐protein kinase in colanic acid export
wzc
putative protein‐tyrosine‐phosphatase in colanic acid export
wzb
putative polysaccharide export protein, outer membrane
wza
STM3919
STM3920
STM3921
STM3922
STM3923
STM3924
STM3925
STM3926
STM3927
STM3928
STM3929
modulator of enterobacterial common antigen (ECA) polysaccharide
UDP‐N‐acetyl glucosamine ‐2‐epimerase
UDP‐N‐acetyl‐D‐mannosaminuronic acid dehydrogenase
dTDP‐glucose 4,6‐dehydratase
glucose‐1‐phosphate thymidyl transferase
lipopolysaccharide biosynthesis protein
TDP‐4‐oxo‐6‐deoxy‐D‐glucose transaminase
O‐antigen translocase in LPS biosyntesis
putative inner membrane protein
TDP‐Fuc4NAc:lipidII transferase
putative UDP‐N‐acetyl‐D‐mannosaminuronic acid transferase
wzzE
wecB
wecC
rffG
rffH
wecD
wecE
wzxE
STM3606
STM3607
STM3608
STM3609
STM3610
STM3611
STM3612
STM3613
STM3614
STM3615
STM3616
STM3617
STM3618
STM3619
STM3620
STM3621
STM3622
STM3623
STM3624
putative transcriptional regulator (LuxR/UhpA familiy)
putative transcriptional regulator, LysR family
putative tRNA‐processing ribonuclease
putative MFS family transport protein
putative inner membrane protein
putative Diguanylate cyclase/phosphodiesterase domain 3
ketodeoxygluconokinase
putative Zn‐dependent peptidase
DAACS family, C4‐dicarboxylic acids transport protein
putative Diguanylate cyclase/phosphodiesterase
putative TPR‐repeat‐containing protein
endo‐1,4‐D‐glucanase
putative cellulose synthase
glycosyltransferase, probably involved in cell wall biogenesis
putative ATPase involved in chromosome partitioning
putative cytoplasmic protein
putative cytoplasmic protein
putative inner membrane protein
putative inner membrane protein
yhjB
yhjC
yhjD
yhjE
yhjG
yhjH
kdgK
yhjJ
dctA
yhjK
yhjL
bcsC
yhjN
yhjO
yhjQ
yhjR
yhjS
yhjT
yhjU
csg
STM1139
STM1140
STM1141
STM1142
STM1143
STM1144
STM1145
putative transcriptional regulator in curly assembly/transport, 2nd
curli production assembly/transport component, 2nd curli operon
curli production assembly/transport component, 2nd curli operon
putative transcriptional regulator (LuxR/UhpA family)
minor curlin subunit precursor, nucleator for assembly
curlin major subunit, coiled surface structures cryptic
putative curli production protein
csgG
csgF
csgE
csgD
csgB
csgA
csgC
0.77964735
‐0.75900143
‐0.86330074
0.098342165
adr
STM0385 putative diguanylate cyclase/phosphodiesterase domain 1 (aka yaiC )
adrA
gly
STM2555 serine hydroxymethyltransferase
glyA
‐0.7095931
wec
yhj/bcs
succinate dehydrogenase, cytochrome b556
succinate dehydrogenase, hydrophobic subunit
succinate dehydrogenase, flavoprotein subunit
succinate dehydrogenase, Fe‐S protein
wecF
wecG
‐1.1092175
‐0.8225715
‐0.46165362
‐1.2891157
Numerator (r)
Denominator q‐value (%)
(s+s0)
0.21987917
12.94102
0.28192386
0.17665482
0.2077704
0.6706345
0.32383624
8.556413
Locus
pgi/pgm
Gene Name
Gene Symbol
sdhC
sdhD
sdhA
sdhB
Operon
0.07164832
‐0.31271487
‐0.17090602
‐0.14950018
‐0.7955477
0.49970412
0.10571416
0.2115535
3.821398
‐0.5923859
‐2.2956998
‐0.43147963
‐0.06639378
‐0.08616231
0.3645222
‐0.15905677
1.2691798
0.3212012
‐2.6516657
‐1.5617541
‐2.3840563
‐1.8586746
‐1.2891157
0.29942727
0.086465225
‐0.66243654
‐0.35225782
‐0.5075489
‐0.46265164
‐0.34493408
0.23592186
0.26919335
0.24981903
0.22555268
0.21289301
0.24891481
0.2675742
0.11737153
14.038219
0
0.066927865
0
0.06410537
0.115076266
0.33265916
‐1.0247878
‐0.2735066
0.26689097
0.22714518
0.25384754
‐1.6581541
‐0.4503259
0.27158266
0.050878678
0.2244196
0.1949813
0.19255586
0.21421777
0.23340331
0.23796788
0.21954177
0.25656268
0.24498908
0.26529017
0.050878678
0.08572143
0.199535
0.15733828
14.038219
1.602521
3.2794652
18.641977
1.9518311
0.18574002
‐0.21702328
‐0.5249004
‐0.1648354
‐0.379019
0.75989574
‐0.2744039
‐0.25473747
‐0.27037552
0.40543115
‐0.004637463
1.6406711
1.4984355
1.0119336
1.1267594
0.24911368
0.59106064
1.0639365
0.36819875
0.29216692
0.19485374
0.24137188
‐0.3923465 ‐0.091574974
‐0.68108827 ‐0.16207713
‐0.57317686 ‐0.12583627
0.06391327
0.1448034
0.2822519
‐1.2774783
‐0.33938333
0.950021
0.21675953
1.2618214
2.5381799
0.42335746
1.2370105
0.28907466
0.51426595
0.123582125
0.45271584
0.22909316
0.2026121
0.29190964
0.36597577
0.115076266
0
7.0054545
0.16040243
‐0.13808168
‐0.17669298
0.019353023
‐0.27506167
0.39898506
0.75786716
0.8503567
‐0.35020438 ‐0.072251335
0.13480397
0.15860808
0.16695112
0.20631191
0.3378672
0.20928216
0.1963307
16.321444
8.556413
0.6706345
0.3835722
‐0.20685117
‐0.15356995
1.6005901
0.89733094
0.40892595
0.32254764
0.2554845
0.35945228
0.048099868
0.29865357
0.67170036
‐0.885439
‐0.4742528
‐0.11016077
‐0.12431578
1.4742607
1.4697394
2.3276753
0.31383693
0.32386404
0.48388755
‐0.17164081
0.14401408
0.2128775
0.22035474
0.20788448
0.292042
0.24760222
0.10496254
0.10378451
0
2.981996
2.0488043
‐3.1918595
‐3.496217
‐2.6320384
‐4.3753157
‐1.0043005
‐0.8307732
‐0.8747101
‐1.3654959
0.31464434
0.23762059
0.3323318
0.31209084
0
0
0
0
0.16054967
‐7.121766
‐1.4728444
0.20680887
0
0.59701335
‐4.324508
‐1.1396213
0.2635262
0
0.59083503
0.21493167
0
‐0.5877265
0.5816348
2.7489436
138
APPENDIX C
DATASET FOR FIGURE 13
139
Gene Name
Gene Symbol
PSLT037
PSLT038
PSLT039
PSLT040
PSLT041
Salmonella plasmid virulence: hydrophilic protein
Salmonella plasmid virulence: hydrophilic protein
Salmonella plasmid virulence: hydrophilic protein
Salmonella plasmid virulence: outer membrane protein
Salmonella plasmid virulence: regulation of spv operon
spvD
spvC
spvB
spvA
spvR
STM1087
STM1088
STM1089
STM1090
STM1091
STM1092
STM1093
STM1094
STM1095
STM1096
STM1097
Pathogenicity island encoded protein: SPI3
Pathogenicity island encoded protein: SPI3
putative inner membrane protein
Pathogenicity island encoded protein: homologous to ipgE
Salmonella outer protein: homologous to ipgD of
putative cytoplasmic protein
putative cytoplasmic protein
Pathogenicity island encoded protein: SPI3
Copper resistance histidine kiUnknownse
Copper resistance transcriptioUnknownl regulatory protein
putative periplasmic or exported protein
pipA
pipB
Unknown
pipC
sopB
orfX
Unknown
pipD
copS
copR
Unknown
STM1379
STM1380
STM1381
STM1382
STM1383
STM1384
STM1385
STM1386
STM1387
STM1388
STM1389
STM1390
STM1391
STM1392
STM1393
STM1394
STM1395
STM1396
STM1397
STM1398
STM1399
STM1400
STM1401
STM1402
STM1403
STM1404
STM1405
STM1406
STM1407
STM1408
STM1409
STM1410
STM1411
STM1412
STM1413
STM1414
STM1415
STM1416
STM1417
STM1418
STM1419
STM1420
STM1421
putative amino acid permease
orf48
orf32
putative hydrolase or acyltransferase
putative cytoplasmic protein
orf245
putative regulatory protein, deoR family
orf408
TetrathioUnknownte reductase complex, subunit A
ttrA
TetrathioUnknownte reductase complex, subunit C
ttrC
TetrathioUnknownte reductase complex, subunit B
ttrB
TetrathioUnknownte reductase complex: sensory transduction histidine kiUnknowttrS
TetrathioUnknownte reductase complex: response regulator
ttrR
putative cytoplasmic protein
orf70
putative inner membrane protein
orf319
putative regulatory proteins, merR family
orf242
Secretion system regulator: transcriptoUnknownl activator, homologous with
ssrB
Secretion system regulator:Sensor component
ssrA
Secretion system apparatus
ssaB
Secretion system apparatus
ssaC
Secretion system apparatus
ssaD
Secretion system effector
ssaE
Secretion system effector
sseA
Secretion system effector
sseB
Secretion system chaparone
sscA
Secretion system effector
sseC
Secretion system effector
sseD
Secretion system effector
sseE
Secretion system chaparone
sscB
Secretion system effector
sseF
Secretion system effector
sseG
Secretion system apparatus
ssaG
Secretion system apparatus
ssaH
Secretion system apparatus
ssaI
Secretion system apparatus: homology with the yscJ/mxiJ/prgK
ssaJ
putative cytoplasmic protein
Unknown
Secretion system apparatus
ssaK
Secretion system apparatus
ssaL
Secretion system apparatus
ssaM
Secretion system apparatus: homology with the LcrD
ssaV
Secretion system apparatus: homology with the YscN
ssaN
Secretion system apparatus
ssaO
Secretion system apparatus
ssaP
Secretion system apparatus
ssaQ
Secretion system apparatus: homology with YscR of
ssaR
Secretion system apparatus: homology with YscS of
ssaS
Secretion system apparatus: homology with YscT of
ssaT
STM2861
STM2862
STM2863
STM2864
STM2865
STM2866
STM2867
STM2868
STM2869
STM2870
STM2871
STM2872
STM2873
STM2874
STM2875
STM2876
STM2877
STM2878
STM2879
STM2880
STM2881
STM2882
STM2883
STM2884
STM2885
STM2886
STM2887
STM2888
STM2889
STM2890
STM2891
STM2892
STM2893
STM2894
STM2895
STM2896
STM2897
STM2898
STM2899
STM2900
STM2901
STM2902
STM2903
STM2904
STM2905
STM2906
STM2907
STM2908
Salmonella iron transporter: fur regulated
Salmonella iron transporter: fur regulated
Salmonella iron transporter: fur regulated
Salmonella iron transporter: fur regulated
putative inner membrane protein
transcriptioUnknownl regulator
bacterial regulatory helix‐turn‐helix proteins, araC family
putative cytoplasmic protein
putative flagellar biosynthesis/type III secretory pathway protein
putative inner membrane protein
cell invasion protein lipoprotein, may link inner
cell invasion protein cytoplasmic
cell invasion protein cytoplasmic
cell invasion protein
regulatory helix‐turn‐helix proteins, araC family
invasion genes transcription activator
cell invasion protein
protein tyrosine phosphate
chaparone, related to virulence
putative cytoplasmic protein
putative acyl carrier protein
cell invasion protein
cell invasion protein
cell invasion protein
cell invasion protein
surface presentation of antigens secretory proteins
surface presentation of antigens secretory proteins
surface presentation of antigens secretory proteins
surface presentation of antigens secretory proteins
surface presentation of antigens secretory proteins
surface presentation of antigens secretory proteins
surface presentation of antigens secretory proteins
surface presentation of antigens secretory proteins
surface presentation of antigens secretory proteins
surface presentation of antigens secretory proteins
invasion protein
invasion protein
invasion protein outer membrane
invasion protein
invasion protein
putative cytoplasmic protein
putative cytoplasmic protein
putative cytoplasmic protein
putative ABC‐type transport system
putative acetyltransferase
putative cytoplasmic protein
serine/threonine specific protein phosphatase 2
putative cytoplasmic protein
sitA
sitB
sitC
sitD
avrA
sprB
hilC
Unknown
orgA
Unknown
prgK
prgJ
prgI
prgH
hilD
hilA
iagB
sptP
sicP
Unknown
iacP
sipA
sipD
sipC
sipB
sicA
spaS
spaR
spaQ
spaP
spaO
invJ
invI
invC
invB
invA
invE
invG
invF
invH
Unknown
Unknown
Unknown
Unknown
Unknown
Unknown
pphB
Unknown
STM3752
STM3753
STM3754
STM3755
STM3756
STM3757
STM3758
STM3759
STM3760
STM3761
STM3762
STM3763
STM3764
putative cytoplasmic protein
ATP binding protein
putative cytoplasmic protein
putative cytoplasmic protein
putative cytoplasmic protein
putative autotransported protein
putative inner membrane protein
putative transcriptioUnknownl regulatory protein
putative cytoplasmic protein
putative inner membrane protein
putative inner membrane protein
Mg2 transport protein
Mg2 transport protein
Unknown
sugR
Unknown
rhuM
rmbA
misL
fidL
marT
Unknown
slsA
cigR
mgtB
mgtC
SPI‐3
SPI‐1
SPI‐2
spv
Locus
SPI‐5
Pathogenicity Island
Expected score (dExp)
Observed score (d)
0.3451125
0.12597384
0.52864
3.73863
3.69344
1.7494527
0.533578
0.1795718
0.857898
0.34778625
‐0.67124
0.6241384
2.89835
‐0.4367854
0.582196
‐0.9798491
0.4992586
‐0.557762
0.478286
‐0.34437576
‐0.4692294
0.382388
Observed score (d)
‐0.43564
0.36591497
‐3.5863433
‐0.32545796
‐0.39771888
1.441267
0.9723333
0.41536158
‐0.18371316
‐0.92264754
‐0.2912236
0.35549143
‐0.4732188
0.373257
0.22726588
0.34995
0.3332265
0
0
0.058067188
0.21516998
‐0.2721435
0.258168
0.277684
0.39057806
0.25100356
0.1232865
0.549752
0.19741683
0.2416341
1.602521
0
0.13251573
0.267453
3.2794652
0.2474459
0.27224
2.0488043
0.18036549
‐1.693815
‐1.8441163
0.15581225
0.7698345
‐0.21243665
‐0.48361963
0.237527
0.2248594
0.19865376
0.262257
1.2710634
11.978601
0.19118953
0.063013285
‐0.2273156
0.2692583
0.6706345
0.19661248
0.2797925
0.2423666
0.21264967
0.44346243
0.1230616
‐3.321381
‐0.9836273
‐1.4643968
‐3.74352
‐4.8352513
‐6.4116616
‐5.22483
‐2.872765
‐2.187747
‐2.1521764
0.94875835
‐0.94357896
‐0.21941125
‐0.3655539
‐0.78974617
‐1.237889
‐1.57193
‐1.1248634
‐0.832631
‐0.48835576
‐0.58988625
0.7282537
0.2542196
0.2849234
0.223634
0.24962762
0.21319415
0.2489697
0.24516734
0.2162347
0.2898113
0.22322313
0.2748823
0.233796
9.568785
0
0.25100356
0.099325456
0
0
0
0
0
0
0
10.890071
‐0.7953813
‐5.91822
‐11.97955
‐7.41666
‐5.643275
‐5.844457
‐3.228976
‐4.3237
‐3.9147432
‐0.162677
‐1.572854
‐2.4865324
‐1.7376173
‐1.568448
‐1.2747184
‐0.98158574
‐1.4888674
‐0.85478
0.237622
0.2664949
0.277138
0.2343444
0.277861
0.219617
0.339929
0.3446157
0.2449561
0.8168742
0
0
0
0
0
0
0
0
‐1.398738
‐0.8512679
‐0.4283639
‐0.1888269
0.9734219
0.22553737
‐2.216393
‐0.6748695
0.3798185
0.22178999
0.29713
0.233578
0.26674393
0.2293868
0.12805222
0.5286912
4.7937937
0.1685139
0
0
0.358913
0.743179
‐0.5265974
‐0.3911136
‐0.2423272
0.28364876
‐0.6895825
0.2181684
0.9547462
‐0.716915
0.8478979
0.9168429
0.57788384
q‐value (%)
‐0.15457898
‐0.3515194
‐0.8197763
0.81142
1.3157438
Denominator (s+s)
‐0.624824
‐1.1292721
0.65599614
0.33842635
‐0.4917346
2.31332
Numerator (r)
0.785688
‐0.13117346
0.18842188
‐0.59271395
‐0.131393
0.1898982
0.4641686
1.19356
0.755373
‐0.33848143
‐0.5332558
‐0.46562156
‐0.267785
0.3826
‐0.1497325
7.42724
9.684762
5.7489934
3.4989843
2.698598
2.66538
1.2546563
1.68272
1.985951
1.445996
0.915324
0.5966483
0.863565
0.3125714
0.22699997
0.245632
0.2515266
0.2615962
0.22173147
0.32417
0.24728456
0
0
0
0
0
0
0.115076266
2.392666
‐0.3761747
1.6843232
2.429555
0.3551381
0.5277148
0.2184914
0.2172513
0.052916735
0
‐7.5789514
‐2.9427886
0.6737911
1.31495
0.385152
0.23712794
0.12110458
‐0.696366
2.439458
0.493937
0.24124567
0
‐0.3317754
2.583535
0.5453996
0.2111852
0
‐0.538284
‐0.4912687
0.2198736
0.63983226
‐0.772837
0.3864253
0.3243237
0.798952
0.748417
1.28687
1.554521
0.4192444
2.5279467
0.6776876
0.4241646
‐0.39816448
0.17691824
0.2348827
0.4571925
0.9843971
0.5134733
0.21224698
0.9342445
‐0.8193529
0.238878
0.2282616
0.2616784
0.2348268
0.231186
0.31319296
0.222331
0.2578252
0.70881206
0.19118953
0.046063263
7.0054545
0
1.1319548
7.0054545
12.94102
‐0.6327656
0.8584856
‐0.14198452
0.22527337
2.0488043
‐0.44472688
0.94338596
0.18169497
0.19259876
0.25100356
‐0.26686937
0.4469964
0.167966
0.2387297
5.396542
0.3236683
0.496327
0.87858
1.685345
0.1874261
0.533298
0.2345273
0.316382
0.4960944
0.052916735
1.1462337
1.242791
0.269519
0.212999
0.199535
0.8882618
1.156954
0.2792278
0.2413475
0.16223158
0.29431117
‐0.47684246
0.31969455
0.4323464
0.5137684
‐0.4145835
0.9432981
2.1396935
1.5254
1.948771
1.766868
1.5712994
0.29729152
0.48596856
0.4139925
0.24619663
0.3677635
0.4469973
0.3151618
0.2271264
0.27235416
0.22486234
0.2814514
0.28447622
0.25100356
0
0.06573839
0.18036549
0.05861933
0.04670303
0.67124
0.25594634
‐0.6973895
‐1.5135429
0.7176173
0.43751
0.719244
0.1684743
0.9286179
‐0.2424582
0.172352
0.23417416
0.21558158
0.2265679
0.2424387
0.8815512
7.0054545
0.19118953
0.8815512
0.38734964
1.3798
0.22465748
0.2164372
0.19118953
‐1.71379
140
APPENDIX D
DATASET FOR FIGURE 15
141
Gene Symbol
Expected score (dExp)
‐0.46287772
0.54299587
STM0370 putative protein in propionate catabolism
STM0371 putative acetyl‐CoA synthetase, propionate catabolism operon
prpD
prpE
STM1383
STM1384
STM1385
STM1386
Tetrathionate reductase complex, subunit A
Tetrathionate reductase complex, subunit C
Tetrathionate reductase complex, subunit B
Tetrathionate reductase complex: sensory transduction histidine kinase
ttrA
ttrC
ttrB
ttrS
‐0.4692294
0.382388
‐0.43564
STM2016
STM2017
STM2018
STM2019
STM2020
STM2021
STM2022
STM2023
STM2024
STM2025
STM2026
STM2027
STM2028
STM2029
STM2030
STM2031
STM2032
STM2033
STM2034
STM2035
nicotinate‐nucleotide dimethylbenzimidazole‐P phophoribosyl transferase
cobalamin 5‐phosphate synthase
bifunctional: cobinamide kinase cobinamide phosphate guanylyltransferase
synthesis of vitamin B12 adenosyl cobalamide precursor
synthesis of vitamin B12 adenosyl cobalamide precursor
synthesis of vitamin B12 adenosyl cobalamide precursor
synthesis of vitamin B12 adenosyl cobalamide precursor
synthesis of vitamin B12 adenosyl cobalamide precursor
synthesis of vitamin B12 adenosyl cobalamide precursor
synthesis of vitamin B12 adenosyl cobalamide precursor
synthesis of vitamin B12 adenosyl cobalamide precursor
synthesis of vitamin B12 adenosyl cobalamide precursor
synthesis of vitamin B12 adenosyl cobalamide precursor
synthesis of vitamin B12 adenosyl cobalamide precursor
synthesis of vitamin B12 adenosyl cobalamide precursor
synthesis of vitamin B12 adenosyl cobalamide precursor
synthesis of vitamin B12 adenosyl cobalamide precursor
synthesis of vitamin B12 adenosyl cobalamide precursor
synthesis of vitamin B12 adenosyl cobalamide precursor
synthesis of vitamin B12 adenosyl cobalamide precursor
cobT
cobS
cobU
cbiP
cbiO
cbiQ
cbiN
cbiM
cbiL
cbiK
cbiJ
cbiH
cbiG
cbiF
cbiT
cbiE
cbiD
cbiC
cibB
cbiA
‐0.3596984
0.125549
‐0.577434
0.132948
‐0.2681435
0.6821211
‐0.177487
‐0.8197763
‐0.2273156
0.2692583
0.6706345
‐0.6364274
‐1.613745
‐0.18234958
‐0.379436
0.2865278
0.2348614
2.0488043
0.048099868
‐0.86849797
‐0.271779
0.23854737
0.44346243
‐2.8734584
‐1.193524
‐1.911219
‐1.9498528
‐0.6194955
‐0.21968375
‐0.48326436
‐0.54513216
0.21559231
0.2155135
0.25419956
0.2795766
0
0.22714518
0.0654669
0.035160456
‐0.3415727
‐1.1164812
0.18976788
‐0.263886
‐0.6444326
‐0.2332939
‐0.23452298
‐0.611676
‐0.19833991
‐1.622655
‐1.763159
‐2.41728
‐1.5197679
‐1.4282357
‐1.1972411
‐1.536577
‐0.64688283
‐0.72592443
‐0.32925114
‐0.41459784
‐0.53393686
‐0.3129892
‐0.3276442
‐0.384656
‐0.4781363
‐0.14634614
‐0.15292
0.229889
0.23514597
0.2288991
0.259454
0.2294473
0.31773597
0.31116977
0.22623284
0.273532
0.048099868
0.05861933
0
0.10616762
0.11451641
0.16223158
0.08572143
1.9518311
1.2710634
‐0.596994
‐2.9346273
‐1.337248
‐2.9236968
‐0.1662132
‐0.6442693
‐0.2936185
‐0.664766
0.2918818
0.2195442
0.219577
0.22711235
6.111435
0
0.12110458
0
pduA
pudB
pduC
pduD
pduE
pduG
pduH
pduJ
pduK
pduL
pduM
pduN
pduO
pduP
pduQ
pduS
pduT
pduU
pduV
pduW
pduX
0.81463695
0.2779956
‐0.691715
0.49715197
STM2337 acetate kinase A (propionate kinase 2)
STM2338 phosphotransacetylase
ackA
pta
0.5191252
0.75595593
STM2973
STM2974
STM2975
STM2976
STM2977
STM2978
STM2979
fucO
fucA
fucP
fucI
fucK
fucU
fucR
‐0.5871229
pdu
STM2038
STM2039
STM2040
STM2041
STM2042
STM2043
STM2044
STM2045
STM2046
STM2047
STM2048
STM2049
STM2050
STM2051
STM2052
STM2053
STM2054
STM2055
STM2056
STM2057
STM2058
House
0.19118953
0.063013285
pocR
pduF
L‐1,2‐propanediol oxidoreductase
L‐fuculose‐1‐phosphate aldolase
L‐fucose permease pseudogene
L‐fucose isomerase
L‐fuculokinase
conserved protein of fucose operon
positive regulator of the fuc operon (DeoR family transcriptional regulator)
Observed Denominator Numerator(r)
q‐value (%)
score(d)
(s+s)
‐1.4725568 ‐0.38424844
0.2693963 0.100403905
‐1.85381
‐0.5133654
0.28511778
0.06083684
0.19865376
0.262257
STM2036 Propanediol utilization: transcriptional regulation, AraC family
STM2037 Propanediol utilization: propanediol diffusion facilitator
Propanediol utilization: polyhedral bodies
Propanediol utilization: polyhedral bodies
Propanediol utilization: dehydratase, large subunit
Propanediol utilization: dehydratase, medium subunit
Propanediol utilization: dehydratase, small subunit
Propanediol utilization: diol dehydratase reactivation
Propanediol utilization: diol dehydratase reactivation
Propanediol utilization: polyhedral bodies
Propanediol utilization: polyhedral bodies
Propanediol utilization
Propanediol utilization
Propanediol utilization: polyhedral bodies
Propanediol utilization: B12 related
Propanediol utilization: CoA‐dependent propionaldehyde dehydrogenase
Propanediol utilization: propanol dehydrogenase
Propanediol utilization: polyhedral bodies
Propanediol utilization: polyhedral bodies
Propanediol utilization: polyhedral bodies
Propanediol utilization
Propanediol utilization: propionate kinase
Propanediol utilization
Observed score(d)
‐0.21243665
‐0.48361963
fuc
Tran
scrit
pion
al prp
Gene Name
ttr
Locus
cbi‐cob
Operon
‐1.693815
‐1.8441163
‐0.2545563
‐2.4453
‐0.769993
0.29452744
0
0.78167754
0.242989
‐3.361834
‐2.8958943
‐0.8561333
‐0.7494269
0.28197682
0.25878945
0
0
0.7955477
‐0.66288
0.134613
‐2.593524
‐3.332989
‐4.498622
‐0.5469762
‐0.746891
‐1.186744
0.21917
0.2114299
0.2638166
0
0
0
0.6272232
0.5557284
‐0.7478967
‐0.4263147
0.2473526
‐0.57325
0.7679843
‐2.2732737
‐2.489522
‐1.757235
‐1.2839699
‐2.86925
‐0.517642
‐0.59797454
‐0.4866713
‐0.33875272
‐0.4437682
0.11952656
0.422674
0.2272317
0.2419843
0.2769866
0.2638323
0.2123185
0.23892361
0.2313112
0
0
0.058067188
0.14613661
0
3.821398
0
‐2.5375
‐2.351337
‐0.458568
‐0.4913177
0.2232548
0.288388
0
0
0.1455015
0.25566864
2.304016
‐2.0800235
‐0.6155243
‐0.4770719 ‐0.110215545
‐0.89110214 ‐0.23629537
0.2959218
0.23102501
0.26517203
0
7.600995
0.4182407
0.0894275
‐0.102252536
‐0.12107843
0.5271
2.87743
0.56910187
142
APPENDIX E
SIGNIFICANT MO GENES DATA FOR CHAPTER 4
143
All Significant Salmonella MO Genes (Delta=0.80701154, False Sig Genes=0, FDR=0%)
Locus
PSLT012
PSLT020
PSLT023
PSLT036
PSLT042
PSLT043
PSLT044
PSLT046
PSLT047
PSLT052
PSLT053
PSLT072
PSLT080
PSLT095
PSLT096
PSLT097
PSLT098
PSLT103
PSLT106
STM0003
STM0004
STM0012
STM0023
STM0027
STM0064
STM0066
STM0067
STM0077
STM0092
STM0096
STM0108
STM0110
STM0113
STM0116
STM0120
STM0134
STM0150
STM0153
STM0157
STM0167
STM0169
STM0171
STM0172
STM0178
STM0181
STM0191
STM0208
STM0216
STM0219
STM0221
STM0223
STM0224
STM0225
STM0228
STM0245
STM0247
STM0259
STM0300
STM0316
STM0319
STM0322
STM0324
STM0351
STM0352
STM0355
STM0362
STM0363
STM0369
STM0370
STM0377
STM0383
STM0385
STM0388
STM0401
STM0402
STM0405
STM0434
STM0436A
STM0447
STM0448
STM0452
STM0457
STM0458
STM0460
STM0461
STM0462
STM0463
STM0469
STM0470
STM0472
STM0475
STM0476
STM0485
STM0488
STM0498
STM0500
STM0508
STM0510
STM0511
STM0528
STM0530
STM0536
STM0558
STM0562
STM0570
GeneN
putative bacterial regulatory proteins, luxR family
hypothetical protein
DNA replication
putative transposase, IS200‐like
putative integrase protein
putative phosphoribulokinase / uridine kinase family
putative integrase protein
putative carbonic anhydrase
putative cytoplasmic protein
plasmid partition protein A
plasmid partition protein B
putative transglycosylase
conjugative transfer: assembly
conjugative transfer: aggregate stability
conjugative transfer
conjugative transfer: assembly
conjugative transfer: fimbrial synthesis
conjugative transfer: surface exclusion
homologue of mvpA, Shigella flexneri
homoserine kinase
threonine synthase
chaperone Hsp70 in DNA biosynthesis/cell division
fimbrial usher
fimbrial chaparone
dihydrodipicolinate reductase
carbamoyl‐phosphate synthetase, glutamine‐hydrolysing small subunit
carbamoyl‐phosphate synthase, large subunit
related to carnitine metabolism
peptidyl‐prolyl cis‐trans isomerase, survival protein
RNA polymerase associated protein, putative SNF2 family
thiamine‐binding periplasmic protein
3‐isopropylmalate isomerase (dehydratase), subunit with LeuC
2‐isopropylmalate synthase
acetolactate synthase III, valine sensitive, large subunit
putative S‐adenosyl methionine adenyltransferase
UDP‐3‐O‐acyl N‐acetylglucosamine deacetylase
APC family, aromatic amino acid transporter
pyruvate dehydrogenase, dihydrolipoyltransacetylase component
putative outer membrane protein
putative periplasmic protein
glucose dehydrogenase
putative carbonic anhydrase
putative ABC‐type multidrug transport system, ATPase component
putative PTS enzyme
pantothenate synthetase
outer membrane protein receptor / transporter for
deoxyguanosine triphosphate triphosphohydrolase
30S ribosomal subunit protein S2
ribosome releasing factor
undecaprenyl pyrophosphate synthetase (di‐trans,poly‐cis‐decaprenylcistransferase)
putative membrane‐associated Zn‐dependent protease
putative outer membrane antigen
histone‐like protein, located in outer membrane
UDP‐N‐acetylglucosamine acetyltransferase
putative outer membrane lipoprotein
putative ABC superfamily (atp_bind) transport system
putative methyltransferase in menaquinone/biotin biosynthesis
putative fimbriae assembly chaparone
aminoacyl‐histidine dipeptidase (peptidase D)
transcriptional regulator of cryptic csgA gene for
gamma‐glutamylphosphate reductase
putative inner membrane protein
putative cation efflux system protein
putative cation efflux pump
putative Copper chaperone
putative cytoplasmic protein
putative transcription regulator, AraC family
putative citrate synthase
putative protein in propionate catabolism
putative outer membrane lipoprotein
putative cytoplasmic protein
putative diguanylate cyclase/phosphodiesterase domain 1
shikimate kinase II
maltodextrin glucosidase
putative thiol ‐ alkyl hydroperoxide reductase
tRNA‐guanine transglycosylase
ketopantoate reductase
IS903 transposase
peptidyl‐prolyl cis/trans isomerase, trigger factor a molecular
proteolytic subunit of clpA‐clpP ATP‐dependent serine protease
peptidyl prolyl isomerase
putative hydrolase
putative cysteine synthase/cystathionine beta‐synthase
putative ABC superfamily (atp) transporter
putative ABC superfamily (atp&membrane) transporter
regulatory protein, P‐II 2, for nitrogen assimilation
putative Amt family, ammonium transport protein
putative 50S ribosomal protein L31 (second copy)
putative 50S ribosomal protein L36 (second copy)
maltose o‐acetyltransferase
RND family, acridine efflux pump
acridine efflux pump
putative cytoplasmic protein
adenylate kinase
putative copper‐transporting ATPase
putative Membrane protein implicated in regulation of
putative inner membrane protein
putative ABC‐type transport system ATPase component/cell division
putative ABC‐type transport system ATPase component/cell division
ureidoglycolate dehydrogenase
putative cytoplasmic protein
peptidyl‐prolyl cis‐trans isomerase B (rotamase B)
putative glycosyltransferase
putative transport protein
outer membrane N‐acetyl phenylalanine beta‐naphthyl ester‐cleaving esterase
GeneS
orf7
repA2
rlgA
parA
parB
finP
traK
traN
trbE
traF
traQ
traT
thrB
thrC
dnaK
bcfC
bcfG
dapB
carA
carB
fixC
surA
hepA
tbpA
leuD
leuA
ilvI
yabC
lpxC
aroP
aceF
yacH
yacC
gcd
yadF
yadG
yadI
panC
fhuA
dgt
rpsB
frr
uppS
yaeL
yaeT
hlpA
lpxA
yaeC
abc
yafE
safB
pepD
crl
proA
prpC
prpD
yaiW
yaiB
yaiC
aroL
malZ
tgt
apbA
tig
clpP
cypD
cof
mdlA
mdlB
glnK
amtB
rpmE2
rpmJ2
maa
acrB
acrA
ybaB
adk
copA
ybbJ
ybbP
sfbA
sfbB
allD
ylbE
ppiB
yfdH
apeE
107808
107809
107810
107811
‐0.21873495
0.19118033
0.59046596
0.42819518
0.5352007
0.52404296
0.6716581
0.29661897
0.39670837
0.37233824
0.44112355
0.27459073
‐0.19855331
0.5083317
0.30819207
0.23419821
0.2876653
0.5539146
0.23498842
‐0.69281363
‐0.314873
‐0.5170135
‐0.33272958
‐0.5230399
‐1.4498417
‐1.1434257
‐1.053431
‐0.21692583
0.3767992
‐0.35401532
0.23577571
1.5279573
2.0958962
0.26020688
‐0.22600807
‐0.25837657
0.33038053
0.43818256
‐0.40804002
‐0.18872282
0.2772285
1.1643332
0.29700285
‐0.24664909
‐0.43498638
0.6176664
0.300246
‐0.4021984
0.2711675
‐0.23628573
0.3049555
0.43271163
0.5923797
0.46926323
0.7503361
0.45306736
0.5335188
0.3435695
0.4249264
0.38255042
‐0.42575482
‐0.34722316
‐0.37917757
‐0.5922731
‐0.26525173
‐0.37270135
0.3706963
‐0.60706687
‐0.35205087
0.25086525
‐1.0665052
‐1.035921
0.6025709
‐0.3888723
‐0.26266083
‐0.23448625
‐0.23700683
‐0.37019327
0.77709967
0.3406515
0.5217175
‐0.199623
‐0.42223638
‐0.4450372
‐0.4977934
‐2.2110238
‐2.5150805
1.3985962
1.5099168
0.2251964
0.39987427
0.3923507
0.42250806
‐0.55290645
‐0.63727254
‐0.33343032
‐0.22696888
1.4184393
0.44251212
‐0.27818152
‐0.42593813
0.28459483
0.277786
‐0.42998475
‐0.37236246
‐0.33098617
0.6662266
0.46488547
0.41039482
0.51944155
0.5330904
0.61639065
0.5118478
0.48000222
0.5566913
0.42865178
0.60735095
‐0.4436235
0.49951515
0.4279481
0.49506816
0.32006288
0.47054815
0.35477102
‐1.2177294
‐0.36514962
‐0.66296506
‐0.21676783
‐0.91175896
‐1.5317243
‐1.2538745
‐1.2448778
‐0.42774284
0.28144532
‐0.5445657
0.33463296
1.7166674
2.0898426
0.4106647
‐0.22315557
‐0.28313807
0.36546996
0.34659097
‐0.4874071
‐0.29264215
0.39958212
1.417171
0.42260903
‐0.28074655
‐0.3594995
0.56935674
0.31568775
‐0.54393405
0.42408898
‐0.25281954
0.31661424
0.52033836
0.6102872
0.32102868
0.9077048
0.27486637
0.54910225
0.30105543
0.6467224
0.48966178
‐0.47432962
‐0.32326004
‐0.66379964
‐0.7305447
‐0.3072882
‐0.35836142
0.37361923
‐1.0282005
‐0.5228659
0.25069094
‐0.96745145
‐1.2856466
0.70973486
‐0.62017125
‐0.2559368
‐0.32816613
‐0.31890327
‐0.461738
0.50235707
0.23828518
0.37075484
‐0.4405928
‐0.2445751
‐0.51094645
‐0.66604364
‐2.2586772
‐2.587126
1.5783657
1.5123256
0.33155555
0.31404147
0.40799665
0.66256225
‐0.41970772
‐0.6506231
‐0.619396
‐0.2539097
1.588685
0.37308457
‐0.28702745
‐0.4512766
0.49165556
0.2642377
‐0.4193589
‐0.644741
‐0.23817043
0.58284324
0.41520572
0.60164636
0.46636653
0.5033524
0.610975
0.47765243
0.5567938
0.31634837
0.39327705
0.4902862
‐0.31377703
0.3619898
0.3715972
0.4314934
0.1999281
0.43895933
0.33978343
‐1.0278673
‐0.41357788
‐0.6681755
‐0.282484
‐0.9254414
‐1.5456456
‐1.1086514
‐1.2725413
‐0.5170514
0.26570287
‐0.43465686
0.26570046
1.583018
2.145787
0.2518642
‐0.22407691
‐0.33918095
0.44108745
0.21256778
‐0.43260288
‐0.27398717
0.4279262
1.3067999
0.3322259
‐0.21187602
‐0.3009579
0.4045455
0.2304402
‐0.7115866
0.5943148
‐0.28313074
0.3075448
0.30236128
0.6410853
0.3484745
0.6976756
0.29837728
0.48765448
0.25424984
0.56409657
0.43527973
‐0.46927315
‐0.32992923
‐0.44164142
‐0.58940333
‐0.21923548
‐0.21547908
0.40769526
‐0.84019566
‐0.27782857
0.26045486
‐0.86840016
‐1.0972964
0.6212581
‐0.49921197
‐0.21505938
‐0.2688599
‐0.3367807
‐0.32148904
0.6469255
0.5413024
0.35298458
‐0.47523832
‐0.37689427
‐0.6286598
‐0.67152846
‐2.2937286
‐2.4561398
1.7735767
1.6645528
0.41882786
0.24001056
0.26487678
0.6792037
‐0.6663243
‐0.69528997
‐0.62821084
‐0.33893412
1.4249496
0.40804917
‐0.23388119
‐0.51883566
0.51679015
0.4636148
‐0.3444349
‐0.6217672
‐1.0850646
‐0.63963336
‐0.6756516
0.6962467
‐0.586795
‐1.4889245
‐0.4208412
‐0.7575558
0.23216134
‐0.34044805
0.31699353
‐1.0760994
‐0.8411851
‐0.28462604
‐0.77392405
‐0.93360496
‐0.93247354
‐1.1038934
0.0844318
0.51616096
0.83274347
0.80367666
‐0.16569032
‐0.572756
2.4256654
0.87991774
0.88545954
‐0.0728656
1.0206679
‐0.24156623
1.0293115
1.4300208
1.6987354
0.93679035
1.1794915
0.31029144
0.42758867
1.0322548
0.45829695
0.16680454
‐0.015725844
0.97402143
0.03287625
‐0.2385491
‐0.73306835
0.14433959
0.47861534
0.57341975
1.1404701
0.19743674
0.6899292
1.415841
0.17894988
1.0336506
0.1374862
0.06541499
‐0.10479076
‐0.059341572
0.30107343
0.59202254
0.93801695
‐0.52142775
‐0.13397627
‐0.52192587
‐1.4730307
‐0.6839262
0.03719335
‐0.5843593
‐0.19599861
0.34953326
‐0.54481554
‐0.5835514
1.2113078
0.06503034
‐0.6453264
0.20476426
0.62007135
‐0.26962534
1.9144396
0.38613337
0.7027212
‐0.18961263
‐0.2916745
‐0.7020355
‐0.6051969
‐2.2217207
‐2.7700706
‐2.935089
‐3.9113479
‐0.046616565
0.2590296
0.18720058
1.3368509
0.6514215
‐0.5962032
‐0.26874873
0.6334251
‐0.004513601
0.26447338
‐0.4211586
‐0.3809063
0.4785309
‐0.05028975
‐0.5965487
0.71657217
107812
107813
Log2 Ratio Means
Ratio
‐1.0817932 ‐0.86064273 ‐0.26263 0.833567
‐0.8767592
‐0.9003971 0.480083 1.394824
‐1.2608273
‐1.1219376 0.490186 1.404626
0.65043
0.6241986 0.480079 1.39482
‐0.5008615 ‐0.35955667 0.507003 1.421095
‐1.3363144
‐1.6471025 0.520162 1.434116
‐0.91123503
‐1.1832428 0.633008 1.550795
‐0.6575734 ‐0.68897706 0.428706 1.346026
‐0.06946793 ‐0.54614925 0.477835 1.392652
‐0.45474067
‐0.6530225 0.415126 1.333415
0.20886631 0.077271126 0.421017 1.338871
‐1.0165291 ‐0.96350557 0.457409 1.373074
‐0.59166986
‐0.5302125 ‐0.31865 0.801819
‐0.80491954 ‐0.71326345 0.456612 1.372316
‐0.7402496 ‐0.84005123 0.369246 1.291677
‐1.044014
‐1.21234 0.38692 1.307599
‐0.75738686
‐0.967667 0.269219 1.205155
‐1.4469562
‐1.0903301 0.487807 1.402312
‐0.062313866 ‐0.31416678 0.309848 1.239577
0.38311204
0.28184104 ‐0.97947 0.507166
0.43817458
0.35283428 ‐0.36453 0.77672
0.7522421
0.704346 ‐0.61605 0.652454
‐0.089326344 ‐0.21570423 ‐0.27733 0.825118
‐0.83642125
‐0.8608931 ‐0.78675 0.57965
1.7328606
1.6991214 ‐1.50907 0.351337
0.5956529
0.71649796 ‐1.16865 0.444837
0.89565265
1.0044138 ‐1.19028 0.438217
‐0.19386353
0.2334121 ‐0.38724 0.764591
1.0740172
1.1923009 0.307982 1.237975
‐0.16503368 ‐0.23358908 ‐0.44441 0.734883
1.1995857
1.1235733 0.278703 1.213104
1.5770993
1.3194692 1.609214 3.050856
1.1851902
1.4400281 2.110509 4.318435
0.98173016
0.5206042 0.307579 1.237629
0.9645097
0.99701464 ‐0.22441 0.855943
0.33947462
0.20077516 ‐0.29357 0.815883
0.153349
0.39013758 0.378979 1.300421
0.9680674
0.9234585 0.332447 1.259147
0.5423217
0.6327726 ‐0.44268 0.735765
0.12027538 0.035354383 ‐0.25178 0.839857
‐0.05477873 ‐0.007675674 0.368246 1.290782
1.0766861
0.98444915 1.296101 2.455644
0.0646959
0.20375274 0.350613 1.275102
‐0.6072303
‐0.3455686 ‐0.24642 0.842983
‐0.5574113
‐0.5896664 ‐0.36515 0.776389
0.161439
0.29092133 0.530523 1.444453
0.3682905
0.12639475 0.282125 1.215984
0.29930934
0.5275517 ‐0.55257 0.681803
0.8477138
1.0069747 0.429857
1.3471
0.23864031
0.3958258 ‐0.25741 0.836587
0.7168318
0.6521502 0.309705 1.239454
1.3570592
0.9922708 0.41847 1.33651
0.18877642
0.2843624 0.614584 1.531117
0.6345175
0.7105296 0.379589 1.300971
‐0.05216601 ‐0.28360838 0.785239 1.723378
0.077230215
0.16295904 0.342104 1.267604
‐0.22239582 ‐0.32202214 0.523425 1.437364
‐0.24911895 ‐0.36154994 0.299625 1.230824
0.07402481
0.2727989 0.545248 1.459272
0.32970014
0.2519256 0.435831 1.352689
0.001985377 ‐0.09746811 ‐0.45645 0.728776
‐0.8202106
‐0.9760636 ‐0.33347 0.793625
‐0.19225281
‐0.2778022 ‐0.49487 0.709624
‐0.07662028 ‐0.067977145 ‐0.63741 0.642867
‐0.7093598 ‐0.71972054 ‐0.26393 0.832819
‐0.7432704 ‐0.79809225 ‐0.31551 0.803565
‐0.073736854
‐0.2841979 0.384004 1.304958
‐0.7967985
‐0.5542958 ‐0.82515 0.564422
‐0.4814676
‐0.3435003 ‐0.38425 0.766178
0.105576865
0.2243431 0.254004 1.192512
‐0.7013361
‐0.8197837 ‐0.96745 0.511408
‐1.0542364 ‐0.85180116 ‐1.13962 0.453879
0.88610744
0.6303237 0.644521 1.56322
0.1100638 ‐0.50275 0.705759
0.059843328
‐0.70945585
‐0.552541 ‐0.24455 0.844078
1.4769859
1.2148346 ‐0.27717 0.825208
0.46394312
0.51389384 ‐0.29756 0.813625
‐0.57110023 ‐0.51646316 ‐0.38447 0.766059
1.7988226
2.2050507 0.642127 1.560629
0.39837956
0.48524043 0.373413 1.295414
0.4547855
0.7326637 0.415152 1.333439
‐0.18991382 ‐0.26375663 ‐0.37182 0.772808
‐0.3193621 ‐0.39003247 ‐0.3479 0.785726
‐0.3485956
‐0.4019517 ‐0.52821 0.693412
‐0.7758657
‐0.6820164 ‐0.61179 0.654385
‐2.6256282
‐2.9934628 ‐2.25448 0.209573
‐3.2622104
‐3.0378387 ‐2.51945 0.17441
‐3.2296724
‐3.5061345 1.583513 2.996987
‐3.6799922
‐3.7337155 1.562265 2.953171
‐0.3229667 ‐0.46000916 0.325193 1.252832
‐0.23273024
‐0.0724034 0.317975 1.24658
0.39140984
0.49807835 0.355075 1.279052
1.0855744
1.02594 0.588091 1.503257
0.62113297
0.2609175 ‐0.54631 0.684768
‐0.2707283
‐0.2668513 ‐0.66106 0.632413
‐0.09927541 ‐0.23757914 ‐0.52701 0.69399
0.7281374
0.53804964 ‐0.27327 0.827441
‐0.0848971 ‐0.06903442 1.477358 2.784384
0.08753406
0.06259792 0.407882 1.326737
‐0.45683774
‐0.5028857 ‐0.26636 0.831413
‐0.32942057 ‐0.41091123 ‐0.46535 0.724295
0.1927756 0.016317612 0.431014 1.34818
‐0.119796574 ‐0.018137489 0.335213 1.261564
‐0.8350702
‐0.8219256 ‐0.39793 0.758948
0.8763294
0.7615438 ‐0.54629 0.684779
144
STM0585
STM0587
STM0603
STM0605
STM0607
STM0608
STM0629
STM0632
STM0633
STM0640
STM0659
STM0661
STM0662
STM0663
STM0664
STM0665
STM0671
STM0680
STM0685
STM0690
STM0692
STM0693
STM0730
STM0737
STM0741
STM0749
STM0756
STM0757
STM0760
STM0764
STM0768
STM0771
STM0772
STM0782
STM0802
STM0803
STM0804
STM0807
STM0819
STM0822
STM0826
STM0828
STM0829
STM0830
STM0833
STM0837
STM0844
STM0845
STM0846
STM0850
STM0852
STM0862
STM0873
STM0887
STM0891
STM0933
STM0934
STM0959
STM0965
STM0966
STM0973
STM0974
STM0985
STM0988
STM0989
STM0995
STM1066
STM1068
STM1070
STM1076
STM1077
STM1079
STM1112
STM1139
STM1140
STM1141
STM1142
STM1145
STM1146
STM1147
STM1150
STM1152
STM1178
STM1179
STM1180
STM1181
STM1183
STM1204
STM1210
STM1211
STM1214
STM1218
STM1237
STM1238
STM1255
STM1261
STM1263
STM1274
STM1284
STM1285
STM1289
STM1295
STM1300
STM1304
STM1305
STM1310
STM1335
STM1336
STM1339
STM1340
outer membrane porin, receptor for ferric enterobactin
fepA
putative cytoplasmic protein
ybdZ
putative aminotransferase
ybdL
putative 3‐phosphoadenosine 5‐phosphosulfate sulfotransferase (PAPS reductase)/FAD synthybdN
periplasmic disulfide isomerase, thiol‐disulphide oxidase
dsbG
alkyl hydroperoxide reductase, C22 subunit detoxification of
ahpC
RNA chaperone, negative regulator of cspA transcription
cspE
putative Sec‐independent protein secretion pathway component
ybeC
lipoate synthase, an iron‐sulfur enzyme
lipA
mrdA
cell elongation specific transpeptidase of penicillin‐binding protein
putative heatshock protein, homolog of hsp70 in
hscC
putative purine nucleoside hydrolase
ybeK
ABC superfamily (atp_bind), glutamate/aspartate transporter
gltL
ABC superfamily (membrane), glutamate/aspartate transporter
gltK
gltJ
ABC superfamily (membrane), glutamate/aspartate transporter
ABC superfamily (bind_prot), glutamate/aspartate transporter
gltI
putative monooxygenase
ubiF
asparagine synthetase B
asnB
Sugar Specific PTS family, n‐acetylglucosamine‐specific enzyme IIABC
nagE
citrate utilization protein b
citB
putative transcriptional regulator, LysR family
transcriptional repressor of iron‐responsive genes (Fur family)
fur
citrate synthase
gltA
2‐oxoglutarate dehydrogenase (dihydrolipoyltranssuccinase E2 component)
sucB
cytochrome d terminal oxidase polypeptide subunit II
cydB
pal
tol protein required for outer membrane integrity
quinolinate synthetase, A protein
nadA
NMN family, nucleoside/purine/pyrimidine transporter
pnuC
3‐deoxy‐D‐arabinoheptulosonate‐7‐phosphate synthase (DAHP synthetase, phenylalanine reparoG
transcriptional regulator, lysR family
Oxalacetate decarboxylase: beta chain
dcoB
putative ABC‐type cobalamin/Fe3 ‐siderophores transport system, ATPase component
phosphoglyceromutase 1
gpmA
ABC superfamily (membrane), molybdate transporter
modB
molybdopterin biosynthesis, protein A
moaA
molybdopterin biosynthesis, protein B
moaB
moaC
molybdopterin biosynthesis, protein C
putative permease
ybhL
putative transcriptional repressor (TetR/AcrR family)
ybiH
putative transferase
ybiB
putative SAM‐dependent methyltransferase
ybiN
ABC superfamily (atp_bind), glutamine high‐affinity transporter
glnQ
glnP
ABC superfamily (membrane), glutamine high‐affinity transporter
ABC superfamily (bind_prot), glutamine high‐affinity transporter
glnH
outer membrane protease, receptor for phage OX2
ompX
putative periplasmic protein
ybiS
putative pyruvate formate lyase activating enzyme
pflE
moeB
molybdopterin biosynthesis
molybdopterin biosynthesis protein
moeA
putative ABC transporter periplasmic binding protein
yliC
putative Fe‐S oxidoreductases family 1
yliG
putative glutathione S‐transferase
yliJ
ybjC
putative inner membrane protein
ABC superfamily (bind_prot), arginine 3rd transport system
artJ
ABC superfamily (atp&memb), arginine transport system
artP
putative nucleoside‐diphosphate‐sugar epimerase
ybjT
L‐allo‐threonine aldolase
ltaA
lrp
regulator for lrp regulon and high‐affinity branched‐chain
anaerobic dimethyl sulfoxide reductase, subunit B
dmsB
anaerobic dimethyl sulfoxide reductase, subunit C
dmsC
pyruvate formate lyase I, induced anaerobically
pflB
focA
putative FNT family, formate transporter (formate channel
tetraacyldisaccharide 4 kinase (lipid A 4kinase)
lpxK
CTP:CMP‐3‐deoxy‐D‐manno‐octulosonate transferase
kdsB
mukF protein (killing factor KicB)
putative periplasmic protein
ycbB
ribosome modulation factor (involved in dimerization of
rmf
putative protease
lonH
putative hydrogenase, membrane component
ompA
methylglyoxal synthase
mgsA
putative periplasmic protein
yccT
putative inner membrane protein
yccV
cbpA
curved DNA‐binding protein
putative transcriptional regulator in curly assembly/transport, 2nd
csgG
curli production assembly/transport component, 2nd curli operon
csgF
curli production assembly/transport component, 2nd curli operon
csgE
csgD
putative transcriptional regulator (LuxR/UhpA family)
putative curli production protein
csgC
putative periplasmic protein
ymdA
putative ACR related to the C‐terminal domain
periplasmic glucans biosynthesis protein
mdoG
yceK
putative outer membrane lipoprotein
flagellar biosynthesis, cell‐proximal portion of basal‐body rod
flgF
flagellar biosynthesis, cell‐distal portion of basal‐body rod
flgG
flagellar biosynthesis, basal‐body outer‐membrane L (lipopolysaccharide layer)
flgH
putative flagella basal body protein
flgI
flagellar biosynthesis, hook‐filament junction protein 1
flgK
outer membrane receptor for Fe(III)‐coprogen, Fe(III)‐ferrioxamine B
fhuE
putative esterase
ycfP
respiratory NADH dehydrogenase 2 cupric reductase
ndh
putative outer membrane protein
ycfR
ycfV
ABC transporter, ATP‐binding protein
putative ribosomal large subunit pseudouridine synthase
ymfC
isocitrate dehydrogenase in e14 prophage, specific for
icdA
putative ABC transporter periplasmic binding protein
putative cytoplasmic protein
putative periplasmic protein
putative inner membrane protein
yeaQ
putative cytoplasmic protein
yeaH
putative Ser protein kinase
yeaG
putative enzymes related to aldose 1‐epimerase
yeaD
protease IV, a signal peptide peptidase
sppA
putative periplasmic protein
arginine succinyltransferase
astA
astD
succinylglutamic semialdehyde dehydrogenase
NAD synthetase, prefers NH3 over glutamine
nadE
50S ribosomal subunit protein L35
rpmI
50S ribosomal subunit protein L20
rplT
integration host factor (IHF), alpha subunit
himA
btuC
ABC superfamily (membrane), vitamin B12 transport protein
0.9580155
1.6586463
0.42625427
0.3849634
0.5100641
0.35502318
‐0.7889897
‐1.1095876
0.26320487
0.22524922
‐0.42572558
‐0.5770081
‐0.673679
‐0.5092478
‐0.5555748
‐0.66387933
‐0.3663575
‐1.5608506
‐0.25067455
‐0.2981579
‐0.25044683
0.58997774
0.6266423
0.26151693
‐0.30366108
0.4004878
‐0.3240194
‐0.3011169
0.54628253
0.2849219
‐0.34293717
0.4087879
0.6452878
‐0.4180693
0.65986574
0.29125378
0.3687425
0.30521566
‐0.41621664
‐0.442354
‐0.4781753
‐0.8392573
‐0.4746565
‐1.635288
0.4758158
‐0.22505845
‐0.30814725
‐0.29099888
‐0.4043882
‐0.22125629
‐0.4049356
0.31162846
‐0.17905602
‐1.4173365
‐0.71155953
‐0.25646675
‐0.30666682
‐0.4318177
‐0.44168755
‐0.28122625
‐1.4719023
‐1.2823764
‐0.39834878
‐0.45908305
‐0.8264857
‐0.35174665
‐1.0369891
0.40872064
1.1558242
‐0.40152797
‐0.5581323
0.3499813
‐0.3099581
‐0.7588283
‐0.9241674
‐1.0519996
‐1.3281112
‐1.4600596
‐1.4272671
‐0.7126416
0.5415282
‐0.36696
‐0.5251709
‐0.41774648
‐0.24669611
‐0.324302
‐0.23739685
0.32385328
‐0.3665278
0.30300504
‐0.47596112
‐0.3584991
‐0.3603536
0.33846152
0.37114596
0.27194655
2.2810953
0.65378964
0.2744936
0.68933046
0.21782845
‐0.2943676
‐0.24713163
‐0.44366714
‐0.24514297
0.29985374
‐1.4608428
‐1.0606834
0.29264265
‐0.2934278
1.0559162
1.7351841
0.64241004
0.48471278
0.70760614
0.4435194
‐0.880915
‐1.0312442
0.33734098
0.47127283
‐0.37190017
‐0.5427533
‐1.0342818
‐0.53041124
‐0.5709684
‐0.76356953
‐0.6821574
‐1.6479359
‐0.3726625
‐0.48714057
‐0.44280136
0.91239756
0.619384
0.40387812
‐0.33722287
0.70452666
‐0.34578836
‐0.2727079
0.40731314
0.56606615
‐0.890913
0.26271224
0.5928036
‐0.33851707
0.6332867
0.49719876
0.1976365
0.29398838
‐0.17864455
‐0.3170274
‐0.7681317
‐0.6363069
‐0.53600425
‐1.5401719
0.26884237
‐0.60718817
‐0.3479092
‐0.8327344
‐0.5576657
‐0.7490953
‐0.65422064
0.32918483
‐0.44594544
‐1.4003847
‐0.5094942
‐0.53386205
‐0.5187434
‐0.33552516
‐0.57411414
‐0.3578153
‐1.5097382
‐1.2160076
‐0.22449249
‐0.34753028
‐0.52779496
‐0.23928219
‐1.025873
0.44216406
1.0283022
‐0.51506615
‐0.5256422
0.36906227
‐0.5270556
‐1.1782665
‐0.7570996
‐0.9824834
‐1.1724006
‐1.4493257
‐1.1628419
‐0.9903692
0.7216828
‐0.46095848
‐0.5935623
‐0.40301433
‐0.45819262
‐0.2887586
‐0.2801575
0.46183276
‐0.65324485
0.2696462
‐0.44852042
‐0.49531895
‐0.3645241
0.38819313
0.3023748
0.56820977
2.2803102
0.6692242
0.40142876
0.7587421
0.27611786
‐0.45289037
‐0.5175908
‐0.64911693
‐0.41127566
0.38263682
‐1.5701078
‐1.1933404
0.24104732
‐0.345843
0.9598503
1.6181923
0.33061343
0.425839
0.53589386
0.49125957
‐0.6495976
‐0.96915185
0.33047995
0.471701
‐0.3907563
‐0.62149066
‐1.0537351
‐0.74785215
‐0.63115054
‐0.7679571
‐0.56265086
‐1.5424268
‐0.25038597
‐0.39032212
‐0.39094642
0.831037
0.86853135
0.231357
‐0.368614
0.46171623
‐0.30040222
‐0.30462992
0.5453931
0.49930444
‐0.94957954
0.4147616
0.6900711
‐0.39626706
0.7044902
0.39910957
0.36066052
0.25006676
‐0.39408445
‐0.22195747
‐0.6186037
‐0.50710005
‐0.54333925
‐1.650116
0.46976787
‐0.3888678
‐0.23795207
‐0.31021452
‐0.41715202
‐0.5501267
‐0.5119743
0.27655312
‐0.4199509
‐1.1767683
‐0.4639384
‐0.556527
‐0.47626817
‐0.38188127
‐0.5876101
‐0.3033928
‐1.4523679
‐1.338426
‐0.46480176
‐0.3542699
‐0.86790794
‐0.32487994
‐0.6459207
0.41327387
0.74478096
‐0.48631975
‐0.4948595
0.4714568
‐0.49807793
‐1.0758065
‐0.8110525
‐0.58964723
‐1.5959761
‐1.5091476
‐1.0917475
‐0.94709754
0.53028905
‐0.4073095
‐0.70547336
‐0.46112373
‐0.36717805
‐0.2424051
‐0.27900034
0.42694753
‐0.37464687
0.24299727
‐0.3523592
‐0.4751201
‐0.34903866
0.34394217
0.3604987
0.43828702
2.2510886
0.8762841
0.3414933
0.6440396
0.24608544
‐0.39618397
‐0.41109887
‐0.6599875
‐0.3780378
0.37407726
‐1.8205353
‐1.3318871
0.32525933
‐0.2620518
0.9709265
0.5550019
‐0.19121508
0.25178462
0.6468124
0.15069991
‐0.20864968
‐1.4278146
0.24327846
0.034822803
‐0.5145188
‐0.47829667
‐0.69161516
‐0.37341556
‐0.6378293
‐1.4089369
1.0897584
‐0.0956105
0.15950722
‐0.40041003
‐0.12072479
0.9073395
1.796742
2.2338598
‐0.41331273
1.5477052
‐0.26702607
‐0.077311166
0.95983857
0.17560285
0.26257965
‐0.3103159
‐0.8919129
1.1440533
‐0.02816065
‐1.042177
‐0.21917652
‐0.09702353
0.3378418
0.005124741
0.08266802
‐0.57792866
‐0.40534726
‐1.7286297
‐1.3159094
0.7924875
‐0.58763456
‐0.43077865
‐0.33460942
0.082801186
‐0.24739324
‐0.78265816
‐0.4170016
‐1.0465586
‐0.048897367
0.08613055
0.6707763
1.0524905
‐0.90780324
‐0.2535967
‐3.645095
‐2.496082
0.13554913
‐0.11640237
‐0.3820342
0.19056635
‐2.939138
0.7258578
‐0.15404917
‐0.74361235
‐0.75453085
‐0.31249458
‐0.4426769
‐1.6324872
‐2.4841034
‐2.2129786
‐2.0441546
‐1.74516
‐1.1675874
‐0.60921794
0.94543475
‐0.16921954
1.0958923
1.3467141
1.1339319
1.9730844
1.619831
0.37853062
0.08399701
0.28233495
‐0.6465189
‐0.108652465
‐0.384855
1.923276
‐0.046311248
‐0.8873787
‐3.407243
‐0.6688221
‐0.30740705
‐0.46575496
‐0.13277811
‐0.58583647
0.27648553
‐0.7756207
‐0.63193977
‐0.5443109
0.19425759
0.15193738
‐0.3852759
‐0.049118973
1.0320842
0.77824533
‐0.23664851
0.12766095
0.81203794
‐0.13732953
‐0.2603843
‐1.6140355
0.18448736
0.054687776
‐0.33737367
‐0.3749117
‐1.0319647
‐0.30032292
‐0.7115269
‐1.6537793
1.1038402
‐0.10355192
0.07047722
‐0.32748368
‐0.20360208
0.80599254
1.4630904
2.410301
‐0.13948935
1.34555
‐0.13559411
‐0.07028874
0.1955221
0.91956943
0.093307786
‐0.23873681
‐0.89992064
0.9742888
‐0.010397093
‐0.9060325
‐0.30484277
‐0.16546385
‐0.12042255
0.074902885
0.46681458
‐0.4704322
‐0.7341103
‐1.7587894
‐1.284921
0.21959558
‐0.52717257
‐0.14306134
‐0.16004929
‐0.065431945
‐0.3684934
‐1.0283278
‐0.74505764
‐1.2539867
‐0.116677105
0.25150496
0.73030025
0.62952006
‐0.8215511
‐0.24641363
‐3.5508404
‐2.7509668
0.2625243
‐0.005751802
‐0.53006834
0.39383805
‐2.43706
0.74335986
‐0.26885107
‐1.0801302
‐0.56906116
‐0.3919469
‐0.4222615
‐2.0239973
‐2.324837
‐2.2709503
‐2.5151248
‐1.4549979
‐0.9190649
‐1.0801338
0.8897964
‐0.23827368
1.1005088
1.4337074
1.7485083
2.096299
1.6788012
0.3217923
‐0.3701707
0.15257327
‐0.5931529
‐0.1991152
‐0.5160779
1.6409713
0.12354395
‐1.1520764
‐3.7447538
‐0.6933789
‐0.47545207
‐0.41566285
‐0.32061452
‐0.5792948
‐0.20017582
‐0.96686655
‐0.52545446
‐0.49825403
0.16109267
0.056686662
‐0.2967572
‐0.15822318
0.93534297
0.8829725
‐0.16877598
0.08455879
0.5543116
‐0.15077637
‐0.114142515
‐1.4850512
0.08720529
‐0.023785954
‐0.4556404
‐0.42480436
‐0.7187726
‐0.80333817
‐0.9004852
‐1.8124185
1.1244713
‐0.023382738
0.028475543
‐0.31356326
‐0.07248604
0.7938867
1.5352359
2.2622237
‐0.24926664
1.2616546
‐0.34239936
0.05537214
0.13860117
0.5009572
0.14219761
‐0.4349714
‐0.737573
1.1510261
‐0.14391999
‐0.90210325
‐0.14593555
‐0.3067349
0.16623312
‐0.033983357
0.4464508
‐0.34354207
‐0.8433608
‐1.8504239
‐1.1680741
1.0621192
‐0.65537995
‐0.22562754
‐0.17734632
‐0.04659729
‐0.1422847
‐0.90984267
‐0.5799282
‐1.3252928
0.08669766
0.50403845
0.8241052
0.6558956
‐0.94185776
‐0.42048126
‐3.386212
‐2.8551254
0.0740137
‐0.081944585
‐0.7149592
0.33149144
‐2.2428668
0.49317136
‐0.38527164
‐0.8070471
‐0.7390381
‐0.63334495
‐0.25903344
‐1.6082772
‐2.4346235
‐2.066302
‐2.4268098
‐1.5759916
‐1.0819148
‐0.9391641
0.79126954
‐0.11798355
0.9917764
1.5044321
1.8011872
2.0200503
1.5202569
0.2793581
‐0.11579435
0.12216826
‐0.60973513
‐0.16417414
‐0.2492648
1.7221025
‐0.018276125
‐0.8446487
‐4.084797
‐0.4495114
‐0.3315415
‐0.36063853
‐0.41818246
‐0.5848898
‐0.04893046
‐0.9297423
‐0.57170576
‐0.5621249
0.096692316
0.05046198
‐0.19504993
‐0.19683614
0.991261
1.670674
0.466426
0.431838
0.584521
0.429934
‐0.77317
‐1.03666
0.310342
0.389408
‐0.39613
‐0.58042
‐0.92057
‐0.59584
‐0.5859
‐0.7318
‐0.53706
‐1.58374
‐0.29124
‐0.39187
‐0.3614
0.777804
0.704853
0.298917
‐0.3365
0.522244
‐0.3234
‐0.29282
0.499663
0.450097
‐0.72781
0.362087
0.642721
‐0.38428
0.665881
0.395854
0.309013
0.28309
‐0.32965
‐0.32711
‐0.62164
‐0.66089
‐0.518
‐1.60853
0.404809
‐0.40704
‐0.298
‐0.47798
‐0.45974
‐0.50683
‐0.52371
0.305789
‐0.34832
‐1.3315
‐0.56166
‐0.44895
‐0.43389
‐0.38307
‐0.53447
‐0.31414
‐1.478
‐1.27894
‐0.36255
‐0.38696
‐0.74073
‐0.3053
‐0.90293
0.421386
0.976302
‐0.46764
‐0.52621
0.396833
‐0.44503
‐1.0043
‐0.83077
‐0.87471
‐1.3655
‐1.47284
‐1.22729
‐0.88337
0.597833
‐0.41174
‐0.60807
‐0.42729
‐0.35736
‐0.28516
‐0.26552
0.404211
‐0.46481
0.271883
‐0.42561
‐0.44298
‐0.35797
0.356866
0.344673
0.426148
2.270831
0.733099
0.339139
0.697371
0.246677
‐0.38115
‐0.39194
‐0.58426
‐0.34482
0.352189
‐1.61716
‐1.1953
0.286316
‐0.30044
1.987921
3.183633
1.381682
1.348951
1.499541
1.347172
0.585131
0.487454
1.240002
1.309856
0.759895
0.66877
0.528302
0.66166
0.666235
0.602151
0.689176
0.333616
0.817199
0.762139
0.77841
1.714519
1.629978
1.230221
0.791961
1.436187
0.799182
0.816306
1.413883
1.366133
0.60382
1.285284
1.561271
0.766159
1.586537
1.315721
1.23886
1.216798
0.79573
0.79713
0.649933
0.632489
0.698339
0.327933
1.323913
0.75417
0.813378
0.717981
0.72712
0.703769
0.695581
1.236094
0.7855
0.397356
0.67752
0.732575
0.740262
0.766802
0.690412
0.804328
0.358985
0.412099
0.77779
0.764739
0.598437
0.809272
0.5348
1.339214
1.967417
0.723148
0.694376
1.316615
0.734569
0.498512
0.562228
0.545363
0.388101
0.360271
0.42712
0.5421
1.513442
0.751715
0.656074
0.743655
0.780594
0.820653
0.8319
1.323365
0.724568
1.207383
0.744522
0.735614
0.780261
1.280641
1.269863
1.343641
4.826012
1.662206
1.265001
1.621547
1.186471
0.767827
0.762104
0.666993
0.787407
1.276496
0.325976
0.436695
1.219523
0.812004
145
STM1345
STM1359
STM1367
STM1368
STM1370
STM1373
STM1374
STM1378
STM1384
STM1398
STM1400
STM1402
STM1407
STM1409
STM1410
STM1411
STM1412
STM1413
STM1419
STM1427
STM1445
STM1450
STM1451
STM1456
STM1466
STM1478
STM1482
STM1486
STM1489
STM1495
STM1496
STM1497
STM1509
STM1525
STM1554
STM1567
STM1572
STM1577
STM1586
STM1592
STM1594
STM1595
STM1606
STM1612
STM1613
STM1614
STM1615
STM1616
STM1628
STM1645
STM1649
STM1660
STM1662
STM1682
STM1686
STM1713
STM1719
STM1721
STM1726
STM1727
STM1736
STM1743
STM1749
STM1751
STM1753
STM1754
STM1780
STM1781
STM1782
STM1793
STM1801
STM1804
STM1812
STM1815
STM1823
STM1825
STM1829
STM1837
STM1838
STM1840
STM1851
STM1888
STM1890
STM1891
STM1901
STM1902
STM1916
STM1959
STM1978
STM1990
STM2017
STM2024
STM2028
STM2031
STM2039
STM2053
STM2056
STM2059
STM2067
STM2071
STM2072
STM2073
STM2076
STM2079
STM2081
STM2083
STM2087
STM2090
STM2091
STM2117
putative cytoplasmic protein
ydiU
putative shikimate 5‐dehydrogenase
ydiB
putative cytoplasmic protein
ydiH
putative Na ‐dicarboxylate symporter
putative ABC transporter
sufB
selenocysteine lyase
sufS
putative SufE protein probably involved in Fe‐S
ynhA
pyruvate kinase I (formerly F), fructose stimulated
pykF
Tetrathionate reductase complex, subunit C
ttrC
sseB
Secretion system effector
Secretion system effector
sseC
Secretion system effector
sseE
Secretion system apparatus
ssaH
Secretion system apparatus: homology with the yscJ/mxiJ/prgK
ssaJ
putative cytoplasmic protein
Secretion system apparatus
ssaK
Secretion system apparatus
ssaL
Secretion system apparatus
ssaM
Secretion system apparatus: homology with YscR of
ssaR
cyclopropane fatty acyl phospholipid synthase
cfa
putative outer membrane lipoprotein
slyB
pyridoxal kinase 2/pyridoxine kinase
pdxY
glutathionine S‐transferase
gst
putative oxidoreductase
ydgO
putative periplasmic protein
ydgA
putative periplasmic protein
ydgH
putative membrane transporter of cations and cationic
ydgF
ynfM
putative MFS familty transport protein
putative dethiobiotin synthase
ynfK
putative component of anaerobic dehydrogenases
ynfI
putative dimethylsulfoxide reductase
putative dimethyl sulphoxide reductase
ydfZ
putative cytoplasmic protein
putative glutaminase
yneH
putative coiled‐coil protein
alcohol dehydrogenase, propanol preferring
adhP
new outer membrane protein predicted bacterial porin
nmpC
nitrate reductase 2, alpha subunit
narZ
putative periplasmic protein
ydcY
putative cytoplasmic protein
ssrAB activated gene
srfB
ssrAB activated gene: predicted coiled‐coil structure
srfC
putative benzoate membrane transport protein
putative cellulase protein
putative PTS system, enzymeIIB component
putative PTS system enzyme IIC component
putative nucleoside triphosphatase
putative Sugar Specific PTS Enzyme II
putative cytoplasmic protein
ynbE
putative outer membrane lipoprotein
putative cytoplasmic protein
transcriptional regulation of aerobic, anaerobic respiration, osmotic
fnr
putative inner membrane protein
ynaJ
thiol peroxidase
tpx
phage shock protein
pspE
cysB
transcriptional regulator for cysteine regulon (LysR familiy)
putative ribosomal large subunit pseudouridine synthase
yciL
trpR controlled transcriptional unit in the 5
trpH
tryptophan synthase, beta protein
trpB
tryptophan synthase, alpha protein
trpA
putative Acyl‐CoA hydrolase
yciA
ABC superfamily (atp‐binding), oligopeptide transport protein
oppD
adhE
iron‐dependent alcohol dehydrogenase of the multifunctional alcohol
DNA‐binding protein HLP‐II (HU, BH2, HD, NS)
hns
Response regulator in protein turnover: mouse virulence
hnr
putative phosphoesterase
ychK
phosphoribosylpyrophosphate synthetase
prsA
putative SulP family transport protein
ychM
ychH
putative inner membrane protein
putative cytochrome oxidase, subunit II
putative CPA1 family, Na:H transport protein
ycgO
putative cytoplasmic protein
ycgB
putative Fumarylacetoacetate (FAA) hydrolase family
ycgM
cell division inhibitor, a membrane ATPase, activates
minD
putative cytoplasmic protein
yoaH
yeaB
putative NTP pyrophosphohydrolase
putative cytoplasmic protein
cold shock protein, multicopy suppresses mukB mutants
cspC
putative cytoplasmic protein
yobF
yobG
putative inner membrane protein
putative cytoplasmic protein
pyruvate kinase II, glucose stimulated
pykA
putative Peptidase
yebA
ABC superfamily (bind_prot) high affinity Zn transport
znuA
aspartate tRNA synthetase
aspS
putative isochorismatase
yecD
chemotaxis regulator, transmits chemoreceptor signals to flagelllar
cheY
flagellar biosynthesis flagellin, filament structural protein
fliC
flagellar biosynthesis
fliO
putative permease
yedA
cobalamin 5‐phosphate synthase
cobS
cbiL
synthesis of vitamin B12 adenosyl cobalamide precursor
synthesis of vitamin B12 adenosyl cobalamide precursor
cbiG
synthesis of vitamin B12 adenosyl cobalamide precursor
cbiE
Propanediol utilization: polyhedral bodies
pudB
pduS
Propanediol utilization: polyhedral bodies
Propanediol utilization
pduV
putative cytoplasmic protein
yeeX
exonuclease I, 3 ‐‐ 5 specific deoxyribophosphodiesterase
sbcB
ATP phosphoribosyltransferase
hisG
histidinal dehydrogenase (also histidinol dehydrogenase activity)
hisD
histidinol phosphate aminotransferase
hisC
N‐(5‐phospho‐L‐ribosyl‐formimino)‐5‐amino‐1‐(5‐phosphoribosyl)‐4‐imidazolecarboxamide ishisA
regulator of length of O‐antigen component of
wzzB
gluconate‐6‐phosphate dehydrogenase, decarboxylating
gnd
LPS side chain defect: phosphomannomutase
rfbK
LPS side chain defect: abequosyltransferase
rfbV
LPS side chain defect: CDP‐6deoxy‐D‐xylo‐4‐hexulose‐3‐dehydrase
rfbH
LPS side chain defect: CDP glucose 4,6‐dehydratase
rfbG
wzb
putative protein‐tyrosine‐phosphatase in colanic acid export
1.1109093
0.23921464
‐1.1607132
0.3481311
1.8288628
1.0143319
0.6949266
1.0706054
‐0.3832782
‐1.6741128
‐0.89993477
‐0.7404304
‐2.5226486
‐1.745902
‐1.2823895
‐1.212782
‐1.1971893
‐0.77967024
‐2.10759
0.53838634
0.54758734
0.5507013
0.41312236
‐0.18982045
0.4062534
0.36855495
‐0.18909168
‐0.23127855
‐1.1623932
‐0.19872937
‐0.3685398
‐0.3500527
‐1.3511477
‐0.31196776
0.43193775
0.4718006
‐0.18370068
‐0.2248073
1.0042905
‐0.38371983
‐0.44180423
‐0.6356835
‐0.2536418
‐0.52231705
‐0.3519927
‐0.33452767
‐0.2504369
‐0.5471751
‐0.30046344
‐0.4214404
‐0.19018997
0.2812335
0.532323
0.6041635
‐0.24195158
0.3855786
‐0.37572515
‐0.31108093
0.6247902
0.42639452
‐0.2479896
0.31725043
‐0.94126964
0.28761715
0.30030814
0.47854376
‐0.30122158
‐0.43034276
‐0.42107615
‐0.20705564
‐0.30309612
0.3659159
0.6757513
0.64360964
‐0.40831774
‐0.38418204
‐0.26884434
‐0.41805288
‐0.30826873
‐0.582477
‐0.30207226
‐0.45786908
0.7314299
1.3631965
‐0.40783373
‐0.3656827
‐0.38359508
0.39477825
‐0.57403517
‐0.28627598
‐0.35943896
‐0.36653033
‐0.35900822
‐0.37218127
‐0.60162073
‐0.49494177
‐0.4730784
0.32313725
0.2899644
1.4977757
0.62781864
0.6341258
‐0.19402218
0.25764465
0.30357298
0.4056601
0.98017097
0.51607764
0.29437086
‐0.14169501
1.4927708
0.44171196
‐1.217718
0.45733228
1.8384182
0.8581476
0.8367215
1.076777
‐0.43991503
‐1.4779617
‐0.95905095
‐0.5855545
‐2.480366
‐1.4621507
‐1.324541
‐0.865683
‐1.7317013
‐0.8322191
‐2.092133
0.5852242
0.6674519
0.25061792
0.4460167
‐0.3831436
0.32921973
0.3679174
‐0.42212728
‐0.39081946
‐1.1485412
‐0.3369662
‐0.37358811
‐0.55640876
‐1.210879
‐0.5324096
0.44049537
0.42413142
‐0.2966894
‐0.4580479
1.1498488
‐0.6083607
‐0.5306051
‐0.41037938
‐0.32784393
‐0.7856752
‐0.3795157
‐0.6439114
‐0.39927378
‐0.6508115
‐0.3825925
‐0.4550827
‐0.399026
0.39288732
0.49079153
0.75391585
‐0.2239119
0.58886385
‐0.30425462
‐0.29586965
0.7092721
0.30337414
‐0.22087821
0.2979059
‐1.0152637
0.39059618
0.38211897
0.34373415
‐0.27414304
‐0.2892813
‐0.33402443
‐0.40138167
‐0.3038189
0.30410102
0.4047032
0.539904
‐0.405646
‐0.38979676
‐0.42344797
‐0.49406308
‐0.44221333
‐0.57865244
‐0.35991398
‐0.6001217
0.6941771
1.3828597
‐0.58696544
‐0.36847875
‐0.43315798
0.5807938
‐0.664406
‐0.53123426
‐0.31011033
‐0.5942693
‐0.5075034
‐0.245728
‐0.6262743
‐0.6589297
‐0.3958133
0.3182445
0.4685992
1.2457414
0.60583025
0.4897871
‐0.42735654
0.44832304
0.5028009
0.53315276
0.9868867
0.44115597
0.305522
‐0.63931817
1.3023136
0.837666
0.87025166
0.8473188 1.301998 2.465701
0.2541867
0.09182452
0.24539095
‐2.26E‐04 0.311704 1.241173
‐0.95250094
‐1.1420289
‐1.0192692
‐1.0349541 ‐1.11031 0.463194
0.27683023
‐0.3665625 ‐0.06849653 ‐0.077386834 0.360765 1.284106
1.7571864
2.0679772
1.9349446
1.9260905 1.808156 3.501943
0.9030303
1.7707404
1.9531987
1.996953 0.92517 1.898908
0.78655946
1.3053304
1.282638
1.2608409 0.772736 1.708507
0.9540288
0.34609383
0.25985903
0.17014986 1.033804 2.047415
‐0.62766564 ‐0.53071415 ‐0.41407105
‐0.2703583 ‐0.48362 0.715181
‐1.5637157
‐1.5679544
‐1.726097
‐1.6248128 ‐1.57193 0.336358
‐0.6318036
‐1.0857143
‐1.2127495
‐1.1596113 ‐0.83026 0.562427
‐0.44367382
‐1.4752728
‐1.1332533
‐1.2630181 ‐0.58989 0.664395
‐2.4565828
‐3.276874
‐3.4141567
‐3.4247928 ‐2.48653 0.178435
‐1.4960818
‐1.9544916
‐1.8679796
‐1.8298781 ‐1.56804 0.337265
‐1.2172247
‐1.8518736
‐2.1207027
‐2.0425308 ‐1.27472 0.413306
‐0.86629224
‐1.5459058
‐1.4453876
‐1.4393945 ‐0.98159 0.506423
‐1.5377116
‐1.1985549
‐1.706445
‐1.4232875 ‐1.48887 0.356292
‐0.78975403
‐2.2722535
‐1.7264606
‐1.8331716 ‐0.80055 0.574131
‐1.865195
‐1.5756209
‐2.0081894
‐1.995713 ‐2.02164 0.246278
0.549235
‐1.1271503
‐1.9751949
‐1.5026411 0.557615 1.471834
0.6889855
0.65983456
0.31934425
0.25440368 0.634675 1.552588
0.38647062
0.35734636
0.3821307
0.22372746 0.39593 1.315791
0.54826 ‐0.70826876
‐0.6502949
‐0.7800278 0.469133 1.384277
‐0.35884932
1.138298
1.0549725
1.025241 ‐0.3106 0.806304
0.2527213
0.38519296
0.18928708
0.2782044 0.329398 1.256489
0.36575988
0.7347037
0.85411257
0.74237645 0.367411 1.290035
‐0.3997874 ‐0.10787598 ‐0.33845413 0.023952104
‐0.337 0.791685
‐0.45196387
‐0.5932076
‐0.7651399
‐0.628818 ‐0.35802 0.780234
‐0.97866875 ‐0.52552414
‐0.760583
‐0.5617785 ‐1.09653 0.467639
‐0.32943332
‐0.6292595 ‐0.54972446
‐0.5097459 ‐0.28838 0.818823
‐0.27664664
‐0.5378545 ‐0.60932666 ‐0.63203114 ‐0.33959 0.790265
‐0.51866335
‐0.7948172
‐1.1683357
‐0.8657208 ‐0.47504 0.719446
‐0.81715876
‐2.0551136
‐2.1272924
‐1.9854239 ‐1.1264 0.458059
‐0.4200531
0.46168852
0.2885842
0.37501928 ‐0.42148 0.74666
0.4944495
0.47160825
0.2640034
0.33904615 0.455628 1.371379
0.3675194 ‐0.26860577 ‐0.33799547 ‐0.37310302 0.42115 1.338995
‐0.34496439
0.4717645
0.0995451
0.10905572 ‐0.27512 0.826383
‐0.31478006
‐0.3036716 ‐0.26014018 ‐0.19998862 ‐0.33255 0.794134
1.263933
0.25987425
0.31525543
0.41740522 1.139357 2.202829
‐0.4058153
‐0.4082041 ‐0.45463413
‐0.3126648 ‐0.46597 0.723987
‐0.6152019
0.138828
‐0.2099058 0.024343297 ‐0.5292 0.692937
‐0.36208963
0.142187 0.106389776
0.11309321 ‐0.46938 0.722273
‐0.26576608
‐0.5791322 ‐0.61242646
‐0.6168841 ‐0.28242 0.822212
‐0.7000317
‐1.3844473
‐1.5026865
‐1.395355 ‐0.66934 0.628794
‐0.40696353
‐0.9162813
‐1.1813852
‐0.9658277 ‐0.37949 0.768709
‐0.49038953
‐0.4312252 ‐0.64045763 ‐0.45143804 ‐0.48961 0.712218
‐0.5593485 ‐0.87528783
‐0.8458499 ‐0.91353655 ‐0.40302 0.756274
‐0.69132197
‐0.9636082
‐1.3039311
‐1.1980091 ‐0.62977 0.64628
‐0.1886261
‐4.07E‐04 ‐0.17345259 ‐0.003326796 ‐0.29056 0.817584
‐0.3689802 ‐0.24922627
‐0.5800033
‐0.6674307 ‐0.41517 0.749932
‐0.3227409 ‐0.76038283 ‐0.75157917 ‐0.78606546 ‐0.30399 0.810012
0.4851172
0.5186295
0.41619164
0.36252376 0.386413 1.307139
0.6095416
0.16564049 ‐0.26653215 ‐0.21402918 0.544219 1.45823
0.6196073
1.0710678
1.1310829
1.1226921 0.659229 1.579238
‐0.2397045
‐0.6327867
‐0.5577372
‐0.6503412 ‐0.23519 0.849574
0.3916322
0.3562029
0.30875078
0.14567114 0.455358 1.371123
‐0.27576232
0.31031558
0.39768574
0.39678493 ‐0.31858 0.801858
‐0.2603506 ‐0.36760768 ‐0.35555023 ‐0.47195932 ‐0.2891 0.818412
0.81449515
0.89797586
0.80832547
0.82315576 0.716186 1.642833
0.2700325
0.39369184
0.01953881
0.15296096 0.333267 1.259863
‐0.2577209 ‐0.24616353 ‐0.14075956
‐0.3137594 ‐0.2422 0.845457
0.22481397
0.12536727 ‐0.055885192 ‐0.016461318 0.27999 1.214187
‐1.0613933
‐3.373034
‐2.9843004
‐2.7309978 ‐1.00598 0.497933
0.5427891 ‐0.038890112 ‐0.14976403 ‐0.05902101 0.407001 1.325927
0.3175498
0.54183644
0.3932172
0.2300782 0.333326 1.259914
0.37279
0.75828016
0.958124
1.0925204 0.398356 1.318005
‐0.3812938
0.81053585
0.5377214
0.43598494 ‐0.31889 0.801689
‐0.40384802
0.1461771 ‐0.02610114 ‐0.10166211 ‐0.37449 0.771378
‐0.37810418 ‐0.18030512 ‐0.13911952 ‐0.16395706 ‐0.37773 0.769645
‐0.38687545
‐0.627598 ‐0.99744743
‐0.6675818 ‐0.33177 0.794561
‐0.3510658
‐0.2795044
‐0.2943152
‐0.5589706 ‐0.31933 0.801444
0.18880795
0.05911469 0.048354328
0.16504192 0.286275 1.219487
0.48674396
0.05535708 0.053606264
0.07697686 0.522399 1.436342
0.46649835
0.57414794
0.5769835
0.12150221 0.550004 1.46409
‐0.46832395 ‐0.15754999 ‐0.45120302 ‐0.45403653 ‐0.42743 0.743586
‐0.440912 ‐0.21480568 ‐0.16558334 ‐0.29719406 ‐0.40496 0.755255
‐0.2660132
‐0.3604281
‐0.6645848
‐0.5956276 ‐0.31944 0.801384
‐0.49191025
‐0.2913259
‐0.3668987 ‐0.23230623 ‐0.46801 0.722962
‐0.34613034 ‐0.49601406
‐0.9558 ‐0.54831296 ‐0.36554 0.77618
‐0.51988935 ‐0.33765703
‐0.6450774
‐0.5211667 ‐0.56034 0.678143
‐0.28196493
‐1.4156271
‐1.2193029
‐1.2874681 ‐0.31465 0.804046
‐0.33456108
‐0.7494681
‐0.7444827 ‐0.60186774 ‐0.46418 0.724881
0.91438
‐1.1120312
‐1.4507257
‐0.8762661 0.779996 1.717126
1.453435
‐3.1004639
‐3.2172017
‐3.3780866 1.39983 2.638706
‐0.2616341
‐0.3228629 ‐0.33112475 ‐0.18849096 ‐0.41881 0.748041
‐0.43531647 ‐0.67360085
‐0.5151873
‐0.6069283 ‐0.38983 0.763222
‐0.39431602
1.5257362
1.6956547
1.9617764 ‐0.40369 0.755923
0.6376977
2.3017983
2.3778193
2.6140275 0.537757 1.451713
‐0.5776367 0.075564675
0.36710957
0.4283571 ‐0.60536 0.657308
‐0.44428456 ‐0.68307203 ‐0.73559564 ‐0.49098048 ‐0.4206 0.747115
‐0.46746382 0.050599314
0.04789822 ‐0.20290194
‐0.379 0.768968
‐0.48899347
‐0.6076826
‐0.9152125
‐0.813943 ‐0.48326 0.715357
‐0.37728187
‐0.4092767
‐0.3165983 ‐0.46636346 ‐0.4146 0.750229
‐0.3650228
‐0.5108238 ‐0.51285577 ‐0.54533434 ‐0.32764 0.796837
‐0.70491284
‐0.6635016
‐0.5572539
‐0.5123162 ‐0.64427 0.639817
‐0.6400521
0.19818437
0.03671358
0.28584102 ‐0.59797 0.660681
‐0.46033874
0.12201987
0.1591279
0.2229881 ‐0.44308 0.735564
0.48112833
‐1.7658125
‐1.9565146
‐1.7855941 0.37417 1.296094
0.24099086
0.17351031
0.15334004 ‐0.18637115 0.333185 1.259791
1.2286866
0.19091474 ‐0.14521758 ‐0.11062954 1.324068 2.503711
0.55097926
0.05327945
0.07998438
0.04636184 0.594876 1.510343
0.31570336
1.2940421
0.5775246
0.44503582 0.479872 1.39462
‐0.42955026
0.31025815
0.2162306
0.29324135 ‐0.35031 0.784416
0.326458
0.54390585
0.6638624
0.47716227 0.344142 1.269396
0.31710204
0.4266141
0.33291423
0.1856702 0.374492 1.296383
0.58841336
0.5132727
0.49226788
0.59198165 0.509075 1.423138
0.9106193
1.3449967
1.3260227
1.4699153 0.959226 1.944266
0.42561674
0.65423524
0.4146966
0.613847 0.46095 1.376448
0.3116214
0.9596773
0.724822
0.79896784 0.303838 1.234424
‐0.55770266 ‐0.48187384
‐0.7830294
‐0.5893673 ‐0.44624 0.733954
146
STM2130
STM2139
STM2146
STM2147
STM2148
STM2199
STM2218
STM2223
STM2224
STM2228
STM2267
STM2278
STM2285
STM2297
STM2302
STM2309
STM2316
STM2317
STM2318
STM2320
STM2321
STM2323
STM2324
STM2326
STM2327
STM2328
STM2337
STM2338
STM2347
STM2352
STM2354
STM2355
STM2362
STM2372
STM2378
STM2381
STM2387
STM2389
STM2390
STM2393
STM2402
STM2405
STM2408
STM2409
STM2428
STM2430
STM2431
STM2432
STM2433
STM2434
STM2467
STM2472
STM2473
STM2479
STM2498
STM2499
STM2510
STM2511
STM2513
STM2521
STM2522
STM2523
STM2544
STM2549
STM2551
STM2552
STM2553
STM2555
STM2567
STM2579
STM2589
STM2592
STM2602
STM2604
STM2605
STM2606
STM2637
STM2639
STM2642
STM2646
STM2663
STM2667
STM2669
STM2670
STM2671
STM2674
STM2676
STM2690
STM2746
STM2763
STM2771
STM2773
STM2774
STM2775
STM2776
STM2777
STM2779
STM2780
STM2788
STM2799
STM2800
STM2805
STM2806
STM2807
STM2811
STM2814
STM2818
STM2820
STM2829
STM2843
sensory kinase in two‐component regulatoyr system wtih
baeS
putative inner membrane protein
bifunctional enzyme: hydroxy‐phosphomethylpyrimidine kinase (HMP‐P kinase) hydroxy‐met thiD
hydoxyethylthiazole kinase (THZ kinase)
thiM
putative periplasmic protein
outer membrane porin, receptor for colicin I
cirA
putative ABC‐type dipeptide/oligopeptide/nickel transport systems, permease component yejE
putative ATP‐dependent helicase
yejH
50S ribosomal subunit protein L25
rplY
putative hydrolase of alkaline phosphatase superfamily
yejM
ompC
outer membrane protein 1b (ibc), porin
ribonucleoside‐diphosphate reductase 1, beta subunit
nrdB
sn‐glycerol‐3‐phosphate dehydrogenase (anaerobic), membrane anchor subunit
glpB
putative DegT/DnrJ/EryC1/StrS family
yfbE
putative inner membrane protein
menD
bifunctional: 2‐oxoglutarate decarboxylase SHCHC synthase
NADH dehydrogenase I chain N
nuoN
NADH dehydrogenase I chain M
nuoM
NADH dehydrogenase I chain L
nuoL
NADH dehydrogenase I chain J
nuoJ
NADH dehydrogenase I chain I
nuoI
NADH dehydrogenase I chain G
nuoG
NADH dehydrogenase I chain F
nuoF
NADH dehydrogenase I chain C,D
nuoC
NADH dehydrogenase I chain B
nuoB
NADH dehydrogenase I chain A
nuoA
acetate kinase A (propionate kinase 2)
ackA
phosphotransacetylase
pta
putative phosphoesterase
yfcE
ABC superfamily (membrane),histidine and lysine/arginine/ornithine transport protein
hisM
ABC superfamily (bind_prot), histidine transport protein
hisJ
ABC superfamily (bind_prot), lysine/arginine/ornithine transport protein
argT
amidophosphoribosyltransferase (PRPP amidotransferase)
purF
putative transport protein
3‐oxoacyl‐[acyl‐carrier‐protein] synthase I
fabB
putative cytoplasmic protein
yfcM
phosphohistidine phosphatase
sixA
paral putative acetyl‐CoA acetyltransferase
yfcY
yfcZ
putative cytoplasmic protein
putative transport
yfdC
putative aminotransferase
yfdZ
putative thiamine pyrophosphate enzymes
Nramp family, manganese/divalent cation transport prortein
mntH
NUP family, nucleoside transport
nupC
cell division protein involved in FtsZ ring
zipA
subunit of cysteine synthase A and O‐acetylserine
cysK
PTS family, Hpr protein, phosphohistidinoprotein‐hexose phosphotransferase
ptsH
General PTS family (Enzyme I) PEP‐protein phosphotransferase
ptsI
PTS family, glucose‐specific IIA component
crr
putative cytoplasmic protein
putative cobalamin adenosyltransferase, ethanolamine utilization
eutT
paral putative transferase
maeB
transaldolase A
talA
putative oxidoreductase
aegA
uracil phosphoribosyltransferase
upp
phosphoribosylaminoimidazole synthetase (AIR synthetase)
purM
GMP synthetase
guaA
IMP dehydrogenase
guaB
similar to the C‐terminal region of AIDA
shdA
putative inner membrane protein
yfgM
histidine tRNA synthetase
hisS
putative protein, involved in density‐dependent regulation of
gcpE
believed to be involved in assembly of
yfhP
asrB
anaerobic sulfide reductase
putative inner membrane protein
putative periplasmic or exported protein
stationary phase inducible protein
csiE
serine hydroxymethyltransferase
glyA
putative periplasmic amino acid binding protein
yfhD
gap repair gene
recO
Gifsy‐1 prophage: similar to host specificity protein‐J
Gifsy‐1 prophage: similar to phage tail component
Gifsy‐1 prophage: similar to DNA packaging protein
Gifsy‐1 prophage: similar to head protein gpshp
Gifsy‐1 prophage: similar to head‐tail preconnector gp5
Gifsy‐1 prophage: similar to head‐tail preconnector gp4
rseC
regulator of sigma E (sigma 24) factor
anti sigma E (sigma 24) factor, negative
rseA
putative transferase
yfiC
putative formate acetyltransferase
yfiD
putative lipoprotein
yfiO
bifuctional: chorismate mutase P prephenate dehydratase
pheA
tyrA
bifunctional: chorismate mutase T prephenate dehydrogenase
3‐deoxy‐D‐arabinoheptulosonate‐7‐phosphate synthase (DAHP synthetase), tyrosine repress aroF
putative periplasmic protein
yfiR
tRNA (guanine‐7‐)‐methyltransferase
trmD
30S ribosomal subunit protein S16
rpsP
putative outer membrane efflux protein
putative Excinuclease ATPase subunit
putative integrase
fljB
Flagellar synthesis: phase 2 flagellin (filament structural
putative glycosyl transferase, related to UDP‐glucuronosyltransferase
iroB
putative ATP binding cassette (ABC) transporter
iroC
Similar to enterochelin esterase of E. coli
iroD
putative hydrolase of the alpha/beta superfamily
iroE
TonB‐dependent siderophore receptor protein
iroN
putative inner membrane protein
Homolog of pipB, putative pentapeptide repeats (8
tricarboxylic transport
DNA‐binding protein with chaperone activity
stpA
putative inner membrane protein
glutaredoxin‐like protein hydrogen donor
nrdH
stimulates ribonucleotide reduction
nrdI
ribonucleoside diphosphate reductase 2, alpha subunit
nrdE
ABC superfamily (bind_prot), glycine/betaine/proline transport protein
proX
emrA
multidrug resistance secretion protein
gamma‐glutamate‐cysteine ligase
gshA
putative phosphoglucomutase
yqaB
DNA strand exchange and recombination protein with
recA
electron transport protein (FeS senter) from formate
hydN
‐0.23525706
‐1.4245783
0.8380818
0.8900621
0.7350009
0.42267513
‐0.2229477
‐0.34153134
‐0.40191922
0.30365953
‐0.3649795
0.45811883
‐0.5205092
0.32749838
‐0.29371068
‐0.5449582
‐0.3797041
‐0.46761006
‐0.8575317
‐0.6258309
‐0.39599353
‐0.55333656
‐0.76764554
‐0.90607184
‐0.40745583
‐0.5014692
‐0.39079365
‐0.4616236
0.5325464
‐0.3382629
‐0.5936473
‐1.400604
0.54774284
‐0.19344439
‐0.70569223
‐0.33975238
‐0.4210802
‐0.43354943
‐1.0053508
0.33464143
0.55602515
‐0.30937022
0.5733523
0.4415167
0.45122093
0.6733387
0.33419007
0.5854015
0.35445872
0.2990498
‐0.5692435
0.31660816
0.5624847
‐0.3615075
‐0.34565735
‐0.19817394
0.45461294
0.5478117
‐0.2064581
0.38129607
0.3655798
0.65346134
1.9767494
‐0.46834084
‐0.50833637
‐0.37134042
‐0.40518212
0.64363766
‐0.26364854
‐0.371346
‐0.4698734
‐0.393688
‐0.3195953
‐0.51528144
‐0.46762577
‐0.4409544
‐0.3276338
‐0.72710884
‐0.21117067
‐2.409216
0.42493463
0.8552046
1.3667911
1.4136881
0.489211
0.4924994
0.42766732
‐0.2827178
0.59398854
0.21955983
0.59391034
1.4615705
1.4685358
0.88882965
0.8541298
1.9108407
‐1.6570932
‐1.0780922
‐0.24668622
0.51035285
‐1.0397096
1.4108615
1.5859082
1.3610189
0.28423262
‐0.6603798
0.30802456
0.5168176
0.36601838
‐2.111915
‐0.30325264
‐1.4444654
0.9110559
0.7898668
0.5211285
0.34250376
‐0.47907624
‐0.28165892
‐0.4752816
0.49258414
‐0.68441063
0.38812217
‐0.48782656
0.28917238
‐0.39288747
‐0.62357396
‐0.71908444
‐0.8066455
‐0.92838544
‐0.58527905
‐0.57785195
‐0.52553827
‐1.3955622
‐0.87389094
‐0.36292687
‐0.5934646
‐0.47798032
‐0.48115346
0.2414636
‐0.48924717
‐0.7646353
‐1.3309743
0.8205257
‐0.538076
‐0.5307672
‐0.44699302
‐0.44985646
‐0.735563
‐1.0411766
0.43004054
0.5908321
‐0.3005613
0.53790146
0.4327222
0.32291824
0.6188528
0.2014798
0.41560653
0.3651713
0.34132865
‐0.638844
0.631907
0.68613225
‐0.49790597
‐0.43354815
‐0.26949763
0.50390565
0.32566613
‐0.4816775
0.30712685
0.28132844
0.19456767
1.9268703
‐0.59718376
‐0.62913424
‐0.31807062
‐0.6434078
0.55979085
‐0.49239382
‐0.561585
‐0.6328658
‐0.36545414
‐0.6365987
‐0.6633785
‐0.6847157
‐0.37403706
‐0.23637518
‐0.83900166
‐0.40218395
‐2.5270565
0.3290534
0.7936667
1.3381793
1.5990025
0.31111732
0.561775
0.22290292
‐0.34084126
0.48456725
0.34764314
0.86389077
1.4559537
1.3882108
0.9238883
0.9028306
2.1902285
‐1.5668646
‐0.8139626
‐0.5167338
0.7136659
‐1.0487089
1.5631614
1.6896712
1.1131215
0.24634005
‐0.61795837
0.2622602
0.22583568
0.616091
‐2.1141264
‐0.3394083
‐0.6639423 ‐0.65042436
‐0.796252 ‐0.29264 0.816407
‐1.3343866
‐1.0207832
‐0.9393163
‐1.1401907 ‐1.40114 0.378629
0.86167157
0.35555798
0.26258653
0.36383238 0.87027 1.828005
0.70109767
0.60119885 ‐0.002512962 0.029784463 0.793676 1.733485
0.64384043
0.46631774
0.67152745
0.49984565 0.633323 1.551134
0.29650134
1.9126965
1.9137075
1.8750834 0.353893 1.278005
‐0.26018736
0.23921727
0.17514017
0.5090737 ‐0.32074 0.800661
‐0.48666865
‐0.602654 ‐0.61617696 ‐0.80372417 ‐0.36995 0.773808
‐0.17719823
0.22545871
0.26638293
0.33103037 ‐0.35147 0.783787
0.4001365
0.4594475
0.4441329
0.20801595 0.398793 1.318405
‐0.5550241
‐1.9298726
‐1.9060316
‐1.8553083 ‐0.5348 0.690252
0.45650494 ‐0.01204091
0.15576616
0.15613848 0.434249 1.351207
‐0.5498602 ‐0.20428927
‐0.3382881 ‐0.54045844 ‐0.5194 0.697663
0.20130165
0.15429819 ‐0.11762217 ‐0.20724286 0.272657 1.208031
‐0.3338009 0.105254896
‐0.2373996
‐0.142814 ‐0.34013 0.789968
‐0.5364034 ‐0.09010234 0.015949069 ‐0.13984679 ‐0.56831 0.674405
‐0.61559105
0.20472471
0.22401272
0.23394392 ‐0.57146 0.672936
‐0.8020342
0.36260724
0.39635876 ‐0.04449083 ‐0.6921 0.618954
‐1.0345399
0.92301166
0.9969052
0.9841413 ‐0.94015 0.521178
‐0.3001663
1.0111129
1.5354394
1.2720251 ‐0.50376 0.705267
0.3335542
0.5885079
0.6079343 ‐0.50265 0.705809
‐0.5341032
‐0.41416374
0.66871697
0.7760612
0.8482847 ‐0.49768 0.708245
‐1.2866403
0.7578795
0.7946701
0.71211123 ‐1.14995 0.450641
‐0.7842597
0.7514559
0.64789313
0.71703404 ‐0.85474 0.552965
‐0.40497294
0.25386277
0.38418785
0.39346194 ‐0.39179 0.762186
‐0.56030476
0.7614176
0.57570356
0.48981956 ‐0.55175 0.682194
‐0.50672805
‐0.3476028
‐0.8295524
‐0.5067927 ‐0.4585 0.727742
‐0.5303182
‐1.0072376
‐0.8412558
‐0.7478572 ‐0.49103 0.711516
0.30317497
0.47926083
0.4151023
0.30556625 0.359062 1.282591
‐0.31882894 ‐0.15360825 ‐0.61077553
‐0.4950088 ‐0.38211 0.767313
‐0.63680995 ‐0.69515795 ‐0.67024964 ‐0.56542164 ‐0.66503 0.630675
‐1.3863664
‐2.6482382
‐2.515496
‐2.4523265 ‐1.37265 0.386182
0.5031891
1.9648407
2.1074753
1.8334143 0.623819 1.540949
‐0.4004039
0.78080255
0.36654153
0.7381135 ‐0.37731 0.769873
‐0.67913485 ‐0.08790274 0.045238234 ‐0.06390487 ‐0.63853 0.642367
‐0.48137915
0.5186413
0.25569984
0.29104447 ‐0.42271 0.746023
‐0.513038
0.26960456
0.11712958 ‐0.08601441 ‐0.46132 0.726319
‐0.5262327 ‐0.51674217 ‐0.44256973 ‐0.07579631 ‐0.56512 0.675902
‐0.97862315
‐1.0113494
‐1.1621034
‐1.4432645 ‐1.00838 0.497103
0.22414994 ‐0.19638361 ‐0.16651835
‐0.2655585 0.329611 1.256674
0.53190136
0.2600624
0.26398492 0.023082407 0.559586 1.473846
‐0.39667216
4.64E‐04 ‐0.018764509 ‐0.18700634 ‐0.33553 0.79249
0.46242976 ‐0.038998865 ‐0.24948457 ‐0.25137687 0.524561 1.438496
0.42390454 0.098293975
0.05965885
0.17366005 0.432714 1.349771
0.2700161
0.84455734
0.3571823
0.43619353 0.348052 1.272841
0.59673494 ‐0.63130504
‐0.819051 ‐0.74938726 0.629642 1.547181
0.49719268 ‐0.20622128 ‐0.10071657 ‐0.07020261 0.344288 1.269524
0.43937817
0.6884998
0.5863998
0.53092635 0.480129 1.394868
0.34319264
0.07999854 0.039455757
0.02775653 0.354274 1.278342
0.36836603
0.06625182 0.045512054 ‐0.19176048 0.336248 1.262469
‐0.6675065
0.6006584
0.4766011
0.48291883 ‐0.6252 0.648331
0.32096383
1.394403
1.3680007
0.95552915 0.42316 1.340861
0.54327565
0.11988245 0.013463078 0.017414007 0.597298 1.51288
‐0.5386727 ‐0.005572236
0.10283049 ‐0.06752354 ‐0.46603 0.723955
‐0.2159622 ‐0.076321065 ‐0.38161 0.767582
‐0.36561623 0.029761888
‐0.27411497
1.6319189
1.404445
1.4160644 ‐0.24726 0.842494
0.22497275
0.52327347
0.73832494
0.9471155 0.394497 1.314484
0.4064823
0.27413726
0.2895384
0.51163965 0.426653 1.344112
‐0.30287918
‐0.4883459
0.07266714
0.15302329 ‐0.33034 0.79535
0.2257414
0.8262161
0.6358742
0.60499936 0.304721 1.23518
0.3583133
0.7556656
1.0426716
0.8955026 0.335074 1.261442
0.5378542
0.30621108
0.5394509
0.5964574 0.461961 1.377413
1.9821848
1.6390253
1.487708
1.5227687 1.961935 3.895841
‐0.55395865 ‐0.75783175
‐0.6825032 ‐0.59163463 ‐0.53983 0.687853
‐0.54535985 ‐0.41308144
‐0.6082869
‐0.7965573 ‐0.56094 0.677859
‐0.21125828
‐0.5125055
‐0.5690386 ‐0.47179893 ‐0.30022 0.812127
‐0.52824616
‐0.7355737
‐0.6372644 ‐0.51503503 ‐0.52561 0.694664
0.5690766
0.85604954
0.9068405
0.8827994 0.590835 1.506118
‐0.25670066
0.23552082
0.22396353
0.25169766 ‐0.33758 0.791367
‐0.52674264
0.40875655
0.21271114
0.6226194 ‐0.48656 0.713726
‐0.6162032 ‐0.16477494 ‐0.46521708 ‐0.24240327 ‐0.57298 0.672226
‐0.35795328
‐0.1642597 ‐0.07226453 ‐0.33703125 ‐0.37237 0.772515
‐0.48812613
‐0.5757709 ‐0.73887795 ‐0.65123403 ‐0.48144 0.716262
‐0.65227646
‐0.8489438 ‐0.92762154
‐1.0008435 ‐0.61031 0.655055
‐0.7068311
‐0.6161648
‐0.6992853 ‐0.51704144 ‐0.61972 0.650795
‐0.5243789
‐0.3866868 ‐0.33483467 ‐0.54304653 ‐0.44646 0.733843
‐0.2256565
‐0.8565542
‐0.7094124
‐0.8726867 ‐0.26322 0.833225
‐0.7159658 ‐0.21629183 ‐0.43168828 ‐0.33610797 ‐0.76069 0.590213
‐0.39635748
‐0.2691202 ‐0.48473087 ‐0.29618627 ‐0.33657 0.791921
‐2.4806406
‐3.539058
‐3.6892347
‐3.8342152 ‐2.4723 0.180203
0.30795994
0.87684643
0.81144875
0.83785975 0.353983 1.278084
0.7369175
0.46165243
0.60133964
0.50020754 0.795263 1.735394
1.1992822
0.88219213
0.9187685
0.909422 1.301418 2.464709
1.3860908
1.164331
1.1723489
0.9882371 1.46626 2.763048
0.40039545
0.29688472
0.06538507
0.11128916 0.400241 1.319729
0.354886
1.571607
0.8121499
0.79679686 0.46972 1.384841
0.27952188
0.37897253
0.30458152
0.47828022 0.310031 1.239734
‐0.26870468 ‐0.47125855
‐0.6280167 ‐0.31454402 ‐0.29742 0.813706
0.820836
0.91573364
0.88280106
1.2101729 0.633131 1.550927
0.51134974 ‐0.33998582 ‐0.24395336
‐0.4226718 0.359518 1.282997
0.62645835
4.4718914
3.0326958
3.278312 0.694753 1.618607
1.3366925
‐0.1385594 ‐0.06457027 ‐0.022934027 1.418072 2.672282
1.4077921
1.0338286
0.83051705
0.97554153 1.421513 2.678663
0.88425475
1.4213401
1.660388
1.6496134 0.898991 1.864761
0.97993296
0.7055156
0.86182636
0.6533429 0.912298 1.882041
2.018897
0.21211101
0.26418743
0.21821526 2.039989 4.112423
‐1.3951266
‐1.5192282
‐1.3188132
‐1.1711544 ‐1.53969 0.343958
‐0.97066003
‐1.3445059
‐1.1444677
‐1.3973186 ‐0.95424 0.516114
‐0.51041025 ‐0.03694854 ‐0.33182222 ‐0.039279483 ‐0.42461 0.74504
0.6639277
1.2195485
1.4674598
1.3035315 0.629315 1.546831
‐0.9491986
‐1.1627603
‐1.7866412
‐1.4778053 ‐1.01254 0.495673
1.6114173
0.2844111
0.23818079
0.09022212 1.52848 2.884818
1.5323713
0.5361342
0.5886238
0.54786766 1.60265 3.037007
1.3807477
1.2840371
1.6497548
1.5424218 1.284963 2.436758
0.27426836
1.0516843
1.2805676
1.3833369 0.26828 1.204371
‐0.6030626
0.14563538 0.105465606
0.05179591 ‐0.62713 0.647462
0.22540766
1.3915378
1.2543832
1.0112273 0.265231 1.201828
0.35993382
0.42678532
0.6108107
0.5289412 0.367529 1.290141
0.48594844
1.2252629
1.1004763
0.8265971 0.489353 1.403815
‐2.1909368
‐0.7292152
‐0.3609178
‐0.662025 ‐2.13899 0.227038
147
STM2844
STM2846
STM2849
STM2851
STM2854
STM2855
STM2856
STM2857
STM2858
STM2861
STM2862
STM2863
STM2864
STM2865
STM2901
STM2911
STM2924
STM2934
STM2935
STM2938
STM2939
STM2946
STM2951
STM2953
STM2954
STM2963
STM2971
STM2976
STM2985
STM2992
STM3003
STM3012
STM3034
STM3040
STM3047
STM3048
STM3049
STM3053
STM3054
STM3055
STM3060
STM3062
STM3063
STM3067
STM3068
STM3073
STM3074
STM3075
STM3076
STM3086
STM3091
STM3128
STM3150
STM3165
STM3175
STM3178
STM3198
STM3217
STM3222
STM3229
STM3231
STM3238
STM3255
STM3272
STM3283
STM3290
STM3296
STM3303
STM3307
STM3310
STM3318
STM3319
STM3321
STM3322
STM3323
STM3330
STM3331
STM3344
STM3345
STM3346
STM3347
STM3348
STM3351
STM3353
STM3356
STM3376
STM3404
STM3409
STM3411
STM3428
STM3444
STM3455
STM3467
STM3468
STM3483
STM3487
STM3494
STM3505
STM3506
STM3507
STM3510
STM3521
STM3541
STM3545
STM3547
STM3559
STM3562
STM3579
STM3583
STM3592
putative periplasmic or exported protein
processing of HycE (part of the FHL
hydrogenase 3, large subunit (part of FHL
hydrogenase 3, membrane subunit (part of FHL
guanine‐nucleotide binding protein in formate‐hydrogenlyase system, functions
hydrogenase‐3 accessory protein, assembly of metallocenter
putative hydrogenase expression/formation protein
putative hydrogenase expression/formation protein
putative hydrogenase expression/formation protein
Salmonella iron transporter: fur regulated
Salmonella iron transporter: fur regulated
Salmonella iron transporter: fur regulated
Salmonella iron transporter: fur regulated
putative inner membrane protein
putative cytoplasmic protein
putative permease
sigma S (sigma 38) factor of RNA
ATP‐sulfurylase, subunit 1 (ATP:sulfate adenylyltransferase)
ATP‐sulfurylase, subunit 1 (ATP:sulfate adenylyltransferase)
putative cytoplasmic protein
putative cytoplasmic protein
3‐phosphoadenosine 5‐phosphosulfate (PAPS) reductase
putative Organic radical activating enzymes
CTP synthetase
putative pyrophosphatase
putative MFS superfamily, D‐glucarate permease
L‐serine dehydratase (L‐threonine deaminase 2)
L‐fucose isomerase
putative SufE protein probably involved in Fe‐S
N‐alpha‐acetylglutamate synthase (amino‐acid acetyltransferase)
General PTS system, enzyme I, transcriptional regulator
putative transcriptional regulator
putative cytoplasmic protein
lysine tRNA synthetase, constitutive
putative cytoplasmic protein
putative aminomethyltransferase
putative hemolysin
glycine cleavage complex protein P, glycine decarboxylase
glycine cleavage complex protein H, carrier of
glycine cleavage complex protein T, aminomethyltransferase, tetrahydrofolate‐dependent
putative cytoplasmic protein
D‐3‐phosphoglycerate dehydrogenase
ribosephosphate isomerase, constitutive
putative membrane protein, involved in stability of
fructose‐bisphosphate aldolase
putative ABC‐type cobalt transport system, permease component
putative ABC‐type cobalt transport system, ATPase component
putative ABC‐type cobalt transport system, ATPase component
transketolase 1 isozyme
arginine decarboxylase
MFS family, galactose:proton symporter
putative oxidoreductase
putative Ni/Fe hydrogenases, small subunit
2,5‐diketo‐D‐gluconate reductase A
putative bacterial regulatory helix‐turn‐helix proteins, araC family
putative sensory histidine kinase in regulatory system
putative inner membrane protein
aerotaxis sensor receptor, senses cellular redox state
putative integral membrane protein
putative inner membrane protein
putative inner membrane protein
putative inner membrane protein
putative phosphotransferase system fructose‐specific component IIB
putative ABC superfamily (membrane) transport protein
30S ribosomal subunit protein S15
argininosuccinate synthetase
ATP‐dependent zinc‐metallo protease
50S ribosomal subunit protein L27
UDP‐N‐acetylglucosamine 1‐carboxyvinyltransferase
putative ABC superfamily (atp&memb), transport protein
putative ABC superfamily (bind_prot) transport protein
putative ABC superfamily (atp_bind) transport protein
putative sigma N modulation factor
sugar specific PTS family, enzyme IIA, also
putative P‐loop‐containing kinase
glutamate synthase, large subunit
glutamate synthase, small subunit
30S ribosomal subunit protein S9
50S ribosomal subunit protein L13
putative ATPase
putative periplasmic protein
serine endoprotease
putative sodium ion pump oxaloacetate decarboxylase beta
putative sodium ion pump oxaloacetate decarboxylase gamma
putative cation transporter
putative oxidoreductase
putative cytoplasmic protein
Trk system transport of potassium
putative cytoplasmic protein
50S ribosomal subunit protein L5
regulatory or redox component complexing with Bfr
FKBP‐type peptidyl prolyl cis‐trans isomerase (rotamase)
putative inner membrane protein
acetylornithine transaminase (NAcOATase and DapATase)
D‐ribulose‐5‐phosphate 3‐epimerase
shikimate kinase I
putative NTP pyrophosphohydrolase
ferrous iron transport protein A
FeoB family, ferrous iron transport protein B
putative cytoplasmic protein
putative amidophosphoribosyltransferase
putative ribonucleoprotein related‐protein
low affinity gluconate permease
putative oxidoreductase
putative transcriptional regulator of sugar metabolism
putative cytoplasmic protein
ABC superfamily (membrane), branched‐chain amino acid transporter
putative integral membrane protein
putative Phosphopantetheinyl transferase
putative POT family, peptide transport protein
hycH
hycE
hycC
hypA
hypB
hypC
hypD
hypE
sitA
sitB
sitC
sitD
avrA
rpoS
cysN
cysD
ygcH
cysH
ygcF
pyrG
mazG
sdaB
fucI
ygdK
argA
ptsP
lysS
ygfY
ygfZ
yqfA
gcvP
gcvH
gcvT
ygfE
serA
rpiA
yggB
fba
tktA
speA
galP
hypO
yqhE
ygiY
aer
ygjQ
yqjD
yqjK
yhaN
yhbS
rpsO
argG
hflB
rpmA
murA
yrbC
yhbN
yhbG
yhbH
ptsN
yhbJ
gltB
gltD
rpsI
rplM
yhcM
yhcB
degQ
oadB
oadG
yhdH
smg
trkA
rplE
bfd
slyD
yhfK
argD
rpe
aroK
yrfE
feoA
feoB
yhgG
yhgH
gntU
yhhX
yhhV
livM
yhhQ
acpT
yhiP
‐1.2787188
‐1.9982865
‐1.5778861
‐1.5309073
‐1.380965
‐1.510201
‐1.6043607
‐1.3017131
‐1.2006162
1.7026858
2.0106812
1.479524
1.0156461
0.6580734
0.28170028
‐0.36350116
1.0578645
0.30372697
0.3542767
‐0.18880545
‐0.20089796
‐0.2020317
0.62965447
0.46347573
0.26385403
0.6211641
‐0.32765755
‐0.40149662
‐0.23369008
‐1.8826816
0.45904133
‐0.19931345
0.39470655
0.5489557
0.22228152
0.37370208
‐0.26975584
‐0.28896147
‐0.44275403
‐0.4154128
‐1.2001287
0.8323728
0.5394156
0.47451338
0.3727042
‐0.7943754
‐0.493748
‐0.499996
‐0.2935491
0.53480905
0.3331002
0.50142735
‐0.19726229
0.20250544
‐0.31041464
‐0.38070723
‐0.22396512
0.35210353
0.2223704
0.3128186
0.44499046
‐0.23153356
0.28756332
‐0.512472
‐0.5601261
‐0.8604555
0.3639048
0.29266664
0.31915554
0.45055595
0.21828444
0.55796766
1.0253689
0.35407287
0.4593303
‐1.2374511
‐1.2325765
‐0.31225324
‐0.42418668
0.46733466
0.27658775
0.29680672
‐0.34602475
‐0.4816189
0.37959757
‐0.38041863
0.55361795
0.45403755
0.61358094
0.27224478
0.29753736
0.29044163
‐0.27054843
‐1.0901717
0.22289732
0.23728496
0.3264107
‐0.8980078
‐0.8008093
‐0.65874517
‐0.40665218
‐0.41907156
‐0.40383425
0.3654765
0.3454789
‐0.51195174
‐0.33340865
‐0.26206633
‐0.23017658
0.42574438
‐1.2830478
‐2.2120636
‐1.6977483
‐1.5929081
‐1.3377738
‐1.5917325
‐1.3384742
‐1.5445496
‐1.1917812
1.6050758
1.9755465
1.534634
0.77281904
0.54348016
0.617756
‐0.28299135
0.65946704
0.48952314
0.29968372
‐0.57485443
‐0.483565
‐0.42270452
0.71734643
0.63191265
0.5658111
0.5561981
‐0.43095577
‐0.7043617
‐0.46151632
‐2.0373597
0.49615526
‐0.23968917
0.5751511
0.705428
0.28155047
0.3103816
‐0.25578
‐0.31050998
‐0.3848467
‐0.34686542
‐1.0961808
0.74745554
0.44647112
0.4381121
0.415672
‐1.0122044
‐0.44734427
‐0.46201798
‐0.7141154
0.4557718
0.47443724
0.29206783
‐0.34846747
0.32095325
‐0.32097733
‐0.16367202
‐0.42934448
0.31415823
0.35430413
0.3589067
0.5090171
‐0.27967775
0.55266887
‐0.2669699
‐0.48675564
‐0.8045967
0.31723154
0.27417678
0.385592
0.6493985
0.24881084
0.51682436
1.2957793
0.44442272
0.5092408
‐1.1750478
‐1.1646444
‐0.2942787
‐0.39810398
0.51619864
0.5025476
0.52625495
‐0.6961095
‐0.7889358
0.36113432
‐0.36449853
0.37892056
0.41118976
0.5232863
0.408246
0.5292295
0.3634315
‐0.34388548
‐1.1069815
0.2771398
0.50706136
0.48532274
‐0.8358187
‐0.7850094
‐0.65858203
‐0.36850718
‐0.19010767
‐0.39919758
0.456926
0.35628942
‐0.36480522
‐0.43975687
‐0.28131464
‐0.21891128
0.24779528
‐1.2518593
‐0.172181
‐0.263596
‐0.3009187 ‐1.27121 0.414313
‐2.144421
‐1.3907449
‐1.029538
‐0.9739851 ‐2.11826 0.230325
‐1.7120734 ‐0.10358425 ‐0.09148506 ‐0.16535304 ‐1.66257 0.315876
0.3335
‐1.6289089
‐0.6390652
‐0.3003945
‐0.3207277 ‐1.58424
‐1.5077561
‐0.6757089 ‐0.86436427
‐1.1842023 ‐1.40883 0.376617
‐1.7514678
‐1.2971075
‐1.0884947
‐1.2998145 ‐1.6178 0.325832
‐1.4685069
‐1.3643197
‐1.0714186
‐1.1026849 ‐1.47045 0.36087
‐1.4773316
‐1.7078265
‐2.026192
‐1.9283416 ‐1.4412 0.368261
‐1.2197933
‐1.1196187
‐0.9748724
‐1.2857137 ‐1.20406 0.434051
1.7330488
‐1.8225362
‐1.4510936
‐1.3076658 1.68027 3.20488
1.9555578
‐1.4567972
‐1.5760242
‐1.6994305 1.980595 3.946559
1.3238136
‐1.2319107
‐1.1149666
‐1.2070023 1.445991 2.724498
0.95749605 ‐0.57300925
‐0.6943098 ‐0.82742065 0.91532 1.885988
0.5883913
0.22636618
0.16684346
0.15857702 0.596648 1.512199
0.7001731
0.37418702
0.13207701
0.19973299 0.53321 1.447145
0.4931611 ‐0.35549 0.781605
0.64968485
0.60937476
‐0.4199722
0.5723216
1.0113361
0.8807009
0.9485627 0.763218 1.697272
0.310964
1.7175845
1.5714319
1.5097268 0.368071 1.290626
0.3409208
0.995818
0.83977145
0.903015 0.331627 1.258432
‐0.3934032
‐0.4256609
‐0.614946 ‐0.59168684 ‐0.38569 0.765414
‐0.53419197 ‐0.12783015
‐0.2431091 ‐0.17925814 ‐0.40622 0.754599
‐0.4029644
0.30678847 ‐0.061309233
0.14378427 ‐0.34257 0.788637
0.33090457
0.9377197
0.94293815
0.70960456 0.559302 1.473556
0.53153473
1.5831877
1.2341961
0.790129 0.542308
1.4563
0.27409884 ‐0.06666602
0.24465722 0.040505618 0.367921 1.290492
0.6033192
0.38301352
0.37756073
0.4378025 0.59356 1.508966
‐0.30523852 ‐0.037356358
0.37048268
0.12657136 ‐0.35462 0.782077
‐0.7407146 ‐0.15369768
‐0.3733546
‐0.3041184 ‐0.61552 0.652693
‐0.40656316 ‐0.50069046 ‐0.66075945
‐0.5349036 ‐0.36726 0.775255
‐1.7753541
‐0.9094354
‐1.0514808
‐0.7714091 ‐1.89847 0.268229
0.4057607
1.61506
1.5269563
1.6946888 0.453652 1.369503
‐0.27772453
‐0.4509196 ‐0.19308375
‐0.1738517 ‐0.23891 0.847386
0.52478904 0.041727323
0.30389428
0.08183529 0.498216 1.412465
0.4235758
0.8250381
0.37911683
0.51252145 0.55932 1.473574
0.33851743 ‐0.39068496 ‐0.45433235
‐0.3793316 0.280783 1.214854
0.36433092
0.09927412
0.18745086
‐0.0856364 0.349472 1.274094
‐0.34860906
‐0.8640276
‐0.6955426
‐0.8497073 ‐0.29138 0.817119
‐0.30673265 ‐0.15525909 ‐0.18276502
‐0.3426088 ‐0.30207 0.811089
‐0.52412593
0.02444239 ‐0.061243914 ‐0.18869832 ‐0.45058 0.731751
‐0.4907852 ‐0.08639197 ‐0.15058707 ‐0.32628548 ‐0.41769 0.748623
‐1.0825833
0.1922612
0.16760007
0.14385821 ‐1.1263 0.45809
0.5936536
0.62308353
0.19925058
0.16718918 0.724494 1.652321
0.42515892
0.54042345
0.7274467
0.54703075 0.470349 1.385444
0.4382247 ‐0.050456624 ‐0.22115836 ‐0.45672375 0.450283 1.366309
0.32199523 ‐0.73165846
‐0.6565856 ‐0.90815854 0.370124 1.292464
‐1.05152
‐1.5030166
‐1.7414619
‐1.6000873 ‐0.9527 0.516665
‐0.5929929 ‐0.24813941 ‐0.07105917 ‐0.14006026 ‐0.51136 0.70156
‐0.28025147 ‐0.20015813 ‐0.12247555 ‐0.17347944 ‐0.41409 0.750494
‐0.5902455 0.039647017 ‐0.14916487 ‐0.12813893 ‐0.53264 0.69129
0.27149752
1.1257912
0.82378703
0.8655421 0.420693 1.33857
0.21365693
0.20429307
0.2514892
0.02743258 0.340398 1.266106
0.27690646 ‐0.18091533 ‐0.32729176 ‐0.22772942 0.356801 1.280583
‐0.46484947
0.25835583 0.033438966
0.2959998 ‐0.33686 0.791763
0.37499368 ‐0.13356934
‐0.2397828 ‐0.17741789 0.299484 1.230704
‐0.36471972 ‐0.15913767 ‐0.16535844
‐0.303867 ‐0.33204 0.794414
‐0.497045
0.14814201
0.10543076 ‐0.24226819 ‐0.34714 0.78614
‐0.3221091 ‐0.24545233
‐0.5870015
‐0.6201221 ‐0.32514 0.798221
0.33692762 ‐0.13237587 ‐0.28828335
8.02E‐04 0.334396 1.26085
0.33712152 ‐0.17460038 ‐0.26037008 ‐0.17399216 0.304599 1.235075
0.59789807 ‐0.42720148
‐0.2842111 ‐0.27550352 0.423208 1.340906
0.3568463 ‐0.09442147 ‐0.13439716 ‐0.43509114 0.436951 1.353741
‐0.27294913
0.3655211
0.22990517
0.3426212 ‐0.26139 0.834286
0.4851381
0.7379055
0.41182685
0.39430737 0.44179 1.358289
‐0.28543532 ‐0.43123624 ‐0.27311894 ‐0.09063242 ‐0.35496 0.781892
‐0.37208533
0.19555874
0.22505854
0.25455463 ‐0.47299 0.72047
0.06927864 ‐0.80491 0.572397
‐0.7496812 ‐0.027040191 ‐0.01537311
0.26751897
0.873671
0.6887258
0.6959391 0.316218 1.245063
0.37332067
0.722275
0.80754155
0.8770581 0.313388 1.242622
0.33516544
0.86490834
0.8380177
0.68250495 0.346638 1.271594
0.37100726
1.0194108
1.4531128
1.1803452 0.490321 1.404757
0.34011468
0.72728646
0.6107526
0.72495925 0.26907 1.205031
0.24608935
0.90596527
0.61113596
0.61389375 0.440294 1.356881
1.0338696
0.12469561 ‐0.14209625 ‐0.21633388 1.118339 2.170969
0.31480545
0.5144853
0.2909794 ‐0.007488954
0.3711 1.293339
0.3930682
0.87617284
0.41066575
0.21388516 0.45388 1.369719
‐1.0209262
0.42223728
0.46917948
0.41576034 ‐1.14448 0.452354
‐1.1944269
0.86034554
0.7685048
0.74538505 ‐1.19722 0.436116
‐0.35574937
0.59703296
0.72727215
0.84410584 ‐0.32076 0.800648
‐0.27671683
0.3355869
0.5297364
0.5527854 ‐0.36634 0.77575
0.4392478
0.48856956
0.5567523
0.3359806 0.47426 1.389206
0.47790214
0.7403273
0.653262
0.6178786 0.419012 1.337012
0.40978143
0.9529764
0.89315414
0.42084214 0.410948 1.329559
‐0.74508744
0.32210544
0.26042974
0.28443214 ‐0.59574 0.661705
‐0.78861606
0.10544067 ‐0.15715173 0.053094957 ‐0.68639 0.621407
0.29512122 ‐0.77252007
0.22669515
0.25414976 0.345284 1.270401
‐0.3964006
‐0.0674355
0.1674601
0.650326 ‐0.38044 0.768204
0.48058265
‐0.3222866 ‐0.36682993 ‐0.42427483 0.47104 1.386109
0.4119724 0.081143364
0.0475558 0.034577005 0.425733 1.343255
0.549325
0.38336587 ‐0.15478486
‐0.0657317 0.562064 1.47638
0.21400793
0.55655867
0.5555049
0.57440585 0.298166 1.229581
0.5117523
1.82E‐04 ‐0.025506811 0.004482636 0.446173 1.362421
0.34046206 0.028055783 0.012357877 0.022738952 0.331445 1.258273
‐0.24580324 ‐0.07410044 ‐0.36324915 ‐0.25896966 ‐0.28675 0.819749
‐1.0186319
‐0.5776001
‐0.8472112
‐0.9248754 ‐1.07193 0.475683
0.25279966
1.1238592
1.5802953
0.8778368 0.250946 1.189987
0.38406584
1.4653877
1.4609106
1.3644738 0.376137 1.297862
0.37126324
1.1182879
1.1681563
0.9867609 0.394332 1.314334
‐0.78202707
‐1.9934821
‐1.9092382
‐1.8104979 ‐0.83862 0.559179
‐0.80909026
‐1.6182702
‐1.514517
‐1.5827016 ‐0.7983 0.575025
‐0.5766391 ‐0.78440833
‐0.9887308
‐0.9772643 ‐0.63132 0.645585
‐0.42183143 ‐0.49081504 ‐0.18121335 ‐0.94985723
‐0.399 0.758385
‐0.36613894
‐0.2944485 ‐0.34561506 ‐0.25370425 ‐0.32511 0.79824
‐0.33831713 ‐0.19777584 0.014297553 ‐0.20688541 ‐0.38045 0.768198
0.22306515
1.4265004
1.4592677
1.38696 0.348489 1.273227
0.42460406
‐1.5679135
0.1685269 0.027284415 0.375457 1.297251
‐0.3218064
‐0.8147165
‐0.6967587
‐0.6396708 ‐0.39952 0.75811
‐0.4066767
1.1676672
0.695106
0.74952626 ‐0.39328 0.761396
‐0.31972826
0.8972435
0.9045855
1.2626444 ‐0.2877 0.819205
‐0.23699446
0.6221992
1.0144118
0.95787734 ‐0.22869 0.853407
0.3458033
0.2915216 0.100314565
0.44760516 0.339781 1.265564
148
STM3622
STM3630
STM3647
STM3649
STM3650
STM3659
STM3663
STM3664
STM3666
STM3679
STM3682
STM3689
STM3693
STM3694
STM3695
STM3699
STM3713
STM3727
STM3728
STM3733
STM3738
STM3753
STM3767
STM3780
STM3794
STM3796
STM3808
STM3810
STM3828
STM3832
STM3842
STM3850
STM3862
STM3866
STM3877
STM3879
STM3887
STM3898
STM3899
STM3901
STM3902
STM3903
STM3904
STM3905
STM3909
STM3918
STM3919
STM3920
STM3956
STM3964
STM3965
STM3967
STM3970
STM3972
STM3973
STM3974
STM3986
STM3987
STM3996
STM3998
STM3999
STM4001
STM4002
STM4006
STM4007
STM4021
STM4042
STM4044
STM4050
STM4068
STM4074
STM4075
STM4080
STM4085
STM4089
STM4091
STM4096
STM4100
STM4103
STM4105
STM4106
STM4110
STM4121
STM4122
STM4123
STM4147
STM4151
STM4152
STM4159
STM4160
STM4161
STM4162
STM4163
STM4170
STM4181
STM4182
STM4190
STM4201
STM4220
STM4222
STM4226
STM4237
STM4248
STM4256
STM4263
STM4270
STM4271
STM4274
STM4282
STM4331
putative cytoplasmic protein
yhjS
ABC superfamily (peri_perm), dipeptide transport protein
dppA
putative outer membrane lipoprotein
yiaF
major cold shock protein 7.4, transcriptional activator
cspA
putative periplasmic or exported protein
putative inner membrane protein
yiaB
gene transcribed divergently from malS
bax
alpha‐amylase
malS
paral putative oxidoreductase
ysaA
putative cytoplasmic protein
selenocysteinyl‐tRNA‐specific translation factor
selB
putative cytoplasmic protein
yibL
putative transcriptional regulator for lct operon (GntR
lldR
lldD
L‐lactate dehydrogenase
putative tRNA/rRNA methyltransferase
yibK
serine acetyltransferase
cysE
O‐antigen ligase
rfaL
50S ribosomal subunit protein L33
rpmG
50S ribosomal subunit protein L28
rpmB
orotate phosphoribosyltransferase
pyrE
putative inner membrane protein
yigC
ATP binding protein
sugR
putative cytoplasmic protein
putative fructose‐bisphosphate aldolase class‐II
putative regulatory protein, deoR family
acetolactate synthase I, large subunit, valine sensitive
ilvB
small heat shock protein
ibpB
putative outer membrane lipoprotein
yidQ
galactonate dehydratase in bifunctional: 2‐oxo‐3‐deoxygalactonate 6‐phosphate aldolase
dgoA
putative permease
putative Preprotein translocase subunit YidC
yidC
putative oxidoreductase
yieF
N‐acetyl glucosamine‐1‐phosphate uridyltransferase and glucosamine‐1‐phosphate acetyl traglmU
membrane‐bound ATP synthase, F1 sector, gamma‐subunit
atpG
asparagine synthetase A
asnA
paral putative regulator protein
yieN
putative MFS family tranport protein (1st mdule)
yieO
putative LysR type transcriptional regulator with pssR
yifE
putative magnesium chelatase, subunit ChlI
yifB
acetolactate synthase II, large subunit, fragment 1
ilvG
ilvM
acetolactate synthase II, small subunit
branched‐chain amino‐acid aminotransferase
ilvE
dihydroxyacid dehydratase
ilvD
threonine deaminase
ilvA
ketol‐acid reductoisomerase
ilvC
undecaprenyl‐phosphate N‐acetylglucosaminyltransferase
rfe
modulator of enterobacterial common antigen (ECA) polysaccharide
wzzE
UDP‐N‐acetyl glucosamine ‐2‐epimerase
wecB
putative protein PaaI, possibly involved in aromatic
yigI
regulator for metE and metH (LysR family)
metR
5‐methyltetrahydropteroyltriglutamate‐homocysteine S‐methyltransferase
metE
dlhH
putative dienelactone hydrolase family
S‐adenosylmethionine : 2‐DMK methyltransferase and 2‐octaprenyl‐6‐methoxy‐1,4‐benzoqui ubiE
putative regulator in ubiquinone biosynthesis
aarF
component of Sec‐independent protein secretion pathway
tatA
component of Sec‐independent protein secretion pathway
tatB
Trk family, potassium transport protein, requires TrkE
trkH
protoporphyrin oxidase
hemG
putative homoserine kinase type II, protein kinase
yihE
putative endonuclease
yihG
DNA polymerase I, 3 ‐‐ 5 polymerase
polA
putative GTPase, involved in coordination of cell
yihA
putative cytoplasmic protein
sensory kinase (phosphatase) in two‐component regulatory system
glnL
glutamine synthetase
glnA
putative isomerase
yihS
putative branched‐chain amino acid permease
putative iron‐containing alcohol dehydrogenase
DMT Superfamily, L‐rhamnose:H symporter protein
rhaT
putative regulatory protein, gntR family
putative ABC‐type sugar, aldose transport system, ATPase
ego
putative ABC superfamily (membrane), sugar transport protein
ydeY
putative ribulose‐5‐phosphate 3‐epimerase
unknown function in glycerol metabolism
glpX
menG
putative methyltransferase in menaquinone biosynthesis protein
ATPase component of the HslUV protease
hslU
50S ribosomal subunit protein L31
rpmE
cystathionine gamma‐synthase
metB
putative cytoplasmic protein
5,10‐methylenetetrahydrofolate reductase
metF
catalase hydroperoxidase HPI(I)
katG
General PTS family, enzyme I
ptsA
N‐acetyl‐gamma‐glutamylphosphate reductase
argC
acetylglutamate kinase
argB
argininosuccinate lyase
argH
preprotein translocase IISP family, membrane subunit
secE
50S ribosomal subunit protein L10
rplJ
50S ribosomal subunit protein L7/L12
rplL
deoxyxylulose‐5‐P thi‐S‐COSH tyrosine
thiH
deoxyxylulose‐5‐P thi‐S‐COSH tyrosine
thiG
putative involved in thiamine biosynthesis
catalyzes the adenylation of thisS as part
thiF
thiamin phosphate synthase (thiamine phosphate pyrophosphorylase)
thiE
DNA‐binding protein HU‐alpha (HU‐2)
hupA
putative acetyltransferase
yjaB
metA
homoserine transsuccinylase
(alpha)‐aspartyl dipeptidase
pepE
putative phage tail protein
aspartokinase III, lysine sensitive
lysC
putative outer membrane protein
yjbE
putative inner membrane protein
yjbA
SOS response regulator, transcriptional repressor (LexA family)
lexA
tyrosine aminotransferase, tyrosine repressible
tyrB
ssDNA‐binding protein controls activity of RecBCD nuclease
ssb
putative inner membrane protein
yjcB
putative transcriptional regulator, LysR family
putative inner membrane protein
yjcH
putative inner membrane protein
part of formate‐dependent nitrite reductase complex involved
nrfG
putative outer membrane lipoprotein
yjeI
0.47895348
0.65638983
0.26586452
0.18005908
0.22452152
‐0.1970659
‐0.19354104
‐0.24996409
‐0.3849482
‐0.29648966
‐0.46270218
0.36531964
‐0.40226498
‐0.31891036
‐0.38597736
0.2519985
0.36301234
0.6258041
0.5031419
0.22934297
0.24687901
0.43738025
‐0.3511006
0.20207778
0.37849623
1.5609252
‐0.28224045
0.28135958
0.21327987
0.50030506
‐0.23485981
0.23937899
0.36955515
0.54671985
‐1.8288294
0.5740368
0.30532005
0.47292084
0.32598174
0.6425514
1.0454634
0.79254895
0.775312
0.5118394
‐0.25719902
0.28181234
0.38888365
0.2827122
0.29129466
0.496016
2.0208678
0.57621735
0.5451342
0.38699812
0.39415374
0.3267777
0.43091
0.4650082
0.36842012
0.6362146
0.37616727
0.46204188
1.8951077
‐0.6108326
‐0.53651893
‐0.2704055
‐0.31133318
‐0.45278054
0.36642
‐0.4316753
0.33004305
0.28925765
0.34366462
‐0.24018738
‐0.32543272
‐0.21740294
‐0.52524084
0.3551766
0.4829309
1.0520654
‐0.22332722
‐0.3237488
‐1.6799085
‐1.2066184
‐1.35849
0.37733194
‐0.32769844
‐0.27338395
0.49387768
0.5696071
0.74364185
0.42741707
0.4782781
0.6041425
0.41277462
0.83211875
‐0.19743058
‐0.22076447
‐1.1065358
‐2.0814438
‐0.3906223
0.4908214
0.48781145
0.5871153
0.1971912
‐0.30131537
‐0.42716506
‐0.3073611
‐0.3483499
0.28103364
0.5198404
0.7135767
0.36045036
0.46725303
0.22606935
‐0.28612143
‐0.29071295
‐0.2857351
‐0.3260673
‐0.65751076
‐0.58953184
0.36450312
‐0.21572231
‐0.38540933
‐0.43957305
0.23225242
0.49145386
0.38240027
0.37100726
0.43212935
0.47976634
0.56249774
‐0.57912034
0.57365334
0.35960653
1.3317875
‐0.41326177
0.27978045
0.3637907
0.40592232
‐0.22943561
0.3455915
0.5402315
0.3996228
‐2.0108335
0.4551856
0.37606826
0.7659487
0.2897434
0.59973615
0.92444766
0.75233585
0.45393547
0.3958778
‐0.60160685
0.31976473
0.4176267
0.28895012
0.37405178
0.6067155
2.130202
0.6570585
0.7330351
0.4446431
0.21388204
0.4204216
0.36631954
0.2570255
0.5877408
0.32162002
0.5917273
0.4504875
1.6498793
‐0.4447654
‐0.5801261
‐0.27652904
‐0.27132848
‐0.5214348
0.51521206
‐0.72215956
0.6452359
0.38426402
0.20211396
‐0.3257725
‐0.19806375
‐0.32428992
‐0.6936451
0.58232796
0.17199175
1.1641366
‐0.277701
‐0.2876717
‐1.9183506
‐1.330715
‐1.4856558
0.25517297
‐0.29879412
‐0.21300955
0.4242009
0.6524479
0.74524623
0.5229101
0.52834356
0.6515002
0.27361307
0.9562479
‐0.3404635
‐0.44376224
‐1.0743078
‐2.1460955
‐0.23616368
0.36775026
0.43012685
0.5578599
0.3038759
‐0.3492216
‐0.3473108
‐0.35714027
‐0.38001975
0.37520134
0.45286873
0.6953107
0.25343433
0.35170114
0.32060763
‐0.3498788
‐0.32134485
‐0.34253663
‐0.4641717
‐0.54979634
‐0.3083847
0.6098935
‐0.25337076
‐0.21543375
‐0.34641305
0.25430465
0.43890908
0.33417016
0.459275
0.260425
0.24572635
0.4580277
‐0.62720615
0.4473668
0.31703052
1.3896406
‐0.2579473
0.4666824
0.2827768
0.43314388
‐0.2112078
0.36063868
0.4510921
0.33254293
‐1.9725355
0.3761866
0.31825593
0.66173244
0.27166605
0.58618224
0.91379493
0.7646743
0.49352932
0.5679266
‐0.39823884
0.20916136
0.29808593
0.30483842
0.2899537
0.5417827
2.026502
0.70042425
0.5664514
0.40212184
0.36006528
0.35949153
0.36982083
0.34211197
0.24637876
0.23502919
0.34549972
0.47532624
2.0633426
‐0.4580785
‐0.66090095
‐0.22166605
‐0.3750686
‐0.524722
0.3493159
‐0.47238067
0.38345605
0.41718525
0.28522003
‐0.29373208
‐0.2541264
‐0.26945928
‐0.5349336
0.62016344
0.51570684
1.1934389
‐0.4115189
‐0.5148504
‐1.8451334
‐1.3596027
‐1.4299273
0.2670554
‐0.45284906
‐0.3425917
0.39095336
0.5532246
0.5477212
0.4220712
0.46170875
0.70391434
0.4795135
0.87414855
‐0.32733977
‐0.37578574
‐0.7839398
‐2.0887516
‐0.29530108
0.3812299
0.6478722
0.6316421
0.34870505
‐0.20983638
‐0.47306418
‐0.34812275
‐0.5585485
0.2916052
1.1361014
0.10715337
0.39822218
1.7636927
0.17822671
0.18167017
0.20326287
‐0.002784849
‐0.42707002
‐0.6548299
‐0.26028427
0.07639939
‐0.2106168
‐0.21499631
‐0.31762493
0.25100732
1.906771
1.5091441
0.8283098
1.0674946
‐0.44474292
0.6982648
0.43108487
0.43595454
0.51292825
1.216307
‐0.46361297
0.059726506
0.54554945
‐0.4325301
0.29219565
‐0.04232111
1.0702175
1.437102
‐0.7493705
0.11855396
0.08260533
0.116377756
0.19326666
0.6117585
0.80081606
0.65603364
1.5322919
1.3083211
0.7675543
0.2355924
0.90911055
0.05869467
0.50552374
0.08060953
1.3302777
0.3934541
1.9925156
0.6121604
0.49250725
1.2409211
0.42558333
0.7979541
0.4794375
0.24990827
0.86111623
0.23006605
‐3.046172
1.014649
‐0.8614913
‐0.14612405
0.043424353
‐0.31382
‐0.05258342
‐0.5438755
0.15237305
‐0.265797
‐0.40540716
‐0.081974894
‐0.35762367
0.18986104
0.9467218
0.8253261
0.69531804
0.0978407
0.15668105
1.2346344
0.13672332
‐0.1591417
0.6250283
0.31977314
‐0.09704229
0.62130743
0.3482004
0.43022105
1.0572369
0.7624599
0.98228496
0.29124603
0.045616366
‐0.3689904
‐0.68625724
‐0.041930385
‐0.067584634
‐2.8885083
‐0.42360932
0.89199054
‐0.06561804
0.87687755
0.089991726
‐0.36365175
‐0.62511533
‐0.4655083
0.75978756
0.09004359
0.71533597
0.08700275
0.4916266
1.7109131
‐0.12572524
‐0.16547696
‐0.047476996
0.078710474
‐0.54028434
‐0.61710554
‐0.1905019
‐0.21415645
‐0.07665873
‐0.050316732
‐0.1700495
0.6143443
1.6350414
1.1095043
0.82460684
0.70575684
‐0.5762905
0.39981353
0.4718336
0.43045422
0.26912284
1.1003712
‐0.44752392
‐0.20296866
0.53348064
‐0.25363237
0.4062164
‐0.041951276
0.9851888
1.0038995
‐1.1015068
‐0.3955661
0.003871119
0.11979651
0.1352363
0.62401396
0.38492376
0.3946524
1.1240008
1.0906904
0.856862
0.29574695
0.9141631
0.62140656
0.38928434
0.0294121
1.5007643
0.23191008
1.8771598
0.6710387
0.6424895
0.96708983
0.49539125
0.6967339
0.736238
0.039901324
0.68715334
‐0.038399022
‐3.429997
0.8775167
‐1.0806694
‐0.25875008
0.24703322
‐0.29780543
0.003506932
‐0.7996518
0.16123646
‐0.14742954
‐0.30971038
‐0.25006828
‐0.55476916
‐0.1350702
1.1588022
1.0059774
0.47887748
0.00562335
0.12392089
1.1793113
‐0.16850032
0.27497667
0.31935942
0.64295644
0.088375315
0.52880853
0.4624054
0.564055
0.97125435
0.87814826
1.009627
0.097995125
‐0.2692408
‐0.77333647
‐0.47755364
‐0.31664777
‐0.18820454
‐2.8630266
‐0.43033835
0.7649744
‐0.10670616
0.63089496
0.028018676
‐0.4410995
‐0.61022663
‐0.2816491
0.52543026
0.042432725
0.33328858
‐0.06425898
0.46281114
1.7175866
‐0.057249717
‐0.13611113
‐0.14926338
4.09E‐04
‐0.6653222
‐0.7088889
‐0.067840494
0.15354414
‐0.05643029
‐0.11105678
‐0.037356976
0.4956306
1.0828239
1.1165243
0.77496606
0.77110326
‐0.37029564
0.04603538
0.60070896
0.32178733
0.28366348
0.9060913
‐0.4528699
‐0.011735023
0.3950154
‐0.32690707
0.49257448
‐0.35066804
0.66823614
0.9538133
‐1.0090463
0.075530075
‐0.2290431
‐0.030671012
0.10118432
0.6385095
0.60558546
0.4817307
1.3032608
1.2207458
1.0445279
0.16008376
0.60147023
0.43969116
0.29344177
‐0.06707674
1.636712
0.13222028
1.2903749
0.8239563
0.9343452
0.6855373
0.6512143
0.5071127
0.29896173
0.068191454
0.30518755
0.15837023
‐3.3333795
0.7090234
‐1.1501278
‐0.20933959
0.14072745
‐0.38358757
‐0.13109052
‐0.63016534
‐0.050507206
‐0.066055015
‐0.53250366
‐0.34049258
‐0.5807771
0.20300889
1.4138205
0.8184255
0.5695407
‐0.06088176
‐0.045554634
0.982827
‐0.14625329
‐0.016878612
‐0.008788543
0.6141499
0.08313876
0.45028988
0.44730914
0.51288176
0.83276814
0.69689643
0.9916104
0.20224686
‐0.17483352
‐0.9920574
‐0.43082675
‐0.19647604
‐0.12233027
‐2.601704
‐0.6432603
0.68065786
‐0.05398615
0.65885246
0.008216077
‐0.3154152
‐0.7487976
‐0.21799472
0.35321736
‐0.09096117
0.483888
0.688426
0.29325
0.333004
0.257066
‐0.27769
‐0.26853
‐0.29275
‐0.39173
‐0.50127
‐0.45354
0.446572
‐0.29045
‐0.30658
‐0.39065
0.246185
0.431125
0.447458
0.444475
0.307299
0.324124
0.485969
‐0.51914
0.407699
0.351711
1.427451
‐0.31782
0.342607
0.286616
0.446457
‐0.22517
0.315203
0.453626
0.426295
‐1.9374
0.46847
0.333215
0.633534
0.295797
0.60949
0.961235
0.769853
0.574259
0.491881
‐0.41901
0.270246
0.368199
0.292167
0.318433
0.548171
2.059191
0.644567
0.614874
0.411254
0.3227
0.368897
0.389017
0.354715
0.400847
0.397621
0.437798
0.462619
1.869443
‐0.50456
‐0.59252
‐0.2562
‐0.31924
‐0.49965
0.410316
‐0.54207
0.452912
0.363569
0.277
‐0.28656
‐0.25921
‐0.27038
‐0.58461
0.519223
0.39021
1.136547
‐0.30418
‐0.37542
‐1.81446
‐1.29898
‐1.42469
0.299853
‐0.35978
‐0.27633
0.436344
0.59176
0.67887
0.457466
0.489443
0.653186
0.388634
0.887505
‐0.28841
‐0.34677
‐0.98826
‐2.10543
‐0.30736
0.413267
0.521937
0.592206
0.283257
‐0.28679
‐0.41585
‐0.33754
‐0.42897
0.315947
1.398507
1.611524
1.225397
1.259634
1.195046
0.824912
0.830163
0.816347
0.762216
0.706487
0.730249
1.362798
0.817645
0.808554
0.762783
1.186067
1.348285
1.363636
1.360819
1.237389
1.251904
1.400526
0.697787
1.326569
1.276073
2.689711
0.802283
1.268046
1.219776
1.36269
0.855496
1.244187
1.369478
1.343778
0.261087
1.383641
1.259817
1.551361
1.227563
1.52572
1.946976
1.705096
1.488912
1.406277
0.747935
1.206014
1.29074
1.224478
1.246976
1.462231
4.167524
1.56327
1.531424
1.329842
1.250669
1.291365
1.309501
1.278733
1.320282
1.317334
1.354535
1.378041
3.653915
0.704876
0.663186
0.83729
0.80149
0.70728
1.328977
0.686784
1.3688
1.286605
1.211672
0.819852
0.835547
0.829099
0.666831
1.433183
1.310584
2.198542
0.809901
0.770879
0.28431
0.406414
0.372499
1.231019
0.779283
0.82569
1.353171
1.507084
1.600885
1.373128
1.403903
1.572637
1.309153
1.849974
0.818803
0.786342
0.504085
0.232382
0.808118
1.331698
1.435882
1.50755
1.216939
0.819723
0.749579
0.791389
0.742791
1.244828
149
STM4333
STM4336
STM4343
STM4351
STM4356
STM4362
STM4363
STM4374
STM4375
STM4409
STM4414
STM4419
STM4446
STM4469
STM4473
STM4486
STM4490
STM4492
STM4498
STM4511
STM4514
STM4549
STM4550
STM4552
STM4594
STM4598
STY0070
STY0402
STY0439
STY0586
STY0936
STY0963
STY1472
STY1488
STY1505
STY1567
STY2099
STY2115
STY2258
STY2261
STY2303
STY2345
STY2703
STY2717
STY2751
STY2867
STY2893
STY2894
STY2897
STY3403
STY3470
STY3653
STY3724
STY3725
STY4091
STY4175
STY4259
STY4260
STY4754
STY4846
putative aminomutase
putative entericidin B precursor
fumarate reductase, anaerobic, flavoprotein subunit
putative arginine‐binding periplasmic protein
putative sugar kinase
putative GTP‐ase, together with HflCK possibly involved
with HflC, part of modulator for protease
putative inner membrane protein
putative inner membrane protein
putative outer membrane protein
inorganic pyrophosphatase
sugar (and other) transporter
putative selenocysteine synthase [L‐seryl‐tRNA(Ser) selenium transferase
ornithine carbamoyltransferase 1
putative acetyltransferase
putative alcohol dehydrogenase
putative Mrr restriction endonuclease
putative cytoplasmic protein
putative inner membrane protein
putative transcriptional regulator, LysR family
putative inner membrane protein
putative cytoplasmic protein
ferric hydrozamate transport, involved in reduction of
putative inner membrane protein
putative fimbrial chaparone protein
response regulator (OmpR family) in two‐component regulatory
citrate lyase alpha chain
PrpD protein
maltodextrin glucosidase
putative membrane protein
putative virK protein
anaerobic dimethyl sulfoxide reductase chain B
putative virulence effector protein
respiratory nitrate reductase 2 alpha chain
putative glycogen debranching protein
putative dimethyl sulphoxide reductase subunit
high‐affinity zinc uptake system periplasmic binding protein
putative copper homeostasis protein
putative ferredoxin
putative propanediol utilization protein PduV
putative reductase RfbI
hypothetical protein
putative cobalamin adenosyltransferase
putative oxidoreductase
GMP synthase (glutamine‐hydrolyzing)
hypothetical protein
putative exported protein
TonB‐dependent outer membrane siderophore receptor protein
conserved hypothetical protein
possible oxidoreductase
argininosuccinate synthetase
dihydroxyacid dehydratase
thiamine biosynthesis protein
thiamine biosynthesis protein
2,3‐bisphosphoglycerate‐independent phosphoglycerate mutase
hypothetical protein
hypothetical protein
gamma‐glutamyltranspeptidase precursor
D‐serine/D‐alanine/glycine transporter
putative outer membrane protein
yjeK
ecnB
frdA
yjeF
hflX
hflK
yjfL
yjfM
ytfM
ppa
argI
yjgM
yjgB
yjiE
yjiH
fhuF
sthA
arcA
citF2
prpD
malZ
ybcI
ybjX
dmsB
srfA
narZ
glgX
dmsB
yebL
cutC
pduS
pduV
rfbI
aegA
guaA
iroE
iroN
argG
ilvD
thiS
thiG
ggt
cycA
0.34275535
0.4911552
‐0.43022296
0.26687232
‐0.26104313
0.7876796
0.8000094
‐0.4443888
‐0.27731678
0.27382404
0.45368612
0.46449316
‐0.42905918
‐1.3485008
0.28985777
0.5597197
0.3887054
0.5707446
0.38002673
‐0.29897767
‐0.4175689
0.54050124
0.77914
1.443204
0.3393081
0.26712856
‐0.18545978
‐0.49298972
‐0.26598063
‐0.39932278
0.8266219
‐0.45513213
‐0.29640138
‐0.5651388
‐0.31610373
‐0.21789041
1.6600322
‐0.83848965
‐0.36159647
‐0.33628783
0.6925853
‐0.37001657
‐0.38120845
‐0.4300859
0.67157376
0.19530237
0.93417346
1.2964964
‐1.4992087
0.22387105
‐0.8413535
0.40515068
0.34690958
0.6056575
‐1.0078194
‐0.70266485
0.39459327
0.68399864
0.26940024
0.33641014
0.3663677
0.6025157
‐0.47210342
0.34219256
‐0.4351466
0.86858255
0.7273756
‐0.4237964
‐0.36688748
0.24136394
0.5373738
0.41518277
‐0.6164485
‐1.5603379
0.4287503
0.5544405
0.24690713
0.7728898
0.44331577
‐0.650452
‐0.52337974
0.567556
0.80690694
1.5985178
0.6615488
0.25683007
‐0.42093408
‐0.5892416
‐0.5112237
‐0.33200687
1.0932217
‐0.3605968
‐0.41446215
‐0.5857039
‐0.41061938
‐0.28208828
1.9473672
‐0.75747293
‐0.36156255
‐0.35360885
1.1637181
‐0.31735414
‐0.6780023
‐0.67344296
0.55280757
0.37931833
0.86765563
1.9452901
‐1.4673667
0.2886808
‐0.9153108
0.26249734
0.4336048
0.7192756
‐1.3371959
‐0.7875038
0.43763816
0.5683288
0.34920967
0.40311894
0.2541502
0.19885266
0.31783143
0.28968376 0.321091 1.249275
0.8024351
‐0.2815821
‐0.3991241 ‐0.51115614 0.632035 1.54975
‐0.6185513 ‐0.21412861 ‐0.26285717 ‐0.34201923 ‐0.50696 0.703704
0.2355721
0.68633914
0.41939098
0.22016367 0.281546 1.215496
‐0.538389
0.7492662
0.9724459
1.2659442 ‐0.41153 0.751828
0.6201337
1.1325591
0.79570717
0.7112566 0.758799 1.692081
0.7477214
0.5571832
0.5122535
0.6720588 0.758369 1.691577
‐0.2376784
‐0.652044
‐0.0996806
‐0.4925044 ‐0.36862 0.774522
‐0.25895834 ‐0.17989731 ‐0.46148422 ‐0.40780795 ‐0.30105 0.811659
0.2284955
0.13155776
0.21557996
0.25771213 0.247894 1.187473
0.53940153
0.3797464
‐0.3178469
0.38645786 0.510154 1.424202
0.4278109
0.22889353
0.2702437
0.31595305 0.435829 1.352688
‐0.60982305
0.66548145
0.8008127
0.578856 ‐0.55178 0.682179
‐1.2840261 ‐0.16654044 ‐0.58588463
‐0.5805293 ‐1.39762 0.379554
0.37574795
0.35791102
0.51642
0.2898662 0.364785 1.28769
0.44027153 0.009001294
‐0.2096884 ‐0.47505113 0.518144 1.432112
0.34024322
1.0261223
0.5276918
0.43209174 0.325285 1.252912
0.60287035
1.3183347
1.072003
0.84367573 0.648835 1.567901
0.40515405
0.48088077
0.47889808
0.20146409 0.409499 1.328224
‐0.55105835 ‐0.23040657
‐0.4647893 ‐0.06686011 ‐0.50016 0.707027
‐0.5656572 ‐0.031217387 ‐0.057554044
‐0.2564576 ‐0.5022 0.706028
0.5888282
0.24952032 ‐0.31520516 ‐0.02025315 0.565628 1.480032
0.757924
0.18168716
0.1969045
0.1514706 0.781324 1.718707
1.8143021
0.11738137 ‐0.31504673 ‐0.18409345 1.618675 3.070928
0.5412092 ‐0.20185731
‐0.2049984
‐0.3331284 0.514022 1.428026
0.21130179 ‐0.022407375 ‐0.14870913 ‐0.23917845 0.245087 1.185164
‐0.50465536
‐0.5581128
‐0.5847175 ‐0.53381014 ‐0.37035 0.773595
‐0.48051035
0.985427
0.4965236
0.6967143 ‐0.52091 0.69693
‐0.4539998
0.6373062
0.10209008
0.34853366 ‐0.4104 0.752414
‐0.3538852 ‐0.42742905 ‐0.47057682
‐0.4057785 ‐0.36174 0.778226
0.9094505
0.14976603 ‐0.38822445
‐0.7432075 0.943098 1.922652
‐0.49858785
‐0.8189377 ‐0.69091284
‐0.9507103 ‐0.43811 0.738103
‐0.4728805 0.003883983 0.025953632 ‐0.17169361 ‐0.39458 0.76071
‐0.35057256 ‐0.50144684 ‐0.51809454 ‐0.43401277 ‐0.50047 0.706876
‐0.40923125 ‐0.92813474
‐1.0527322
‐0.9623939 ‐0.37865 0.769156
‐0.34394017
‐0.3544724 ‐0.47628576 ‐0.63092494 ‐0.28131 0.822846
1.7970768
‐3.3868663
‐3.5019495
‐3.6352866 1.801492 3.485805
‐0.65187526 ‐0.46578476
‐0.5861411 ‐0.32073995 ‐0.74928 0.594901
‐0.74739695
0.2783675 0.034208395 ‐0.27177742 ‐0.49019 0.711934
‐0.6888912
‐0.5082773
‐0.4873949 ‐0.38296574 ‐0.4596 0.72719
0.61202896
2.163033
1.9231256
1.4972976 0.822777 1.768808
‐0.22864625 ‐0.22236492 ‐0.073161565 ‐0.027449075 ‐0.30534 0.809252
‐0.5178964
0.5951261
0.49704218
0.5939658 ‐0.5257 0.694621
‐0.6773814 ‐0.17396946
‐0.3890439 ‐0.42055735 ‐0.59364 0.66267
0.42809445
0.23781666
0.1643857
0.07279256 0.550825 1.464923
0.29865903
0.6023217
0.53004766
0.28801653 0.291093 1.223567
0.87125075
0.83267385
0.7676555
0.7568699 0.891027 1.854495
1.7477167
0.34931105
0.36523324
0.3093109 1.663168 3.167112
‐1.5548842
‐1.1871341
‐1.3526785
‐1.3884839 ‐1.50715 0.351805
0.42742115 ‐0.32889977 ‐0.21418169
‐0.1868183 0.313324 1.242568
‐0.9074922 0.007016142 ‐0.10949153 ‐0.014826099 ‐0.88805 0.540343
0.2621436
1.4708517
0.88730145
0.8937096 0.309931 1.239648
0.3258385
1.424583
0.9494153
0.7918123 0.368784 1.291264
0.60881543
0.69907445
0.65668464
0.52331895 0.644583 1.563287
‐1.3815194
0.02113587 ‐0.10393594 ‐0.092662506 ‐1.24218 0.422734
‐0.7313358 ‐0.36298174 ‐0.58551556 ‐0.66896117 ‐0.7405 0.598531
0.31719965 ‐0.15451665
‐0.3308565
‐0.3029147 0.383144 1.304181
0.5021433
‐0.154856
0.14545798 ‐0.07953447 0.584824 1.499856
0.22701757
0.55573344
0.3729122
0.14492114 0.281876 1.215775
0.23571685 ‐0.53900665
‐0.9099165
‐1.2299426 0.325082 1.252736
150
APPENDIX F
SIGNIFICANT LT2 GENES DATA FOR CHAPTER 4
151
All Significant Salmonella LT2 Genes (Delta=0.77666634, False Sig Genes=0, FDR=0%)
Locus
Obsolete
PSLT002
PSLT004
PSLT005
PSLT008
PSLT011
PSLT012
PSLT015
PSLT016
PSLT018
PSLT020
PSLT023
PSLT026
PSLT027
PSLT036
PSLT042
PSLT043
PSLT044
PSLT045
PSLT046
PSLT048
PSLT049
PSLT050
PSLT051
PSLT052
PSLT055
PSLT068
PSLT072
PSLT077
PSLT079
PSLT080
PSLT083
PSLT085
PSLT091
PSLT092
PSLT093
PSLT095
PSLT096
PSLT097
PSLT098
PSLT099
PSLT100
PSLT103
PSLT107
STM0004
STM0009
STM0012
STM0013
STM0018
STM0019
STM0024
STM0027
STM0028
STM0043
STM0048
STM0049
STM0064
STM0066
STM0067
STM0089
STM0090
STM0091
STM0092
STM0093
STM0094
STM0107
STM0108
STM0110
STM0113
STM0116
STM0120
STM0125
STM0127
STM0129
STM0131
STM0132
STM0136
STM0152
STM0153
STM0157
STM0158
STM0166
STM0168
STM0171
STM0173
STM0177
STM0181
STM0190
STM0193
STM0213
STM0216
STM0217
STM0219
STM0222
STM0223
STM0224
STM0227
STM0228
STM0229
STM0230
STM0236
STM0257
STM0264
STM0289
STM0313
STM0324
STM0330
STM0337
STM0355
STM0362
STM0369
STM0378
STM0383
STM0384
STM0385
STM0388
STM0392
STM0399
STM0400
STM0402
STM0405
STM0406
STM0407
STM0418
STM0422
STM0425
STM0434
STM0439
STM0440
STM0441
STM0443
STM0447
STM0448
GeneN
GeneS
Obsolete
putative phospholipase D
DNA replication
repA3
replication of plasmid
tap
sdiA‐regulated geneputative bacterial regulatory helix‐turn‐helix proteins, araC
srgC
sdiA‐regulated gene putative thiol‐disulfide isomerase or thioredoxin
srgA
putative bacterial regulatory proteins, luxR family
orf7
putative outer membrane protein
orf5
plasmid‐encoded fimbriaechaperone
pefD
plasmid‐encoded fimbriae major fimbrial subunit
pefA
hypothetical protein
DNA replication
repA2
putative periplasmic protein
ccdA
toxin addiction system: antidote
putative transposase, IS200‐like
putative integrase protein
putative phosphoribulokinase / uridine kinase family
putative integrase protein
rlgA
putative resolvase
rlgA
putative carbonic anhydrase
alpha‐helical coiled coil protein
tlpA
putative DNA polymerase III epsilon subunit (3‐5
putative cytoplasmic protein
putative cytoplasmic protein
samB
plasmid partition protein A
parA
mutagenesis by UV and mutagens related to
samA
putative ParB‐like nuclease domain
putative transglycosylase
finP
conjugative transfer: fimbrial subunit
traA
conjugative transfer: assembly
traE
conjugative transfer: assembly
traK
conjugative transfer:
trbD
conjugative transfer
traR
conjugative transfer: assembly
traW
conjugative transfer: assembly
traU
conjugative transfer:
conjugative transfer: aggregate stability
traN
conjugative transfer
trbE
conjugative transfer: assembly
traF
conjugative transfer: fimbrial synthesis
traQ
conjugative transfer
trbB
conjugative transfer: assembly
traH
conjugative transfer: surface exclusion
traT
putative cytoplasmic protein
threonine synthase
thrC
putative regulator
yaaH
chaperone Hsp70 in DNA biosynthesis/cell division
dnaK
heat shock protein, DnaJ and GrpE stimulates
dnaJ
putative exochitinase
putative hydroxymethyltransferase
fimbrial subunit
bcfD
fimbrial chaparone
bcfG
putative thiol‐disulfide isomerase
bcfH
30S ribosomal subunit protein S20
rpsT
FKBP‐type peptidyl‐prolyl cis‐trans isomerase (rotamase)
slpA
regulates the activity of guanosine 3,5‐bispyrophosphate synthetase
lytB
dihydrodipicolinate reductase
dapB
carbamoyl‐phosphate synthetase, glutamine‐hydrolysing small subunit
carA
carbamoyl‐phosphate synthase, large subunit
carB
putative cytoplasmic protein
apaG
S‐adenosylmethionine‐6‐N,N‐adenosyl (rRNA) dimethyltransferase kasugamycin resistance ksgA
NAD‐dependent dehydrogenase/carboxylase pyridoxine phosphate biosynthetic protein PdxJpdxA
peptidyl‐prolyl cis‐trans isomerase, survival protein
surA
Organic solvent tolerance protein
imp
DnaJ like chaperone protein
djlA
putative binding‐protein‐dependent transport system inner membrane component
yabK
thiamine‐binding periplasmic protein
tbpA
3‐isopropylmalate isomerase (dehydratase), subunit with LeuC
leuD
2‐isopropylmalate synthase
leuA
acetolactate synthase III, valine sensitive, large subunit
ilvI
putative S‐adenosyl methionine adenyltransferase
yabC
phospho‐N‐acetylmuramoyl‐pentapeptide transferase
mraY
essential cell division gene, stablilzes FtsZ ring
ftsW
L‐alanine adding enzyme, UDP‐N‐acetyl‐muramate:alanine ligase
murC
cell division protein ingrowth of wall at
ftsQ
ATP‐binding cell division protein, septation process, complexes
ftsA
preprotein translocase secretion protein of IISP family
secA
pyruvate dehydrogenase, decarboxylase component
aceE
pyruvate dehydrogenase, dihydrolipoyltransacetylase component
aceF
putative outer membrane protein
yacH
aconitate hydratase 2
acnB
spermidine synthase (putrescine aminopropyltransferase)
speE
putative multicopper oxidase
cueO
putative carbonic anhydrase
yadF
putative ABC superfamily (membrane) transport protein
yadH
putative fimbrial subunit
stiA
pantothenate synthetase
panC
transpeptidase of penicillin‐binding protein 1b (peptidoglycan synthetase)
mrcB
ABC superfamily (bind _prot), hydroxamate‐dependent iron uptake
fhuD
2,3,4,5‐tetrahydropyridine‐2‐carboxylate N‐succinyltransferase
dapD
30S ribosomal subunit protein S2
rpsB
protein chain elongation factor EF‐Ts
tsf
ribosome releasing factor
frr
CDP‐diglyceride synthase
cdsA
putative membrane‐associated Zn‐dependent protease
yaeL
putative outer membrane antigen
yaeT
(3R)‐hydroxymyristol acyl carrier protein dehydratase
fabZ
UDP‐N‐acetylglucosamine acetyltransferase
lpxA
tetraacyldisaccharide‐1‐P
lpxB
RNAse HII
rnhB
cell cycle protein
mesJ
putative drug efflux protein (perhaps for chloramphenicol)
DNA polymerase III, epsilon subunit, 3‐5 exonucleolytic
dnaQ
putative cytoplasmic protein
DNA polymerase IV, devoid of proofreading, damage‐inducible
dinP
putative inner membrane protein
putative 3‐isopropylmalate isomerase (dehydratase), subunit with LeuC
putative fimbriae usher
stbD
putative Copper chaperone
putative cytoplasmic protein
putative citrate synthase
prpC
putative inner membrane protein
yaiY
putative cytoplasmic protein
yaiB
induced by phosphate starvation
psiF
putative diguanylate cyclase/phosphodiesterase domain 1
yaiC
shikimate kinase II
aroL
putative exonuclease involved in removal of stalled
rdgC
LIVCS family, branched chain amino acid transporter
brnQ
putative APC family, proline transporter
proY
putative thiol ‐ alkyl hydroperoxide reductase
tRNA‐guanine transglycosylase
tgt
preprotein translocase IISP family, membrane subunit
yajC
preprotein translocase, IISP family, part of the
secD
transcription termination L factor
nusB
1‐deoxyxylulose‐5‐phosphate synthase flavoprotein
dxs
sulfur transfer protein (from cys to ThiS
thiI
ketopantoate reductase
apbA
protohaeme IX farnesyltransferase (haeme O biosynthesis)
cyoE
cytochrome o ubiquinol oxidase subunit IV
cyoD
cytochrome o ubiquinol oxidase subunit III
cyoC
cytochrome o ubiquinol oxidase subunit II
cyoA
peptidyl‐prolyl cis/trans isomerase, trigger factor a molecular
tig
proteolytic subunit of clpA‐clpP ATP‐dependent serine protease
clpP
107808
107809
107810
107811
107812
107813
Log2 Ratio Means
Ratio
‐0.024515491
‐0.56913185
0.26097435
0.14039512
‐0.08653011
0.017582217
‐0.21873495
0.32027528
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‐8.57E‐04
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0.008465212
0.05489772
‐1.5317243
‐1.2538745
‐1.2448778
‐0.37726894
0.07971882
0.25723776
0.28144532
0.23846218
‐0.02423773
‐0.11707239
0.33463296
1.7166674
2.0898426
0.4106647
‐0.22315557
0.09187374
‐0.011474098
‐0.047314465
‐0.14612615
‐0.155406
‐0.06436498
‐4.26E‐05
0.34659097
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0.05181466
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1.417171
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‐0.32326004
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‐0.26524666
‐0.3072882
‐0.35836142
‐1.0282005
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‐0.96745145
‐0.118161425
‐1.2856466
0.70973486
0.087086454
‐0.026942851
‐0.15446708
‐0.2559368
‐0.32816613
0.034208562
0.37148115
‐0.017852247
‐0.028791165
‐0.009968681
‐0.31890327
‐0.2491674
‐0.19011502
0.18307544
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‐0.035030454
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‐0.005062324
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‐0.12937424
0.10145542
0.31634837
0.17513727
‐0.27145207
0.4902862
0.22106652
0.03563294
‐0.31377703
‐0.2461052
‐0.114045255
‐0.16829999
‐0.00748688
0.08862781
0.3619898
0.3715972
0.4314934
0.1999281
0.122797824
0.2385979
0.43895933
0.11592378
‐0.41357788
‐0.17039281
‐0.6681755
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0.15926483
‐0.020479208
‐0.41533518
‐0.9254414
‐0.09210748
‐0.098945215
‐0.015216936
0.009544011
‐1.5456456
‐1.1086514
‐1.2725413
‐0.17708895
0.02302706
0.29398572
0.26570287
0.055939388
0.09690074
‐0.23706743
0.26570046
1.583018
2.145787
0.2518642
‐0.22407691
‐0.19211438
‐0.18126376
‐0.027416121
‐0.076396585
‐0.25006297
0.14492969
0.5556925
0.21256778
‐0.43260288
‐0.19665106
0.19224705
‐0.31378183
1.3067999
‐0.038382508
‐0.04382514
‐0.3009579
‐0.003396956
‐0.05192486
‐0.08721535
‐0.7115866
0.060426794
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0.2029817
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‐0.42936707
‐0.21505938
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0.09624046
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0.005142221
0.012762454
‐0.3367807
‐0.33575934
‐0.1998862
0.06552855
‐0.10590536
0.6469255
0.5413024
‐0.3178753
‐0.7012004
‐0.44108105
‐0.46645153
‐0.86112
‐1.0260054
‐1.0850646
‐0.63325745
‐0.3770909
‐0.5968133
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‐0.6756516
‐0.8314
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0.6962467
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‐1.4889245
‐0.4208412
‐1.2752275
‐0.7575558
‐0.3740288
‐1.0907441
‐1.0865803
‐1.1690465
‐0.34044805
‐0.44043934
‐0.37463763
‐1.0760994
‐0.7422059
‐0.55611783
‐0.8411851
‐0.7080694
‐1.0022832
‐0.61945295
‐0.77961516
‐0.38843426
‐0.28462604
‐0.77392405
‐0.93360496
‐0.93247354
‐0.9666945
‐0.9970439
‐1.1038934
‐0.5798514
0.83274347
0.8916415
0.80367666
0.8971304
‐0.46230847
‐0.44477814
‐0.41096395
‐0.572756
‐0.37815225
0.4716167
0.40721318
0.55788106
2.4256654
0.87991774
0.88545954
0.7085653
1.2748251
1.7484965
1.0206679
0.8907043
0.7086819
1.1448509
1.0293115
1.4300208
1.6987354
0.93679035
1.1794915
1.0492826
1.7430907
0.7847641
1.0218602
0.62190914
0.8546085
1.3482674
1.0322548
0.45829695
1.3556936
0.45519966
‐1.0482265
0.97402143
‐0.38512462
‐0.7245394
‐0.73306835
0.8579666
0.87246543
1.0971526
0.57341975
1.1490176
1.1404701
1.5885047
0.6899292
1.415841
0.6900964
1.0336506
0.71775705
0.80364996
0.60620975
‐0.43852103
0.5090484
1.4514205
‐0.55591816
‐0.52142775
‐0.75975925
‐0.4925068
‐1.4730307
‐0.6839262
‐0.5843593
‐0.66106755
‐0.54481554
‐0.5045892
‐0.5835514
1.2113078
0.33080214
0.47835243
0.79900515
‐0.6453264
0.20476426
1.142839
1.1477289
0.90064746
0.87931055
1.1883136
0.62007135
1.2340465
1.390631
1.495569
0.64498657
1.9144396
0.38613337
‐0.5590353
‐0.8732664
‐0.49048424
‐0.67465156
‐0.8363603
‐1.2005081
‐1.0817932
‐0.8036808
‐0.35168564
‐0.7367811
‐0.8767592
‐1.2608273
‐0.65585476
‐0.6941175
0.65043
‐0.5008615
‐1.3363144
‐0.91123503
‐1.2566822
‐0.6575734
‐0.6530334
‐0.93230665
‐1.2578626
‐1.3365123
‐0.45474067
‐0.4705424
‐0.6261268
‐1.0165291
‐0.54335165
‐0.57119286
‐0.59166986
‐0.7858825
‐1.0243008
‐0.95396143
‐1.084095
‐0.7221319
‐0.80491954
‐0.7402496
‐1.044014
‐0.75738686
‐1.2760592
‐1.0738035
‐1.4469562
‐0.61901164
0.43817458
0.87591946
0.7522421
0.9123665
‐0.7128606
‐0.58665085
‐0.58373487
‐0.83642125
‐0.45147872
0.41125882
0.41153362
0.8107692
1.7328606
0.5956529
0.89565265
0.86141175
1.3571906
1.782081
1.0740172
0.931686
0.44692767
1.1841683
1.1995857
1.5770993
1.1851902
0.98173016
0.9645097
0.841995
1.3378145
0.788876
1.2807578
0.77353925
1.0449086
1.0821278
0.9680674
0.5423217
1.6505774
0.32902807
‐0.7835071
1.0766861
‐0.3639681
‐0.65723234
‐0.5574113
0.79675347
0.9673261
0.8437279
0.29930934
1.0189682
0.8477138
1.1740962
0.7168318
1.3570592
0.41285872
0.6345175
0.65910125
0.88572997
0.38494682
‐0.37103057
0.325833
1.3280559
‐0.44036174
‐0.8202106
‐0.97403556
‐0.55290353
‐0.7093598
‐0.7432704
‐0.7967985
‐0.56807154
‐0.7013361
‐0.4854659
‐1.0542364
0.88610744
0.38405833
0.671455
0.78537035
‐0.70945585
1.4769859
0.7577437
1.2874233
0.8751357
0.6138723
0.8481654
0.46394312
1.2247059
1.3016087
1.284953
0.3547519
1.7988226
0.39837956
‐0.47630873
‐0.84985125
‐0.44274163
‐0.728913
‐1.0207927
‐1.4041059
‐0.86064273
‐0.58809394
‐0.4151503
‐0.6808149
‐0.9003971
‐1.1219376
‐0.698623
‐0.3980606
0.6241986
‐0.35955667
‐1.6471025
‐1.1832428
‐1.4972923
‐0.68897706
‐0.84832406
‐0.8935997
‐1.0860307
‐1.1462287
‐0.6530225
‐0.61812747
‐0.47696564
‐0.96350557
‐0.5648818
‐0.70043534
‐0.5302125
‐0.6939375
‐1.3184862
‐1.08258
‐0.97996753
‐0.8119023
‐0.71326345
‐0.84005123
‐1.21234
‐0.967667
‐1.2982337
‐0.97136444
‐1.0903301
‐0.9647307
0.35283428
0.67216027
0.704346
1.0958174
‐0.46364868
‐0.58377564
‐0.53525835
‐0.8608931
‐0.56505764
0.47513437
0.33195403
0.8278819
1.6991214
0.71649796
1.0044138
0.7316711
1.1179612
1.7441692
1.1923009
0.25266615
0.7739203
1.0670031
1.1235733
1.3194692
1.4400281
0.5206042
0.99701464
0.7592049
0.9643548
0.71410125
0.9755648
0.7106285
1.0284092
1.1139914
0.9234585
0.6327726
1.4447147
0.36136717
‐0.74054164
0.98444915
‐0.41794303
‐0.70912886
‐0.5896664
0.616637
0.99694276
1.0483469
0.5275517
0.80457145
1.0069747
0.8087542
0.6521502
0.9922708
0.50637925
0.7105296
0.67716736
0.91760117
0.5957402
‐0.3734191
0.4978041
0.8551662
‐0.4913373
‐0.9760636
‐0.5715621
‐0.39480707
‐0.71972054
‐0.79809225
‐0.5542958
‐0.5048042
‐0.8197837
‐0.5983404
‐0.85180116
0.6303237
0.49439356
0.32832554
0.3985292
‐0.552541
1.2148346
0.9905058
1.0090208
1.1148609
0.645033
0.8839316
0.51389384
1.1463679
1.2867326
1.3487186
0.5125706
2.2050507
0.48524043
‐0.45107
‐0.80811
‐0.4581
‐0.62334
‐0.90609
‐1.21021
‐1.00917
‐0.67501
‐0.38131
‐0.67147
‐0.8056
‐1.01947
‐0.72863
‐0.54845
0.656958
‐0.4824
‐1.49078
‐0.83844
‐1.34307
‐0.70137
‐0.62513
‐0.97222
‐1.14349
‐1.21726
‐0.48274
‐0.5097
‐0.49258
‐1.01871
‐0.61681
‐0.60925
‐0.65436
‐0.7293
‐1.11502
‐0.88533
‐0.94789
‐0.64082
‐0.60094
‐0.78474
‐1.06332
‐0.88584
‐1.18033
‐1.01407
‐1.21373
‐0.7212
0.541251
0.81324
0.753422
0.968438
‐0.54627
‐0.5384
‐0.50999
‐0.75669
‐0.4649
0.45267
0.383567
0.732177
1.952549
0.73069
0.928509
0.767216
1.249992
1.758249
1.095662
0.691685
0.643177
1.132007
1.11749
1.442196
1.441318
0.813042
1.047005
0.883494
1.34842
0.76258
1.092728
0.702026
0.975975
1.181462
0.974594
0.544464
1.483662
0.381865
‐0.85743
1.011719
‐0.38901
‐0.69697
‐0.62672
0.757119
0.945578
0.996409
0.46676
0.990852
0.998386
1.190452
0.686304
1.255057
0.536445
0.792899
0.684675
0.868994
0.528966
‐0.39432
0.444229
1.211548
‐0.49587
‐0.77257
‐0.76845
‐0.48007
‐0.96737
‐0.74176
‐0.64515
‐0.57798
‐0.68865
‐0.52947
‐0.82986
0.909246
0.403085
0.492711
0.660968
‐0.63577
0.965528
0.963696
1.148058
0.963548
0.712739
0.97347
0.532636
1.201707
1.326324
1.376414
0.504103
1.972771
0.423251
0.731499
0.571131
0.727943
0.649167
0.533629
0.432207
0.496833
0.626328
0.767741
0.627867
0.572125
0.493297
0.603478
0.683755
1.576755
0.715784
0.35582
0.559248
0.394182
0.614988
0.648362
0.509722
0.452663
0.430098
0.715619
0.702367
0.710755
0.493557
0.65211
0.655538
0.635359
0.603198
0.461684
0.541363
0.518389
0.641347
0.659326
0.580456
0.47853
0.541171
0.441251
0.495147
0.431153
0.606594
1.455234
1.757154
1.685786
1.956721
0.684787
0.688533
0.702229
0.591853
0.724523
1.368571
1.304563
1.661144
3.870578
1.659432
1.903307
1.701982
2.378402
3.382873
2.137111
1.615169
1.561764
2.191635
2.169692
2.717343
2.715688
1.756912
2.066236
1.844838
2.546331
1.696522
2.132769
1.626787
1.966971
2.268065
1.965088
1.458478
2.796577
1.303025
0.551937
2.016312
0.763652
0.616868
0.647649
1.690112
1.92596
1.995028
1.382003
1.987359
1.997764
2.282242
1.609155
2.386766
1.450394
1.732553
1.60734
1.826389
1.442894
0.760846
1.360586
2.315859
0.709133
0.585375
0.587047
0.716942
0.511437
0.598008
0.639426
0.669901
0.620436
0.692812
0.562583
1.878064
1.322332
1.407086
1.581143
0.643595
1.952778
1.9503
2.216153
1.9501
1.638912
1.963558
1.44657
2.300116
2.507629
2.596222
1.418241
3.925213
1.340946
Expected Observed Numerato Denomina q‐value score score(d)
r(r)
tor (s+s0)
(%)
(dExp)
‐0.60076
0.061582
0.9208
‐0.29929
0.128603
‐0.85605
0.870234
0.713429
0.481909
0.118159
0.398341
0.069159
0.865692
‐1.45763
0.863839
1.232557
‐0.07928
‐0.414
0.701186
0.5544
‐0.26489
0.591169
1.600897
‐1.05141
0.313744
‐0.94071
0.989512
0.428741
0.301009
0.736635
1.234405
0.470677
‐0.28705
‐0.35589
0.038165
0.351722
0.12158
0.044502
‐0.61534
0.056153
0.29929
0.340537
‐0.04703
‐0.43169
‐0.2902
‐0.50458
‐0.29209
0.439491
0.23731
‐0.22329
0.086029
0.494818
0.074434
0.365644
0.743661
0.337449
‐0.06001
0.593543
0.095578
1.071704
0.275075
0.708205
0.33358
‐1.21286
0.495699
0.077786
‐0.12609
0.162481
0.709606
‐0.50555
0.876007
‐0.16342
‐0.45196
‐1.14584
‐0.08476
0.330477
1.880968
0.632487
‐0.19833
0.729416
0.448135
‐1.01347
0.378644
0.377207
‐0.78615
‐0.13855
0.35118
0.244168
‐0.23685
‐0.66863
0.182031
‐0.50764
0.597365
‐0.47236
0.104747
‐0.57737
‐0.16902
‐0.5921
‐0.79903
2.179022
0.097248
‐0.14131
1.061023
‐0.54133
0.377815
‐0.54969
‐0.25634
0.188743
‐0.77298
‐0.17628
1.714808
0.400907
‐0.56586
‐0.82656
0.768363
‐0.05615
0.576001
‐0.3244
0.05056
0.975941
‐0.29444
1.258977
‐0.22272
‐0.84382
0.153391
0.834841
1.349896
0.096314
1.113066
0.384153
‐2.30068
0.806797
‐2.17902
‐1.38154
‐2.60992
‐1.68452
‐1.8566
‐2.88984
‐3.31558
‐3.05792
‐2.10027
‐1.39067
‐2.26523
‐2.37631
‐2.3584
‐2.36108
‐1.60719
2.373382
‐1.49818
‐4.31521
‐1.75103
‐4.03266
‐2.45862
‐1.58914
‐3.07608
‐3.65408
‐3.8553
‐1.39093
‐1.64074
‐1.49826
‐3.53387
‐1.93508
‐2.02039
‐1.86514
‐2.56492
‐3.11738
‐2.24831
‐2.74675
‐1.6663
‐1.4442
‐2.75287
‐3.15721
‐2.76156
‐3.25376
‐3.53924
‐3.25894
‐1.90773
1.341179
2.491274
2.648883
3.030242
‐1.61121
‐1.77944
‐1.66011
‐2.17447
‐1.49908
1.637261
1.362165
2.134394
3.964501
2.161062
3.16017
2.529416
3.835314
6.567223
3.575174
1.454411
1.808378
3.901099
3.663932
4.365401
3.56763
2.019765
3.244978
2.583163
2.80562
2.723324
3.11576
2.342176
3.082485
3.478389
3.39195
1.778551
4.324608
1.300689
‐2.43619
3.508376
‐1.43308
‐2.52425
‐2.02339
2.307029
3.224012
2.988814
1.370746
2.781953
2.933237
2.474989
2.50011
3.232734
1.590971
2.097013
2.507112
2.999714
1.613574
‐1.41915
1.410087
2.769479
‐1.71472
‐1.98534
‐2.06565
‐1.59065
‐1.90204
‐2.56919
‐1.94283
‐1.91937
‐2.05333
‐1.8218
‐2.11664
2.145138
1.326272
1.387675
1.707804
‐2.11012
1.500231
2.620717
3.415642
2.904321
2.099254
2.676822
1.764959
4.238075
4.602279
4.3269
1.484227
5.238511
1.475024
‐0.45107
‐0.80811
‐0.4581
‐0.62334
‐0.90609
‐1.21021
‐1.00917
‐0.67501
‐0.38131
‐0.67147
‐0.8056
‐1.01947
‐0.72863
‐0.54845
0.656958
‐0.4824
‐1.49078
‐0.83844
‐1.34307
‐0.70137
‐0.62513
‐0.97222
‐1.14349
‐1.21726
‐0.48274
‐0.5097
‐0.49258
‐1.01871
‐0.61681
‐0.60925
‐0.65436
‐0.7293
‐1.11502
‐0.88533
‐0.94789
‐0.64082
‐0.60094
‐0.78474
‐1.06332
‐0.88584
‐1.18033
‐1.01407
‐1.21373
‐0.7212
0.541251
0.81324
0.753422
0.968438
‐0.54627
‐0.5384
‐0.50999
‐0.75669
‐0.4649
0.45267
0.383567
0.732177
1.952549
0.73069
0.928509
0.767216
1.249992
1.758249
1.095662
0.691685
0.643177
1.132008
1.11749
1.442197
1.441318
0.813042
1.047005
0.883494
1.34842
0.76258
1.092728
0.702026
0.975975
1.181462
0.974594
0.544464
1.483662
0.381865
‐0.85743
1.011719
‐0.38901
‐0.69697
‐0.62672
0.757119
0.945578
0.996409
0.46676
0.990852
0.998386
1.190452
0.686304
1.255057
0.536445
0.792899
0.684675
0.868994
0.528966
‐0.39432
0.444229
1.211548
‐0.49587
‐0.77257
‐0.76845
‐0.48007
‐0.96737
‐0.74176
‐0.64515
‐0.57798
‐0.68865
‐0.52947
‐0.82986
0.909246
0.403085
0.492711
0.660968
‐0.63577
0.965528
0.963696
1.148058
0.963548
0.712739
0.97347
0.532636
1.201707
1.326324
1.376414
0.504103
1.972771
0.423251
0.326501
0.309628
0.271948
0.335742
0.313544
0.365006
0.330018
0.321392
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0.296424
0.339011
0.432273
0.308599
0.341246
0.276803
0.321994
0.345471
0.478825
0.333048
0.28527
0.393376
0.316057
0.312936
0.315737
0.347061
0.310654
0.328767
0.288271
0.318753
0.30155
0.350834
0.284335
0.357679
0.393776
0.345096
0.384577
0.416103
0.285063
0.33679
0.320776
0.362759
0.286522
0.37243
0.37804
0.403563
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0.319591
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0.302569
0.3072
0.347988
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0.343038
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0.306128
0.343074
0.293587
0.351953
0.288372
0.271452
0.276109
0.309735
0.328179
0.293292
0.333379
0.340516
0.356171
0.34037
0.480993
0.274509
0.388234
0.337181
0.378109
0.273093
0.289692
0.327822
0.277859
0.315036
0.437464
0.289185
0.389136
0.372015
0.30181
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STM0449
STM0450
STM0452
STM0456
STM0461
STM0462
STM0463
STM0468
STM0469
STM0470
STM0485
STM0486
STM0488
STM0492
STM0508
STM0513
STM0523
STM0528
STM0542
STM0546
STM0561
STM0562
STM0568
STM0570
STM0583
STM0585
STM0587
STM0592
STM0594
STM0595
STM0596
STM0597
STM0598
STM0599
STM0600
STM0607
STM0617
STM0626
STM0632
STM0643
STM0645
STM0648
STM0655
STM0659
STM0660
STM0661
STM0662
STM0664
STM0665
STM0671
STM0688
STM0689
STM0693
STM0717
STM0718
STM0730
STM0732
STM0733
STM0734
STM0736
STM0737
STM0738
STM0739
STM0748
STM0749
STM0750
STM0772
STM0782
STM0783
STM0795
STM0803
STM0811
STM0812
STM0816
STM0828
STM0829
STM0830
STM0833
STM0837
STM0844
STM0847
STM0862
STM0865
STM0871
STM0873
STM0874
STM0878
STM0887
STM0888
STM0890
STM0892
STM0908
STM0934
STM0937
STM0938
STM0948
STM0954
STM0958
STM0959
STM0965
STM0968
STM0973
STM0974
STM0975
STM0979
STM0981
STM0982
STM0989
STM1009
STM1020
STM1021
STM1026
STM1027
STM1028
STM1032
STM1044
STM1045
STM1059
STM1061
STM1062
STM1064
STM1066
STM1067
STM1068
STM1072
STM1076
STM1077
STM1096
STM1097
STM1098
STM1125
STM1139
STM1140
STM1141
STM1142
STM1145
STM1146
STM1147
specificity component of clpA‐clpP ATP‐dependent serine protease
clpX
DNA‐binding, ATP‐dependent protease la cleaves RcsA and
lon
peptidyl prolyl isomerase
cypD
putative ABC transporter periplasmic binding protein
ybaE
putative ABC superfamily (atp&membrane) transporter
mdlB
regulatory protein, P‐II 2, for nitrogen assimilation
glnK
putative Amt family, ammonium transport protein
amtB
putative diguanylate cyclase/phosphodiesterase domain 2
ylaB
putative 50S ribosomal protein L31 (second copy)
rpmE2
putative 50S ribosomal protein L36 (second copy)
rpmJ2
putative cytoplasmic protein
ybaB
putative recombination protein, gap repair
recR
adenylate kinase
adk
putative CPA2 family transport protein
ybaL
putative inner membrane protein
ybbP
putative ATPase
ybbB
allantoinase
allB
ureidoglycolate dehydrogenase
allD
bifunctional 5,10‐methylene‐tetrahydrofolate dehydrogenase and 5,10‐methylene‐tetrahydr folD
outer membrane usher protein
fimD
Sensor protein
putative transport protein
APC family, phenylalanene transporter
pheP
outer membrane N‐acetyl phenylalanine beta‐naphthyl ester‐cleaving esterase
apeE
putative cytoplasmic protein
ybdK
outer membrane porin, receptor for ferric enterobactin
fepA
putative cytoplasmic protein
ybdZ
ABC superfamily (membrane), ferric enterobactin (enterochelin) transporter
fepD
ABC superfamily (peri_perm), ferric enterobactin (enterochelin) tranporter
fepB
isochorismate synthetase, enterochelin biosynthesis
entC
2,3‐dihydroxybenzoate‐AMP ligase
entE
2,3‐dihydro‐2,3‐dihydroxybenzoate synthetase, isochorismatase
entB
2,3‐dihydro‐2,3‐dihydroxybenzoate dehydrogenase
entA
putative protein PaaI, possibly involved in aromatic
ybdB
carbon starvation protein
cstA
periplasmic disulfide isomerase, thiol‐disulphide oxidase
dsbG
RNase I, cleaves phosphodiester bond between any
rna
response regulator in two‐component regulatory system with
dpiA
putative Sec‐independent protein secretion pathway component
ybeC
alpha ribazole‐5‐P phosphatase in cobalamin synthesis
cobC
putative Nicotinic acid mononucleotide adenylyltransferase
nadD
leucine tRNA synthetase
leuS
putative cytoplasmic protein
ybeR
putative heatshock protein, homolog of hsp70 in
hscC
putative cytoplasmic protein
putative purine nucleoside hydrolase
ybeK
ABC superfamily (atp_bind), glutamate/aspartate transporter
gltL
ABC superfamily (membrane), glutamate/aspartate transporter
gltJ
ABC superfamily (bind_prot), glutamate/aspartate transporter
gltI
putative monooxygenase
ubiF
putative lipoprotein
ybfN
citrate‐proton symporter
citA
transcriptional repressor of iron‐responsive genes (Fur family)
fur
putative inner membrane protein
putative cytoplasmic protein
citrate synthase
gltA
succinate dehydrogenase, cytochrome b556
sdhC
succinate dehydrogenase, hydrophobic subunit
sdhD
succinate dehydrogenase, flavoprotein subunit
sdhA
2‐oxoglutarate dehydrogenase (decarboxylase component)
sucA
2‐oxoglutarate dehydrogenase (dihydrolipoyltranssuccinase E2 component)
sucB
succinyl‐CoA synthetase, beta subunit
sucC
succinyl‐CoA synthetase, alpha subunit
sucD
tol protein required for outer membrane integrity
tolB
tol protein required for outer membrane integrity
pal
putative periplasmic protein
ybgF
phosphoglyceromutase 1
gpmA
ABC superfamily (membrane), molybdate transporter
modB
ABC superfamily (atp_bind), molybdate transporter
modC
7‐keto‐8‐aminopelargonic acid synthetase
bioF
molybdopterin biosynthesis, protein B
moaB
putative negative regulator
ybhN
cardiolipin (CL) synthase
ybhO
putative ABC superfamily (membrane) transport protein
ybhS
ABC superfamily (atp_bind), glutamine high‐affinity transporter
glnQ
ABC superfamily (membrane), glutamine high‐affinity transporter
glnP
ABC superfamily (bind_prot), glutamine high‐affinity transporter
glnH
outer membrane protease, receptor for phage OX2
ompX
putative periplasmic protein
ybiS
putative pyruvate formate lyase activating enzyme
pflE
putative asparaginase
ybiK
putative glutathione S‐transferase
yliJ
putative permease
ybjG
putative inner membrane protein
ybjM
putative inner membrane protein
ybjC
oxygen‐insensitive NADPH nitroreductase
mdaA
ABC superfamily (atp_bind), putrescine transporter
potG
ABC superfamily (bind_prot), arginine 3rd transport system
artJ
ABC superfamily (membrane), arginine 3rd transport system
artM
ABC superfamily (bind_prot), arginine transport system
artI
putative lipoprotein
ybjP
Fels‐1 prophage
L‐allo‐threonine aldolase
ltaA
hybrid cluster protein similar to prismane‐protein homolog
hcp
putative inner membrane protein
ybjE
putative cytoplasmic protein
putative inner membrane protein
thioredoxin reductase
trxB
regulator for lrp regulon and high‐affinity branched‐chain
lrp
anaerobic dimethyl sulfoxide reductase, subunit B
dmsB
putative MFS family transport protein
ycaD
pyruvate formate lyase I, induced anaerobically
pflB
putative FNT family, formate transporter (formate channel
focA
putative cytoplasmic protein
ycaO
putative Zn‐dependent protease with chaperone function
ycaL
30S ribosomal subunit protein S1
rpsA
integration host factor (IHF), beta subunit site‐specific
himD
mukF protein (killing factor KicB)
Gifsy‐2 prophage exodeoxyribonuclease
Gifsy‐2 prophage
Gifsy‐2 prophage
Gifsy‐2 prophage
Gifsy‐2 prophage
Gifsy‐2 prophage lysozyme
Gifsy‐2 prophage
Gifsy‐2 prophage: superoxide dismutase precursor (Cu‐Zn)
sodC
Gifsy‐2 prophage probable minor tail protein
putative cytoplasmic protein
ycbW
putative N6‐adenine‐specific DNA methylase
ycbY
putative ATPase component of ABC transporters with
uup
paraquat‐inducible protein B
pqiB
ribosome modulation factor (involved in dimerization of
rmf
beta‐hydroxydecanoyl thioester dehydrase (trans‐2‐decenoyl‐ACP isomerase)
fabA
putative protease
lonH
putative DNA transformation protein
yccR
methylglyoxal synthase
mgsA
putative periplasmic protein
yccT
Copper resistance transcriptional regulatory protein
copR
putative periplasmic or exported protein
4‐hydroxyphenylacetate catabolism
hpaC
SSS family, major sodium/proline symporter
putP
putative transcriptional regulator in curly assembly/transport, 2nd
csgG
curli production assembly/transport component, 2nd curli operon
csgF
curli production assembly/transport component, 2nd curli operon
csgE
putative transcriptional regulator (LuxR/UhpA family)
csgD
putative curli production protein
csgC
putative periplasmic protein
ymdA
putative ACR related to the C‐terminal domain
152
0.2764029
0.21014813
0.5217175
0.013862575
‐0.4977934
‐2.2110238
‐2.5150805
0.18790144
1.3985962
1.5099168
0.42250806
0.1383543
‐0.55290645
‐0.18466538
‐0.22696888
0.18248695
0.04045679
‐0.27818152
‐0.23547623
‐0.2289422
‐0.16640389
‐0.42998475
‐0.12897126
‐0.37236246
0.136302
0.9580155
1.6586463
‐0.089237794
0.15964195
‐0.041376133
‐0.16569774
‐0.03610212
0.26830655
‐0.037574347
0.006246797
0.5100641
‐0.16996862
‐0.07584326
‐1.1095876
0.028894002
‐0.10901003
0.20801476
0.074464895
‐0.42572558
‐0.20414087
‐0.5770081
‐0.673679
‐0.5555748
‐0.66387933
‐0.3663575
‐0.02801992
‐0.19560848
0.58997774
‐0.12471457
0.23774374
0.6266423
0.008798748
‐0.13162221
‐0.13651139
0.06386573
0.26151693
0.13465412
‐0.05691173
0.09232277
0.4004878
‐0.0552178
0.6452878
‐0.4180693
‐0.15239358
0.32754552
0.29125378
‐0.1731959
‐0.2027896
‐0.121631615
‐0.8392573
‐0.4746565
‐1.635288
0.4758158
‐0.22505845
‐0.30814725
‐0.123217225
0.31162846
‐0.07805403
‐0.16829391
‐0.17905602
0.053176016
‐0.14448799
‐1.4173365
‐0.13690579
0.09460141
0.07022612
‐0.18527438
‐0.30666682
0.13254821
‐0.023494873
‐0.3081
‐0.37670466
0.14916131
‐0.4318177
‐0.44168755
‐0.022586863
‐1.4719023
‐1.2823764
0.19294322
0.004482293
0.1129186
0.0826966
‐0.8264857
‐0.016730106
‐0.053763438
‐0.30851012
‐0.035161383
‐0.136989
0.1707156
0.01930838
‐0.46788502
0.13166812
‐0.020034539
0.021966599
0.009675218
0.44150075
‐1.0369891
0.1901781
0.40872064
‐0.006722272
‐0.40152797
‐0.5581323
‐0.26226795
‐0.41177925
‐0.09466166
‐0.028754672
‐0.7588283
‐0.9241674
‐1.0519996
‐1.3281112
‐1.4600596
‐1.4272671
‐0.7126416
0.25895515
0.16719347
0.37075484
0.17962728
‐0.66604364
‐2.2586772
‐2.587126
‐0.0858201
1.5783657
1.5123256
0.66256225
0.3955859
‐0.41970772
‐0.19477
‐0.2539097
0.098355666
0.105447866
‐0.28702745
‐0.17731822
‐0.026289761
‐0.07622832
‐0.4193589
‐0.002069403
‐0.644741
0.19414575
1.0559162
1.7351841
‐0.25716263
0.25267553
‐0.37923864
‐0.13061993
0.057909448
0.1754265
‐0.11972696
‐0.18393022
0.70760614
‐0.2836915
‐0.08754068
‐1.0312442
‐0.2483012
0.027530616
0.21691012
‐0.022565901
‐0.37190017
‐0.2077432
‐0.5427533
‐1.0342818
‐0.5709684
‐0.76356953
‐0.6821574
0.13353829
‐0.100571804
0.91239756
‐0.103127725
0.40668654
0.619384
0.09971459
‐0.44384727
‐0.20356365
0.10227226
0.40387812
‐0.09066245
0.06843569
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‐4.17707
1.371388
‐2.01538
1.402844
‐2.77622
‐1.63159
‐1.59983
‐1.6569
1.376686
2.730687
‐3.56155
‐1.5809
‐3.1604
‐1.59821
‐2.51926
2.469304
‐1.66729
‐2.737
‐1.51081
2.231939
2.329099
1.9852
‐3.05401
‐1.39494
‐10.644
‐7.45239
1.525848
2.310902
1.60857
‐1.88694
‐1.54055
‐1.64337
‐1.49637
‐2.67527
‐1.79416
‐3.80702
‐3.1934
‐1.88827
‐4.59009
‐1.49097
‐2.21213
1.824976
1.745266
2.04436
‐5.48301
1.428523
1.944574
‐1.57322
‐2.44279
‐2.18157
‐1.89599
‐4.84312
‐2.9873
2.345891
‐4.49439
‐7.97367
‐6.89538
‐5.81757
‐4.68393
‐3.21386
‐2.21652
0.492511
0.49426
0.630057
‐0.58131
‐0.68769
‐2.6136
‐3.02337
‐0.65326
‐3.22363
‐3.77502
1.149455
1.426275
0.511157
0.619314
0.633204
0.577897
‐0.41394
‐0.46029
‐0.51653
‐0.43301
‐0.80487
‐0.75118
0.422959
0.784815
1.222761
0.979451
0.73874
1.63966
0.742317
0.49244
0.986745
1.054377
1.15626
0.9719
1.486009
0.671054
‐0.57393
‐0.5024
‐1.50897
‐0.77595
‐0.53305
0.748672
‐0.46788
‐0.43584
‐0.41092
‐0.426
‐0.81412
‐0.74995
‐1.62504
1.106023
‐0.45548
‐0.4595
0.83574
‐0.60669
‐0.53894
1.598356
1.072875
0.923936
1.55092
1.756607
2.302128
2.040118
1.630101
1.040664
1.38497
0.82329
‐0.84314
1.089789
0.676467
1.644842
‐0.9501
‐0.49871
‐0.56537
‐0.67764
‐0.46397
‐0.66094
‐1.77928
‐1.2563
0.691401
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0.524833
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0.363785
0.726847
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0.741727
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0.693682
0.69804
0.779302
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‐3.52738
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0.485254
0.76447
0.520861
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STM1148
STM1150
STM1155
STM1164
STM1165
STM1166
STM1174
STM1176
STM1178
STM1179
STM1180
STM1181
STM1183
STM1185
STM1190
STM1194
STM1195
STM1214
STM1220
STM1228
STM1232
STM1238
STM1254
STM1261
STM1263
STM1274
STM1285
STM1290
STM1295
STM1304
STM1305
STM1310
STM1320
STM1324
STM1325
STM1326
STM1342
STM1345
STM1348
STM1350
STM1353
STM1354
STM1367
STM1370
STM1373
STM1374
STM1375
STM1388
STM1391
STM1398
STM1400
STM1402
STM1404
STM1405
STM1407
STM1409
STM1410
STM1411
STM1412
STM1413
STM1419
STM1427
STM1428
STM1449
STM1451
STM1452
STM1456
STM1467
STM1471
STM1472
STM1477
STM1478
STM1485
STM1486
STM1489
STM1495
STM1496
STM1497
STM1500
STM1501
STM1504
STM1507
STM1509
STM1528
STM1532
STM1533
STM1534
STM1536
STM1537
STM1539
STM1546
STM1549
STM1556
STM1558
STM1559
STM1565
STM1571
STM1582
STM1585
STM1588
STM1606
STM1612
STM1613
STM1614
STM1615
STM1616
STM1617
STM1627
STM1632
STM1638
STM1639
STM1642
STM1647
STM1649
STM1660
STM1663
STM1672
STM1676
STM1680
STM1682
STM1686
STM1690
STM1692
STM1697
STM1702
STM1714
STM1726
STM1746
STM1749
STM1754
STM1761
STM1780
STM1784
STM1785
STM1792
STM1793
STM1797
STM1802
putative phospholipase
periplasmic glucans biosynthesis protein
lauroyl/myristoyl acyltransferase involved in lipid A biosynthesis
putative outer membrane lipoprotein
glutaredoxin 2
putative MFS superfamily transport protein
flagellar biosynthesis, cell‐proximal portion of basal‐body rod
flagellar biosynthesis, initiation of hook assembly
flagellar biosynthesis, cell‐proximal portion of basal‐body rod
flagellar biosynthesis, cell‐distal portion of basal‐body rod
flagellar biosynthesis, basal‐body outer‐membrane L (lipopolysaccharide layer)
putative flagella basal body protein
flagellar biosynthesis, hook‐filament junction protein 1
RNase E
putative metal‐binding
malonyl‐CoA‐[acyl‐carrier‐protein] transacylase
3‐oxoacyl‐[acyl‐carrier‐protein] reductase
putative outer membrane protein
putative regulator (NagC/XylR family)
putative periplasmic protein
adenylosuccinate lyase
isocitrate dehydrogenase in e14 prophage, specific for
putative outer membrane lipoprotein
putative cytoplasmic protein
putative periplasmic protein
putative inner membrane protein
putative Ser protein kinase
glyceraldehyde‐3‐phosphate dehydrogenase A
protease IV, a signal peptide peptidase
arginine succinyltransferase
succinylglutamic semialdehyde dehydrogenase
NAD synthetase, prefers NH3 over glutamine
part of a kinase, putative domain shared
putative cytoplasmic protein
putative cytoplasmic protein
6‐phosphofructokinase II
ABC superfamily (binding protein), vitamin B12 transport
putative cytoplasmic protein
putative inner membrane protein
Homolog of a plant pathogenicity factor
putative electron transfer flavoprotein
putative electron transfer flavoprotein
putative cytoplasmic protein
putative ABC transporter
selenocysteine lyase
putative SufE protein probably involved in Fe‐S
putative LysM domain
putative cytoplasmic protein
Secretion system regulator: transcriptonal activator, homologous with
Secretion system effector
Secretion system effector
Secretion system effector
Secretion system effector
Secretion system effector
Secretion system apparatus
Secretion system apparatus: homology with the yscJ/mxiJ/prgK
putative cytoplasmic protein
Secretion system apparatus
Secretion system apparatus
Secretion system apparatus
Secretion system apparatus: homology with YscR of
cyclopropane fatty acyl phospholipid synthase
putative MFS family transport protein
tyrosine tRNA synthetase
glutathionine S‐transferase
putative POT family, peptide transport protein
putative oxidoreductase
mannose‐6‐phosphate isomerase
sensory histidine kinase in two‐component regulatory system
putative periplasmic protein
putative amino acid transporter
putative periplasmic protein
acid shock protein
putative MFS familty transport protein
putative dethiobiotin synthase
putative component of anaerobic dehydrogenases
putative dimethylsulfoxide reductase
putative dimethyl sulphoxide reductase
putative outer membrane protein
putative inner membrane lipoprotein
putative inner membrane lipoprotein
putative transport protein
putative cytoplasmic protein
putative outer membrane protein
putative dehydrogenase protein
putative hydrogenase
putative hydrogenase
putative hydrogenase maturation protease
putative Ni/Fe‐hydrogenase 1 b‐type cytochrome subunit
putative hydrogenase‐1 small subunit
putative monooxygenase
putative translation initiation inhibitor
putative Na /H antiporter
putative glycosyl hydrolase
putative glycosyl hydrolase
30S ribosomal subunit protein S22
putative permease
putative arylamine N‐acetyltransferase
putative outer membrane lipoprotein
putative regulatory protein, gntR family
putative benzoate membrane transport protein
putative cellulase protein
putative PTS system, enzymeIIB component
putative PTS system enzyme IIC component
putative nucleoside triphosphatase
putative Sugar Specific PTS Enzyme II
putative ribulose‐phosphate 3‐epimerase
alcohol dehydrogenase class III
putative inner membrane protein
putative SAM‐dependent methyltransferases
cytochrome b(561)
acyl carrier protein phosphodiesterase
fermentative D‐lactate dehydrogenase, NAD‐dependent
putative cytoplasmic protein
transcriptional regulation of aerobic, anaerobic respiration, osmotic
putative integral membrane protein
putative cytoplasmic protein
putative aldo/keto reductase family
putative carboxypeptidase
thiol peroxidase
phage shock protein
phage shock protein negative regulatory gene for
ABC superfamily (periplasm), peptide transport protein
putative Diguanylate cyclase/phosphodiesterase domain 2
RNase II, mRNA degradation
DNA topoisomerase type I, omega protein
tryptophan synthase, beta protein
ABC superfamily (periplasm), oligopeptide transport protein with
iron‐dependent alcohol dehydrogenase of the multifunctional alcohol
putative phosphoesterase
nitrate reductase 1, cytochrome b(NR), gamma subunit
phosphoribosylpyrophosphate synthetase
putative GTP‐binding protein
putative cytoplasmic protein
putative cytochrome oxidase, subunit I
putative cytochrome oxidase, subunit II
putative transglycosylase‐associated protein
alanine racemase 2, catabolic
ymdC
mdoG
htrB
yceB
grxB
yceL
flgB
flgD
flgF
flgG
flgH
flgI
flgK
rne
yceD
fabD
fabG
ycfR
ycfX
purB
icdA
yeaQ
yeaG
gapA
sppA
astA
astD
nadE
ydjN
ydiZ
pfkB
btuD
ydiU
ydiA
ydiD
ydiR
ydiQ
ydiH
sufB
sufS
ynhA
ynhG
orf70
ssrB
sseB
sseC
sseE
sseF
sseG
ssaH
ssaJ
ssaK
ssaL
ssaM
ssaR
cfa
ydhC
tyrS
gst
ydgR
ydgO
manA
rstB
ydgI
ydgH
ynfM
ynfK
ynfI
ynfD
ynfC
ynfA
ydfJ
ydfZ
rpsV
yddG
nhoA
yncC
cybB
acpD
ldhA
fnr
ynaI
ycjI
tpx
pspE
pspA
sapA
rnb
topA
trpB
oppA
adhE
ychK
narI
prsA
ychF
ymgE
dadX
153
0.054068517
0.5415282
‐0.1604228
0.029775366
0.16463952
‐0.20057508
‐0.24398626
‐0.31164765
‐0.5251709
‐0.41774648
‐0.24669611
‐0.324302
‐0.23739685
0.02921594
0.21810497
0.117961995
0.15777712
‐0.47596112
0.058407985
‐0.005889685
‐0.31009138
0.33846152
0.015791897
0.27194655
2.2810953
0.65378964
0.68933046
0.03538778
‐0.2943676
‐0.44366714
‐0.24514297
0.29985374
0.046802618
0.095578276
0.15465511
0.13333306
‐0.080898724
1.1109093
‐0.008475127
‐0.37968674
‐0.21897374
‐0.17257172
‐1.1607132
1.8288628
1.0143319
0.6949266
0.2030428
0.09683996
‐0.045912962
‐1.6741128
‐0.89993477
‐0.7404304
‐0.08034967
‐0.18586467
‐2.5226486
‐1.745902
‐1.2823895
‐1.212782
‐1.1971893
‐0.77967024
‐2.10759
0.53838634
‐0.086790815
0.14966837
0.41312236
‐0.08561341
‐0.18982045
0.09934974
‐0.23468739
0.001483276
‐0.3116799
0.36855495
‐0.055210296
‐0.23127855
‐1.1623932
‐0.19872937
‐0.3685398
‐0.3500527
‐0.2840113
‐0.12229592
‐0.13590805
‐0.15804242
‐1.3511477
‐0.12595634
‐0.15376502
0.06782231
‐0.13515557
‐0.18552598
‐0.2032689
‐0.21789321
0.20372333
0.106838144
‐0.007203043
‐0.089331925
‐0.034019895
‐0.42334127
0.09303354
0.09087757
‐0.08836462
‐0.23514542
‐0.2536418
‐0.52231705
‐0.3519927
‐0.33452767
‐0.2504369
‐0.5471751
‐0.19925678
0.3018156
0.10058872
0.011606389
‐0.010859509
‐0.10919571
‐0.102360666
‐0.19018997
0.2812335
‐0.007718208
0.08616393
‐0.031380136
‐0.14750583
0.6041635
‐0.24195158
‐0.15976194
‐0.1263535
0.27374637
0.24852581
0.13929856
0.6247902
0.10556983
‐0.94126964
0.47854376
‐0.17575248
‐0.30122158
0.1969354
0.057605747
‐0.004706493
‐0.20705564
‐0.074945815
0.093311004
‐0.108016655
0.7216828
‐0.2713051
0.071547635
0.15097828
‐0.13999118
‐0.15891434
‐0.12191109
‐0.5935623
‐0.40301433
‐0.45819262
‐0.2887586
‐0.2801575
‐0.18947308
0.16459917
‐0.1920138
‐0.012130227
‐0.44852042
‐0.1285463
0.13874896
0.03655681
0.38819313
0.26073694
0.56820977
2.2803102
0.6692242
0.7587421
‐0.07432849
‐0.45289037
‐0.64911693
‐0.41127566
0.38263682
0.038091604
0.12058025
‐0.029846352
0.20857969
0.021437347
1.4927708
‐0.11085564
‐0.02649557
‐0.20456798
0.07833293
‐1.217718
1.8384182
0.8581476
0.8367215
0.0627239
0.281905
‐0.07884433
‐1.4779617
‐0.95905095
‐0.5855545
0.07565084
‐0.16700755
‐2.480366
‐1.4621507
‐1.324541
‐0.865683
‐1.7317013
‐0.8322191
‐2.092133
0.5852242
‐0.105173916
‐0.02462159
0.4460167
‐0.09977127
‐0.3831436
‐0.06953407
‐0.255906
‐0.023751773
‐0.013351898
0.3679174
‐0.093497545
‐0.39081946
‐1.1485412
‐0.3369662
‐0.37358811
‐0.55640876
‐0.157557
‐0.09390689
‐0.23647597
‐0.15857194
‐1.210879
‐0.35776296
‐0.10208606
0.15546015
‐0.0418269
‐0.20655942
‐0.21031234
‐0.033842675
0.10701732
0.20268254
‐0.08502233
‐0.06959273
0.005380407
‐0.596213
‐0.12684515
0.17604361
0.099436425
0.041621055
‐0.32784393
‐0.7856752
‐0.3795157
‐0.6439114
‐0.39927378
‐0.6508115
‐0.1544576
‐0.007162598
0.031953044
‐0.004490397
0.120846935
0.041565914
‐0.05225767
‐0.399026
0.39288732
‐0.10974138
0.109365046
0.16731921
‐0.27840137
0.75391585
‐0.2239119
‐0.010411385
‐0.25867128
0.016170513
‐0.061163615
0.12498835
0.7092721
0.14339177
‐1.0152637
0.34373415
‐0.091930225
‐0.27414304
0.21479593
0.08438086
‐0.24098572
‐0.40138167
‐0.18277146
0.06541252
‐0.14861533
0.53028905
‐0.18319903
0.09752407
0.095054746
‐0.28870073
‐0.31864962
‐0.23948023
‐0.70547336
‐0.46112373
‐0.36717805
‐0.2424051
‐0.27900034
‐0.11561472
0.14148992
‐0.18482763
‐0.04840321
‐0.3523592
0.007555843
‐0.04143879
‐0.25444815
0.34394217
0.26242307
0.43828702
2.2510886
0.8762841
0.6440396
‐0.23907097
‐0.39618397
‐0.6599875
‐0.3780378
0.37407726
0.03691275
0.19640777
0.17462827
0.32062015
‐0.019437123
1.3023136
0.00335303
‐0.23027726
0.048657984
‐0.08649514
‐0.95250094
1.7571864
0.9030303
0.78655946
0.10129302
0.21109246
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‐1.5637157
‐0.6318036
‐0.44367382
0.06725627
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‐2.4565828
‐1.4960818
‐1.2172247
‐0.86629224
‐1.5377116
‐0.78975403
‐1.865195
0.549235
‐0.39397734
‐0.093539745
0.54826
‐0.048650537
‐0.35884932
0.16549467
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‐0.1438854
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0.36575988
0.034639798
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‐0.97866875
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‐0.81715876
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‐0.04879934
0.13181192
0.0409649
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‐0.21605578
0.15740846
0.22907755
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0.007884459
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0.14440401
0.06889076
0.023392105
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‐0.7000317
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‐0.5593485
‐0.69132197
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0.2390924
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‐0.60621
0.354729
0.300824
0.269805
0.287693
0.399047
0.334619
0.329758
0.382854
0.291249
0.30136
0.469929
0.291652
0.302015
0.332887
0.435091
0.325342
0.309585
0.271519
0.404106
0.288988
0.307332
0.339664
0.377379
0.351898
0.451343
0.333271
0.286105
0.300628
0.257791
0.3143
0.286578
0.274779
0.349171
0.37551
0.302832
0.282208
0.321142
0.265413
0.299173
0.279486
0.276683
0.317178
0.294322
0.301641
0.325023
0.268594
0.461002
0.462172
0.324872
0.301998
0.292584
0.355435
0.334852
0.282859
0.303382
0.292616
0.335586
0.290298
0.402688
0.422761
0.397905
0.501093
0.272299
0.285221
0.293271
0.323646
0.289587
0.263063
0.280127
0.285185
0.409882
0.294337
0.321937
0.308144
0.328814
0.290874
0.284125
0.370282
0.297634
0.286465
0.29751
0.312853
0.296706
0.28987
0.335876
0.348102
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0.307829
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STM1814
STM1821
STM1829
STM1838
STM1840
STM1844
STM1845
STM1846
STM1849
STM1851
STM1852
STM1863
STM1864
STM1874
STM1878
STM1879
STM1888
STM1890
STM1891
STM1892
STM1893
STM1894
STM1897
STM1902
STM1904
STM1916
STM1917
STM1919
STM1920
STM1921
STM1922
STM1926
STM1927
STM1932
STM1936
STM1953
STM1956
STM1958
STM1959
STM1960
STM1970
STM1975
STM1979
STM1980
STM1990
STM1996
STM2001
STM2006
STM2011
STM2021
STM2023
STM2024
STM2031
STM2035
STM2039
STM2059
STM2063
STM2070
STM2073
STM2079
STM2080
STM2082
STM2083
STM2087
STM2090
STM2091
STM2096
STM2117
STM2130
STM2139
STM2140
STM2148
STM2194
STM2199
STM2200
STM2203
STM2214
STM2217
STM2223
STM2236
STM2237
STM2267
STM2272
STM2280
STM2299
STM2300
STM2304
STM2318
STM2320
STM2321
STM2323
STM2324
STM2326
STM2328
STM2331
STM2333
STM2337
STM2338
STM2341
STM2347
STM2354
STM2355
STM2362
STM2363
STM2366
STM2368
STM2369
STM2372
STM2390
STM2392
STM2424
STM2428
STM2430
STM2432
STM2442
STM2443
STM2467
STM2472
STM2499
STM2500
STM2501
STM2506
STM2510
STM2512
STM2521
STM2522
STM2523
STM2536
STM2538
STM2540
STM2543
STM2544
STM2549
STM2551
STM2552
STM2553
STM2555
STM2571
cell division inhibitor activated MinC inhibits FtsZ
putative DNA helicase
putative cytoplasmic protein
putative cytoplasmic protein
putative inner membrane protein
heat shock protein, integral membrane protein
carboxy‐terminal protease for penicillin‐binding protein 3
activator of proP
putative inner membrane protein
putative cytoplasmic protein
putative inner membrane lipoprotein
putative inner membrane protein
putative inner membrane protein
putative inner membrane protein
DNA exonuclease X, degrades ss and ds
protease II
pyruvate kinase II, glucose stimulated
putative Peptidase
ABC superfamily (bind_prot) high affinity Zn transport
ABC superfamily (atp_bind) high affinity Zn transport
ABC superfamily (atp_bind) high affinity Zn transport
Holliday junction helicase, subunit B
putative periplasmic protein
putative isochorismatase
putative inner membrane protein
chemotaxis regulator, transmits chemoreceptor signals to flagelllar
methyl esterase, response regulator for chemotaxis (cheA
methyl accepting chemotaxis protein II, aspartate sensor‐receptor
purine‐binding chemotaxis protein regulation
sensory histitine protein kinase, transduces signal between
enables flagellar motor rotation, linking torque machinery
putative cytoplasmic protein
putative universal stress protein
ferritin‐like protein
putative cytoplasmic protein
putative 1‐cyclopropane‐carboxylate deaminase
sigma F (sigma 28) factor of RNA
N‐methylation of lysine residues in flagellin
flagellar biosynthesis flagellin, filament structural protein
flagellar biosynthesis filament capping protein
flagellar biosynthesis, component of motor switching and
flagellar biosynthesis
flagellar biosynthesis
flagellar biosynthesis
putative permease
putative cold‐shock protein
putative inner membrane protein
putative branched chain amino acid transport protein
putative cytoplasmic protein
synthesis of vitamin B12 adenosyl cobalamide precursor
synthesis of vitamin B12 adenosyl cobalamide precursor
synthesis of vitamin B12 adenosyl cobalamide precursor
synthesis of vitamin B12 adenosyl cobalamide precursor
synthesis of vitamin B12 adenosyl cobalamide precursor
Propanediol utilization: polyhedral bodies
putative cytoplasmic protein
Hydrogen sulfide production: membrane anchoring protein
putative dehydratase
histidinol phosphate aminotransferase
regulator of length of O‐antigen component of
UDP‐glucose/GDP‐mannose dehydrogenase
LPS side chain defect: bifunctional enzyme: undecaprenol‐phosphate
LPS side chain defect: phosphomannomutase
LPS side chain defect: abequosyltransferase
LPS side chain defect: CDP‐6deoxy‐D‐xylo‐4‐hexulose‐3‐dehydrase
LPS side chain defect: CDP glucose 4,6‐dehydratase
TDP‐rhamnose synthetase
putative protein‐tyrosine‐phosphatase in colanic acid export
sensory kinase in two‐component regulatoyr system wtih
putative inner membrane protein
putative diacylglycerol kinase catalytic domain
putative periplasmic protein
putative esterase
outer membrane porin, receptor for colicin I
APC family, lysine‐specific permease
endonuclease IV
putative lipoprotein, suppresses thermosensitivity of prc mutants
putative ABC‐type dipeptide/oligopeptide/nickel transport systems, permease component
putative ATP‐dependent helicase
putative phage protein
putative inner membrane protein
outer membrane protein 1b (ibc), porin
DNA gyrase, subunit A, type II topoisomerase
putative permease
paral putative transformylase
putative cytoplasmic protein
polymyxin resistance protein B
NADH dehydrogenase I chain L
NADH dehydrogenase I chain J
NADH dehydrogenase I chain I
NADH dehydrogenase I chain G
NADH dehydrogenase I chain F
NADH dehydrogenase I chain C,D
NADH dehydrogenase I chain A
putative aminotransferase (ortho), paral putative regulator
putative response regulator
acetate kinase A (propionate kinase 2)
phosphotransacetylase
putative transketolase
putative phosphoesterase
ABC superfamily (bind_prot), histidine transport protein
ABC superfamily (bind_prot), lysine/arginine/ornithine transport protein
amidophosphoribosyltransferase (PRPP amidotransferase)
membrane protein required for colicin V production
acetylCoA carboxylase, beta subunit
pseudouridylate synthase I
putative aspartate‐semialdehyde dehydrogenase
putative transport protein
putative cytoplasmic protein
lipoprotein precursor
putative transcriptional regulator, LysR family
cell division protein involved in FtsZ ring
subunit of cysteine synthase A and O‐acetylserine
General PTS family (Enzyme I) PEP‐protein phosphotransferase
ABC superfamily (membrane), thiosulfate permease W protein
ABC superfamily (membrane), thiosulfate transport protein
putative cobalamin adenosyltransferase, ethanolamine utilization
paral putative transferase
phosphoribosylaminoimidazole synthetase (AIR synthetase)
polyphosphate kinase, component of RNA degradosome
polyphosphate kinase, component of RNA degradosome
putative inner membrane protein
GMP synthetase
exonuclease VII, large subunit
putative inner membrane protein
histidine tRNA synthetase
putative protein, involved in density‐dependent regulation of
putative aminopeptidase
[2FE‐2S] ferredoxin, electron carrer protein, believed to
co‐chaperone protein Hsc20, believed to be involved
putative aminotransferase class‐V
believed to be involved in assembly of
anaerobic sulfide reductase
putative inner membrane protein
putative periplasmic or exported protein
stationary phase inducible protein
serine hydroxymethyltransferase
putative aminotransferase
minC
yoaA
yobF
yobG
htpX
prc
proQ
yebW
exoX
ptrB
pykA
yebA
znuA
znuC
zunB
ruvB
yebB
yecD
yecN
cheY
cheB
cheM
cheW
cheA
motB
yecG
ftnB
yecH
yedO
fliA
fliB
fliC
fliD
fliG
fliL
fliP
fliQ
yedA
cspB
yeeI
cboQ
cbiM
cbiL
cbiE
cbiA
pudB
yeeX
phsC
yeeZ
hisC
wzzB
udg
rfbP
rfbK
rfbV
rfbH
rfbG
rfbD
wzb
baeS
yegS
yeiG
cirA
lysP
nfo
spr
yejB
yejH
ompC
gyrA
yfbG
pmrD
nuoL
nuoJ
nuoI
nuoG
nuoF
nuoC
nuoA
yfbQ
yfbS
ackA
pta
yfcE
hisJ
argT
purF
cvpA
accD
truA
usg
yfcZ
vacJ
yfeR
zipA
cysK
ptsI
cysW
cysU
eutT
maeB
purM
purN
ppk
guaA
xseA
yfgM
hisS
gcpE
pepB
fdx
hscB
nifS
yfhP
asrB
csiE
glyA
154
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‐0.26884434
‐0.30826873
‐0.582477
0.069191605
0.23165391
0.07755703
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‐0.18065819
0.1864297
0.27213326
0.14664434
0.1810388
0.4198059
‐0.45786908
0.7314299
1.3631965
0.25144094
‐0.03187781
‐0.14616849
‐0.2446566
‐0.3656827
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‐0.38359508
0.021205017
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‐0.16131973
0.106536426
‐0.05808545
‐0.19881563
0.046041377
‐0.14805304
‐0.39661565
0.14875863
0.31583518
0.1414723
0.39477825
0.046875205
‐0.33502188
‐0.15826781
‐0.020009601
0.017453767
‐0.28627598
0.18569529
0.07780213
‐0.102783434
‐0.29447466
0.026401527
‐0.18780291
‐0.36653033
‐0.37218127
‐0.12346863
‐0.60162073
0.32313725
‐0.08552289
0.32365817
0.6341258
0.25764465
0.014545129
‐0.18199804
0.4056601
0.98017097
0.51607764
0.29437086
0.26496527
‐0.14169501
‐0.23525706
‐1.4245783
0.26698622
0.7350009
0.054421656
0.42267513
0.05140927
‐0.045610104
0.01517154
‐0.05366419
‐0.34153134
0.18049029
‐0.014838871
‐0.3649795
0.080137804
0.03252856
‐0.033254035
0.06925537
‐0.2081248
‐0.8575317
‐0.6258309
‐0.39599353
‐0.55333656
‐0.76764554
‐0.90607184
‐0.5014692
0.10471456
‐0.061281778
‐0.39079365
‐0.4616236
‐0.018777054
0.5325464
‐0.5936473
‐1.400604
0.54774284
‐0.1076371
0.22395338
0.016327815
0.15879549
‐0.19344439
‐1.0053508
0.08148945
‐0.049995497
0.45122093
0.6733387
0.5854015
0.06484899
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0.31660816
‐0.19817394
‐0.061437722
0.15320905
0.22724605
0.45461294
0.22466974
0.38129607
0.3655798
0.65346134
‐0.040686227
‐0.10597995
0.20873909
0.2126126
1.9767494
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‐0.50833637
‐0.37134042
‐0.40518212
0.64363766
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0.22262585
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‐0.42344797
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‐0.57865244
0.1054979
0.09220145
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‐0.35991398
‐0.2861385
0.036686923
0.19440068
0.100961916
0.105976425
0.152566
‐0.6001217
0.6941771
1.3828597
0.24517128
‐0.2856091
‐0.3093324
0.04280575
‐0.36847875
‐0.07851224
‐0.43315798
‐0.5573388
‐0.3472248
‐0.58123994
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0.093669176
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0.043752573
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0.06791354
0.053942945
0.3278289
0.5807938
0.07710468
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0.30097237
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0.058238026
0.039250746
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‐0.6262743
0.3182445
0.07946232
0.16975561
0.4897871
0.44832304
0.05432841
‐0.16203153
0.53315276
0.9868867
0.44115597
0.305522
0.15737686
‐0.63931817
‐0.30325264
‐1.4444654
0.18609942
0.5211285
‐0.03454032
0.34250376
‐0.116212964
‐0.075764045
0.048784353
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0.2621859
0.058021955
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0.0748521
0.16715702
0.018600065
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0.2414636
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0.003586193
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0.4313549
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0.32291824
0.6188528
0.41560653
0.0624721
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0.631907
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0.14973487
0.039916545
0.50390565
0.2103931
0.30712685
0.28132844
0.19456767
‐0.12126932
‐0.17619285
0.013661562
0.37317967
1.9268703
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0.55979085
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0.16397606
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1.453435
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1.1776893
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0.92301166
1.0111129
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0.9858371
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1.9648407
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STM2582
STM2583
STM2600
STM2601
STM2602
STM2604
STM2605
STM2613
STM2625
STM2626
STM2629
STM2637
STM2638
STM2646
STM2647
STM2648
STM2663
STM2665
STM2667
STM2669
STM2670
STM2674
STM2678
STM2681
STM2692
STM2746
STM2771
STM2774
STM2775
STM2776
STM2779
STM2780
STM2784
STM2799
STM2800
STM2803
STM2806
STM2807
STM2810
STM2811
STM2817
STM2818
STM2820
STM2827
STM2829
STM2830
STM2838
STM2843
STM2846
STM2854
STM2855
STM2856
STM2857
STM2858
STM2861
STM2862
STM2863
STM2864
STM2911
STM2922
STM2924
STM2925
STM2928
STM2934
STM2935
STM2938
STM2948
STM2951
STM2952
STM2953
STM2963
STM2985
STM2992
STM3001
STM3002
STM3003
STM3040
STM3041
STM3047
STM3049
STM3058
STM3063
STM3066
STM3068
STM3069
STM3073
STM3086
STM3099
STM3109
STM3115
STM3120
STM3180
STM3189
STM3195
STM3200
STM3202
STM3203
STM3208
STM3209
STM3211
STM3221
STM3223
STM3225
STM3250
STM3255
STM3261
STM3265
STM3280
STM3282
STM3285
STM3286
STM3288
STM3293
STM3296
STM3303
STM3304
STM3307
STM3310
STM3318
STM3319
STM3330
STM3331
STM3333
STM3341
STM3344
STM3345
STM3346
STM3347
STM3348
STM3370
STM3372
STM3374
STM3377
STM3379
STM3380
STM3403
STM3407
STM3414
leader peptidase (signal peptidase I), serine protease
lepB
GTP‐binding elongation factor
lepA
Gifsy‐1 prophage: similar to minor tail protein
Gifsy‐1 prophage: similar to minor capsid protein
Gifsy‐1 prophage: similar to DNA packaging protein
Gifsy‐1 prophage: similar to head protein gpshp
Gifsy‐1 prophage: similar to head‐tail preconnector gp5
Gifsy‐1 prophage
Gifsy‐1 prophage: similar to dnaC Homolog in
Gifsy‐1 prophage: similar to replication protein 15
Gifsy‐1 prophage
regulator of sigma E (sigma 24) factor
rseC
anti sigma E (sigma 24) factor, negative
rseB
putative formate acetyltransferase
yfiD
uracil‐DNA‐glycosylase
ung
putative tRNA/rRNA methyltransferase
yfiF
putative lipoprotein
yfiO
ribosome associated factor, stabilizes ribosomes against dissociation
yfiA
bifuctional: chorismate mutase P prephenate dehydratase
pheA
bifunctional: chorismate mutase T prephenate dehydrogenase
tyrA
3‐deoxy‐D‐arabinoheptulosonate‐7‐phosphate synthase (DAHP synthetase), tyrosine repress aroF
tRNA (guanine‐7‐)‐methyltransferase
trmD
putative cytochrome c‐type biogenesis protein (heme exporter
corE
molecular chaparone heat shock protein
grpE
putative HlyD family secretion protein
putative Excinuclease ATPase subunit
Flagellar synthesis: phase 2 flagellin (filament structural
fljB
putative ATP binding cassette (ABC) transporter
iroC
Similar to enterochelin esterase of E. coli
iroD
putative hydrolase of the alpha/beta superfamily
iroE
putative inner membrane protein
Homolog of pipB, putative pentapeptide repeats (8
tricarboxylic transport: regulatory protein
tctE
DNA‐binding protein with chaperone activity
stpA
putative inner membrane protein
putative regulatory protein, gntR family
stimulates ribonucleotide reduction
nrdI
ribonucleoside diphosphate reductase 2, alpha subunit
nrdE
ABC superfamily (membrane), glycine/betaine/proline transport protein
proW
ABC superfamily (bind_prot), glycine/betaine/proline transport protein
proX
quorum sensing protein, produces autoinducer ‐ acyl‐homoserine
luxS
gamma‐glutamate‐cysteine ligase
gshA
putative phosphoglucomutase
yqaB
alanyl‐tRNA synthetase
alaS
DNA strand exchange and recombination protein with
recA
putative cytoplasmic protein
ygaD
putative polysialic acid capsule expression protein
gutQ
electron transport protein (FeS senter) from formate
hydN
processing of HycE (part of the FHL
hycH
guanine‐nucleotide binding protein in formate‐hydrogenlyase system, functions
hypA
hydrogenase‐3 accessory protein, assembly of metallocenter
hypB
putative hydrogenase expression/formation protein
hypC
putative hydrogenase expression/formation protein
hypD
putative hydrogenase expression/formation protein
hypE
Salmonella iron transporter: fur regulated
sitA
Salmonella iron transporter: fur regulated
sitB
Salmonella iron transporter: fur regulated
sitC
Salmonella iron transporter: fur regulated
sitD
putative permease
putative 3‐polyprenyl‐4‐hydroxybenzoate decarboxylase and related decarboxylase
sigma S (sigma 38) factor of RNA
rpoS
lipoprotein
nlpD
paral putative hydrogenase subunit
ygbO
ATP‐sulfurylase, subunit 1 (ATP:sulfate adenylyltransferase)
cysN
ATP‐sulfurylase, subunit 1 (ATP:sulfate adenylyltransferase)
cysD
putative cytoplasmic protein
sulfite reductase, beta (flavoprotein) subunit
cysJ
putative Organic radical activating enzymes
ygcF
enolase
eno
CTP synthetase
pyrG
putative MFS superfamily, D‐glucarate permease
putative SufE protein probably involved in Fe‐S
ygdK
N‐alpha‐acetylglutamate synthase (amino‐acid acetyltransferase)
argA
thymidylate synthetase
thyA
phosphatidylglycerol‐prolipoprotein diacylglyceryl transferase
lgt
General PTS system, enzyme I, transcriptional regulator
ptsP
lysine tRNA synthetase, constitutive
lysS
peptide chain release factor RF‐2
prfB
putative cytoplasmic protein
ygfY
putative hemolysin
yqfA
proline aminopeptidase P II
pepP
ribosephosphate isomerase, constitutive
rpiA
putative LYSE family, amino acid transport protein
yggA
fructose‐bisphosphate aldolase
fba
phosphoglycerate kinase
pgk
putative ABC‐type cobalt transport system, permease component
arginine decarboxylase
speA
putative protein transport
yggR
putative S‐adenosylmethionine‐dependent methyltransferase
yggH
putative inner membrane protein
yqgA
putative transcriptional regulator, LysR family
putative cytoplasmic protein
ygiN
ygiD
putative cytoplasmic protein
3,4 dihydroxy‐2‐butanone‐4‐phosphate synthase
ribB
bifunctional putative sugar nucleotide transferase domain of
rfaE
putative cytoplasmic protein
ygiF
putative SH3 domain protein
ygiM
putative O‐sialoglycoprotein endopeptidase
gcp
30S ribosomal subunit protein S21
rpsU
sigma D (sigma 70) factor of RNA
rpoD
putative metal‐dependent hydrolase
ygjP
putative dehydrogenase
ygjR
putative dicarboxylate permease
ygjU
galactarate dehydrogenase
garD
putative phosphotransferase system fructose‐specific component IIB
galactitol‐1‐phosphate dehydrogenase
putative endonuclease
yraN
cysteine sulfinate desulfinase
deaD
polynucleotide phosphorylase, member of mRNA degradosome
pnp
ribosome‐binding factor, role in processing of 10S
rbfA
protein chain initiation factor IF‐2
infB
putative cytoplasmic protein
yhbC
preprotein translocase IISP family, auxillary membrane component
secG
ATP‐dependent zinc‐metallo protease
hflB
50S ribosomal subunit protein L27
rpmA
50S ribosomal subunit protein L21
rplU
UDP‐N‐acetylglucosamine 1‐carboxyvinyltransferase
murA
putative ABC superfamily (atp&memb), transport protein
yrbC
putative ABC superfamily (bind_prot) transport protein
yhbN
putative ABC superfamily (atp_bind) transport protein
yhbG
glutamate synthase, large subunit
gltB
glutamate synthase, small subunit
gltD
putative purine‐cytosine permease
stringent starvation protein B
sspB
30S ribosomal subunit protein S9
rpsI
50S ribosomal subunit protein L13
rplM
putative ATPase
yhcM
putative periplasmic protein
yhcB
serine endoprotease
degQ
RNase G
cafA
rod shape‐determining protein
mreD
rod shape‐determining protein HSP70 class molecular chaperones
mreB
putative nitrate reductase
acetylCoA carboxylase, BCCP subunit, carrier of biotin
accB
acetyl CoA carboxylase, biotin carboxylase subunit
accC
putative DNA topoisomerase
yrdD
10‐formyltetrahydrofolate:L‐methionyl‐tRNA(fMet) N‐formyltransferase
fmt
50S ribosomal subunit protein L17
rplQ
155
0.09966997
0.005809556
‐0.17638513
‐0.25034606
‐0.3195953
‐0.51528144
‐0.46762577
‐0.0664435
0.04889824
0.002201933
‐0.018076448
‐0.3276338
‐0.012538897
‐2.409216
‐0.02925302
‐0.06344302
0.42493463
‐0.25310317
0.8552046
1.3667911
1.4136881
0.4924994
0.45198253
‐0.25207266
‐0.3458817
0.59398854
0.59391034
1.4685358
0.88882965
0.8541298
‐1.6570932
‐1.0780922
‐0.0024338
0.51035285
‐1.0397096
‐0.14893174
1.5859082
1.3610189
‐0.08571178
0.28423262
0.19017899
0.30802456
0.5168176
0.08696923
0.36601838
‐0.05823111
0.010391856
‐2.111915
‐1.9982865
‐1.380965
‐1.510201
‐1.6043607
‐1.3017131
‐1.2006162
1.7026858
2.0106812
1.479524
1.0156461
‐0.36350116
0.007283965
1.0578645
0.1636027
0.08241676
0.30372697
0.3542767
‐0.18880545
0.17232679
0.62965447
‐0.15794368
0.46347573
0.6211641
‐0.23369008
‐1.8826816
‐0.004866882
‐0.15134822
0.45904133
0.5489557
0.20445457
0.22228152
‐0.26975584
‐0.004089691
0.5394156
‐0.2124776
0.3727042
0.14861359
‐0.7943754
0.53480905
‐0.061858002
‐0.118700884
0.02044422
0.042138446
0.090776965
‐0.03154176
‐0.014588503
0.0378735
‐0.036254928
‐0.03987757
‐0.1840618
‐0.074756615
0.024191434
‐0.1397961
0.2381426
0.37479806
‐0.6256263
0.28756332
‐0.20311347
‐0.240176
0.11226402
0.287719
‐0.005791862
0.108974874
‐0.11697027
0.01768721
0.3639048
0.29266664
0.14947657
0.31915554
0.45055595
0.21828444
0.55796766
‐1.2374511
‐1.2325765
‐0.07350284
0.11391048
‐0.31225324
‐0.42418668
0.46733466
0.27658775
0.29680672
0.32975817
0.11135699
‐0.049545288
0.16395642
0.3264945
0.0967396
0.28743678
0.14425322
‐0.21090123
0.20593268
0.1014333
‐0.2742328
‐0.12566397
‐0.6365987
‐0.6633785
‐0.6847157
‐0.038837463
0.2679128
0.12518373
‐0.06352956
‐0.23637518
0.06686209
‐2.5270565
‐0.025046064
0.060515027
0.3290534
‐0.13701907
0.7936667
1.3381793
1.5990025
0.561775
0.33105728
‐0.219745
‐0.105080955
0.48456725
0.86389077
1.3882108
0.9238883
0.9028306
‐1.5668646
‐0.8139626
‐0.08608077
0.7136659
‐1.0487089
‐0.35169092
1.6896712
1.1131215
0.037242457
0.24634005
0.22966039
0.2622602
0.22583568
‐0.045989398
0.616091
0.002727301
‐0.17322683
‐2.1141264
‐2.2120636
‐1.3377738
‐1.5917325
‐1.3384742
‐1.5445496
‐1.1917812
1.6050758
1.9755465
1.534634
0.77281904
‐0.28299135
‐0.01565569
0.65946704
0.26038495
0.1496541
0.48952314
0.29968372
‐0.57485443
0.09527983
0.71734643
‐0.17798114
0.63191265
0.5561981
‐0.46151632
‐2.0373597
0.26829427
0.028634714
0.49615526
0.705428
0.118721396
0.28155047
‐0.25578
‐0.00613397
0.44647112
0.100207396
0.415672
0.29308948
‐1.0122044
0.4557718
0.024763463
‐0.32781953
‐0.08933705
0.13966922
0.23736475
‐0.08255189
‐0.003988799
‐0.15404993
‐0.33209553
‐0.1330226
‐0.20660804
0.11385263
0.10382196
0.001734606
0.073373266
0.3099094
‐0.25812346
0.55266887
0.21478082
‐0.19994754
0.090695724
0.27095413
‐0.04465242
‐0.012338016
0.20749073
0.019447526
0.31723154
0.27417678
0.18808955
0.385592
0.6493985
0.24881084
0.51682436
‐1.1750478
‐1.1646444
0.0889527
0.09031873
‐0.2942787
‐0.39810398
0.51619864
0.5025476
0.52625495
0.20061354
0.2793191
0.06909308
0.004959014
0.1647305
0.18060349
0.2726006
0.23554099
‐0.13917804
0.05357113
0.21773262
‐0.12595981
‐0.26800135
‐0.48812613
‐0.65227646
‐0.7068311
‐0.054674678
0.15600066
0.008890197
0.27539665
‐0.2256565
‐0.06068614
‐2.4806406
‐0.10279054
0.004911195
0.30795994
0.07632942
0.7369175
1.1992822
1.3860908
0.354886
0.16392724
‐0.16762441
‐0.17565991
0.820836
0.62645835
1.4077921
0.88425475
0.97993296
‐1.3951266
‐0.97066003
‐0.031923085
0.6639277
‐0.9491986
‐0.29418498
1.5323713
1.3807477
‐0.100272834
0.27426836
0.3912015
0.22540766
0.35993382
0.009967996
0.48594844
0.0839029
0.045713007
‐2.1909368
‐2.144421
‐1.5077561
‐1.7514678
‐1.4685069
‐1.4773316
‐1.2197933
1.7330488
1.9555578
1.3238136
0.95749605
‐0.4199722
0.07242312
0.5723216
0.22599287
0.15939096
0.310964
0.3409208
‐0.3934032
0.10417513
0.33090457
‐0.2562994
0.53153473
0.6033192
‐0.40656316
‐1.7753541
‐0.013539204
‐0.11858269
0.4057607
0.4235758
0.15328436
0.33851743
‐0.34860906
‐0.074968375
0.42515892
0.031301398
0.32199523
0.2946258
‐1.05152
0.27149752
‐0.094669834
‐0.23102309
0.021162478
0.030387117
0.18766257
‐0.14289394
0.02529741
‐0.20141844
0.11838128
‐0.06085754
‐0.09481134
0.18511528
0.12358436
0.04273513
0.18642077
0.13743226
‐0.1164927
0.4851381
0.058728024
‐0.17018883
‐0.075012125
0.16514485
‐0.017997647
‐0.01067437
0.14714777
0.1491869
0.26751897
0.37332067
0.28382948
0.33516544
0.37100726
0.34011468
0.24608935
‐1.0209262
‐1.1944269
0.1374948
0.1314835
‐0.35574937
‐0.27671683
0.4392478
0.47790214
0.40978143
0.060122635
0.1755934
‐0.10524708
0.019371338
0.25905517
0.068293154
0.110935025
0.15461309
‐0.16408038
0.5916567
0.57178414
‐0.9957277
‐0.79157364
‐0.5757709
‐0.8489438
‐0.6161648
‐0.5275034
‐0.81746256
‐0.45344615
‐0.58997846
‐0.8565542
0.53380734
‐3.539058
‐0.9064514
1.2615591
0.87684643
‐0.78871423
0.46165243
0.88219213
1.164331
1.571607
0.6109971
0.51942676
‐0.30258146
0.91573364
4.4718914
1.0338286
1.4213401
0.7055156
‐1.5192282
‐1.3445059
‐0.4754369
1.2195485
‐1.1627603
‐0.7921751
0.5361342
1.2840371
0.8111567
1.0516843
‐0.39434144
1.3915378
0.42678532
0.43071222
1.2252629
0.51590735
0.96365744
‐0.7292152
‐1.3907449
‐0.6757089
‐1.2971075
‐1.3643197
‐1.7078265
‐1.1196187
‐1.8225362
‐1.4567972
‐1.2319107
‐0.57300925
0.64968485
‐0.73271036
1.0113361
0.36568114
1.3575366
1.7175845
0.995818
‐0.4256609
0.82691765
0.9377197
‐0.45854482
1.5831877
0.38301352
‐0.50069046
‐0.9094354
1.0519418
0.9341656
1.61506
0.8250381
0.31896365
‐0.39068496
‐0.8640276
1.1865511
0.54042345
0.39912364
‐0.73165846
‐0.4568361
‐1.5030166
1.1257912
0.36173138
0.6009225
‐0.3918133
‐0.46844065
‐0.8831592
‐0.44555646
1.4724897
1.0107374
0.9045049
0.4021744
1.6224974
0.9687112
0.6024334
‐0.46579698
‐0.668651
‐1.0302029
‐0.34901798
0.7379055
0.43816087
0.61774576
0.7503863
1.3900466
0.60618097
0.8832069
1.3815571
1.2449843
0.873671
0.722275
0.82678646
0.86490834
1.0194108
0.72728646
0.90596527
0.42223728
0.86034554
0.44045606
0.5373964
0.59703296
0.3355869
0.48856956
0.7403273
0.9529764
1.1699529
0.94404954
1.2637119
0.8321907
1.0537269
0.69413424
0.6499722
0.8723259
0.47248608
0.6738609
0.62521434
‐0.60188156
‐0.9375658
‐0.73887795
‐0.92762154
‐0.6992853
‐0.71590596
‐1.0576814
‐0.49207753
‐0.6300953
‐0.7094124
0.6663871
‐3.6892347
‐0.9081608
1.2526436
0.81144875
‐0.6562085
0.60133964
0.9187685
1.1723489
0.8121499
0.44705623
0.58000386
‐0.61178833
0.88280106
3.0326958
0.83051705
1.660388
0.86182636
‐1.3188132
‐1.1444677
‐0.5139672
1.4674598
‐1.7866412
‐0.84443575
0.5886238
1.6497548
0.764251
1.2805676
‐0.8224546
1.2543832
0.6108107
0.3911952
1.1004763
0.7166603
0.81719846
‐0.3609178
‐1.029538
‐0.86436427
‐1.0884947
‐1.0714186
‐2.026192
‐0.9748724
‐1.4510936
‐1.5760242
‐1.1149666
‐0.6943098
0.60937476
‐0.7122252
0.8807009
0.6373582
1.3299998
1.5714319
0.83977145
‐0.614946
0.92148805
0.94293815
‐0.46459493
1.2341961
0.37756073
‐0.66075945
‐1.0514808
0.948105
0.7284123
1.5269563
0.37911683
0.7021465
‐0.45433235
‐0.6955426
1.2101642
0.7274467
0.56539404
‐0.6565856
‐0.39942473
‐1.7414619
0.82378703
0.53561974
0.40339646
‐0.7512944
‐0.5192889
‐0.98961717
‐0.48397323
1.0858337
0.6274843
0.6362264
0.3229126
1.5688049
0.8101795
0.39776328
‐0.42401534
‐0.7760198
‐1.0730301
‐0.48722446
0.41182685
0.6339922
1.1174277
0.68511885
1.01867
0.55015844
1.2870035
1.3008317
1.5090841
0.6887258
0.80754155
0.9400084
0.8380177
1.4531128
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0.61113596
0.46917948
0.7685048
0.44140106
0.5705995
0.72727215
0.5297364
0.5567523
0.653262
0.89315414
0.91923195
1.1231475
1.0159082
0.7664692
1.2477264
1.0396188
0.38813308
0.7963802
0.6622497
0.50706035
0.635363
‐0.6572079
‐1.125732
‐0.65123403
‐1.0008435
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‐1.0227988
‐1.2540472
‐0.49332753
‐0.47800833
‐0.8726867
0.37579963
‐3.8342152
‐1.0135117
0.9548015
0.83785975
‐0.54647964
0.50020754
0.909422
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0.61621284
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‐0.5936708
1.2101729
3.278312
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1.6496134
0.6533429
‐1.1711544
‐1.3973186
‐0.46975276
1.3035315
‐1.4778053
‐0.79789424
0.54786766
1.5424218
0.6013942
1.3833369
‐0.88572073
1.0112273
0.5289412
0.36508504
0.8265971
0.77565557
0.92377216
‐0.662025
‐0.9739851
‐1.1842023
‐1.2998145
‐1.1026849
‐1.9283416
‐1.2857137
‐1.3076658
‐1.6994305
‐1.2070023
‐0.82742065
0.4931611
‐0.7171739
0.9485627
0.7776076
1.0254316
1.5097268
0.903015
‐0.59168684
0.96029365
0.70960456
‐0.58150333
0.790129
0.4378025
‐0.5349036
‐0.7714091
0.890139
0.5866112
1.6946888
0.51252145
0.6573744
‐0.3793316
‐0.8497073
0.7337791
0.54703075
0.3302064
‐0.90815854
‐0.38106892
‐1.6000873
0.8655421
0.5765678
0.5492505
‐0.519497
‐0.7870097
‐0.87133825
‐0.60670054
1.001783
0.5105102
1.3067031
0.43900347
1.5368252
0.799553
0.44121185
‐0.5513716
‐0.8261018
‐1.0650597
‐0.3887005
0.39430737
0.3299853
1.2904097
0.5076172
1.3603115
0.5319397
1.2373838
1.2844783
1.5471741
0.6959391
0.8770581
1.1391729
0.68250495
1.1803452
0.72495925
0.61389375
0.41576034
0.74538505
0.31248042
0.437884
0.84410584
0.5527854
0.3359806
0.6178786
0.42084214
0.8932288
1.0040327
1.013385
0.888353
1.1608334
0.99623066
0.35735843
0.49501544
0.5642593
0.590859
0.610787
‐0.75161
‐0.95162
‐0.65529
‐0.9258
‐0.61083
‐0.7554
‐1.04306
‐0.47962
‐0.56603
‐0.81288
0.525331
‐3.6875
‐0.94271
1.156335
0.842052
‐0.6638
0.521067
0.903461
1.108306
1.060185
0.558089
0.495991
‐0.50268
1.002903
3.5943
0.946629
1.577114
0.740228
‐1.3364
‐1.29543
‐0.48639
1.33018
‐1.47574
‐0.8115
0.557542
1.492071
0.725601
1.23853
‐0.70084
1.219049
0.522179
0.395664
1.050779
0.669408
0.901543
‐0.58405
‐1.13142
‐0.90809
‐1.22847
‐1.17947
‐1.88745
‐1.12673
‐1.5271
‐1.57742
‐1.18463
‐0.69825
0.584074
‐0.7207
0.946867
0.593549
1.237656
1.599581
0.912868
‐0.5441
0.9029
0.863421
‐0.50155
1.202504
0.399459
‐0.56545
‐0.91078
0.963395
0.74973
1.612235
0.572225
0.559495
‐0.40812
‐0.80309
1.043498
0.604967
0.431575
‐0.76547
‐0.41244
‐1.61486
0.938373
0.491306
0.517856
‐0.5542
‐0.59158
‐0.9147
‐0.51208
1.186702
0.716244
0.949145
0.38803
1.576043
0.859481
0.48047
‐0.48039
‐0.75692
‐1.0561
‐0.40831
0.51468
0.467379
1.008528
0.647707
1.256343
0.56276
1.135865
1.322289
1.433748
0.752779
0.802292
0.968656
0.795144
1.217623
0.687666
0.710332
0.435726
0.791412
0.398113
0.515293
0.722804
0.472703
0.460434
0.670489
0.755658
0.994138
1.023743
1.097668
0.829004
1.154096
0.909995
0.465155
0.721241
0.566332
1.506144
1.527092
0.593942
0.51705
0.634946
0.526387
0.65482
0.592381
0.485296
0.717168
0.675474
0.569243
1.439264
0.077616
0.520255
2.228904
1.792598
0.631213
1.435016
1.870548
2.155923
2.085198
1.472317
1.410289
0.705794
2.004028
12.07792
1.927364
2.983723
1.67044
0.396008
0.407415
0.713811
2.51434
0.35955
0.569788
1.471759
2.812925
1.653589
2.359579
0.615214
2.327933
1.436123
1.315548
2.071648
1.59042
1.868062
0.667087
0.456465
0.532889
0.426769
0.441512
0.270284
0.457951
0.346974
0.335081
0.439938
0.616321
1.499076
0.606802
1.927681
1.508954
2.358151
3.030553
1.882785
0.68582
1.869821
1.819347
0.706349
2.301388
1.319013
0.675744
0.531899
1.949893
1.681478
3.057251
1.486815
1.473753
0.753607
0.573119
2.061219
1.520944
1.348705
0.588263
0.75135
0.326498
1.916366
1.405717
1.431826
0.681034
0.663616
0.530452
0.701212
2.276318
1.642899
1.930728
1.308605
2.981509
1.814386
1.395198
0.716782
0.591757
0.480931
0.753503
1.428677
1.382596
2.011857
1.566677
2.388894
1.477092
2.197502
2.500626
2.701475
1.685035
1.743869
1.957017
1.73525
2.325632
1.610676
1.63618
1.352591
1.730767
1.317783
1.429285
1.650386
1.387707
1.375956
1.591613
1.688401
1.99189
2.033187
2.140085
1.776459
2.225448
1.879038
1.380465
1.648599
1.480754
0.193614
‐1.13131
‐1.0548
‐0.50162
1.166575
0.423883
1.176908
‐0.02103
‐0.54803
1.099502
0.707396
0.071744
‐0.30566
‐0.22938
‐0.34781
‐0.08696
‐0.74825
0.869194
2.03774
0.138552
0.196317
0.25576
0.114597
‐0.06811
0.253112
0.367586
0.519337
0.011302
0.949245
‐0.24933
0.615961
‐0.56441
0.980468
0.648303
0.304073
‐0.135
0.620905
‐0.46554
‐0.22603
0.750531
‐0.5892
‐0.05813
‐1.31909
‐0.84855
0.385875
1.083664
‐0.88161
‐0.11693
1.897161
‐0.64461
‐0.73811
0.383309
‐0.5179
‐0.06589
0.968613
‐0.39493
‐0.65329
‐0.56358
‐0.23022
‐0.77533
‐0.59736
0.411725
‐0.28808
0.342819
‐0.01385
0.646675
‐0.53211
‐1.55655
0.034731
‐0.49895
2.300679
0.886855
‐0.74281
0.409007
‐0.1279
0.8738
0.557001
1.196408
‐0.94698
0.917672
‐0.15056
‐1.15668
‐0.02263
‐0.39834
0.555024
0.039134
0.298515
‐0.40091
0.089904
0.717622
‐0.54648
‐0.54013
‐0.43768
‐0.1146
‐0.2778
0.28756
0.332433
‐0.91516
‐0.58563
0.556409
‐0.18635
‐0.50906
‐0.72942
‐1.28122
‐0.37281
‐0.31535
0.850341
‐0.30101
0.524708
‐0.711
1.028654
0.480966
1.845169
‐0.63598
‐0.53261
0.930021
‐0.03551
0.302409
0.45741
0.226032
‐1.37684
0.510854
‐0.16058
0.557369
0.879025
0.704058
‐0.24417
0.2697
‐0.57334
0.086961
‐0.04087
‐0.00852
‐0.4769
‐0.98951
0.658374
‐0.10475
‐0.28565
0.403972
1.94424
2.217255
‐1.98391
‐2.69988
‐2.16356
‐3.09004
‐1.98047
‐1.8881
‐2.73059
‐1.78402
‐1.87888
‐2.64185
1.546266
‐10.8151
‐3.23782
3.243129
3.064856
‐2.03758
1.752069
3.387289
3.509201
2.0727
1.792847
1.588449
‐1.41228
2.787235
5.132976
2.993816
4.726163
2.324938
‐3.74747
‐3.89304
‐1.80385
4.048697
‐3.38587
‐2.98018
2.052387
4.095908
2.272389
3.50095
‐1.70902
3.322129
1.690006
1.43969
2.813431
2.002018
3.010509
‐1.58284
‐2.92812
‐2.24687
‐3.7713
‐3.38335
‐5.39426
‐3.26068
‐3.73227
‐4.84174
‐4.06649
‐2.12092
1.929727
‐2.75161
3.226448
1.575808
3.417437
5.039931
3.03213
‐1.72539
3.056969
2.595408
‐1.69576
2.478196
1.452652
‐1.85749
‐2.70579
3.178687
2.102176
5.300085
1.475218
1.485223
‐1.46232
‐2.59327
2.540414
1.908298
1.325661
‐2.31739
‐1.48057
‐4.96913
2.679302
1.527662
1.644555
‐1.53534
‐1.66849
‐3.11802
‐1.68256
2.961656
1.760598
2.106485
1.338034
5.613798
2.768495
1.510872
‐1.63828
‐2.50476
‐3.92748
‐1.37556
1.400577
1.355837
2.204815
1.973007
3.35118
2.023674
2.966572
4.627315
4.087434
2.380466
2.669778
2.791047
2.543634
3.184757
2.337313
2.009029
1.59852
2.720968
1.333413
1.743073
2.209676
1.456129
1.434307
2.29516
1.782019
2.890129
3.319728
3.240115
2.849101
3.70076
2.497213
1.33441
1.944216
1.823703
0.590859
0.610787
‐0.75161
‐0.95162
‐0.65529
‐0.9258
‐0.61083
‐0.7554
‐1.04306
‐0.47962
‐0.56603
‐0.81288
0.525331
‐3.6875
‐0.94271
1.156335
0.842052
‐0.6638
0.521067
0.903461
1.108306
1.060185
0.558089
0.495991
‐0.50268
1.002903
3.5943
0.946629
1.577114
0.740228
‐1.3364
‐1.29543
‐0.48639
1.33018
‐1.47574
‐0.8115
0.557542
1.492071
0.725601
1.23853
‐0.70084
1.21905
0.522179
0.395664
1.050779
0.669408
0.901543
‐0.58405
‐1.13142
‐0.90809
‐1.22847
‐1.17947
‐1.88745
‐1.12674
‐1.5271
‐1.57742
‐1.18463
‐0.69825
0.584074
‐0.7207
0.946867
0.593549
1.237656
1.599581
0.912868
‐0.5441
0.9029
0.863421
‐0.50155
1.202504
0.399459
‐0.56545
‐0.91078
0.963395
0.74973
1.612235
0.572225
0.559495
‐0.40812
‐0.80309
1.043498
0.604967
0.431575
‐0.76547
‐0.41244
‐1.61486
0.938373
0.491306
0.517857
‐0.5542
‐0.59158
‐0.9147
‐0.51208
1.186702
0.716244
0.949145
0.38803
1.576043
0.859481
0.48047
‐0.48039
‐0.75692
‐1.0561
‐0.40831
0.51468
0.467379
1.008528
0.647707
1.256343
0.56276
1.135865
1.322289
1.433748
0.752779
0.802292
0.968656
0.795144
1.217623
0.687666
0.710332
0.435726
0.791412
0.398113
0.515293
0.722804
0.472703
0.460434
0.670489
0.755658
0.994138
1.023743
1.097668
0.829004
1.154096
0.909995
0.465155
0.721241
0.566332
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0.311286
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0.312248
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0.355936
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0.35982
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0.700237
0
0.316195
0
0.333699
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0.318386
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0.356614
0
0.332755
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0.269638
0
0.328545
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0.435851
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0.272299
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0.271655
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0.364283
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0.319312
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0.35377
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0.410083
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0.366948
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0.308981
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0.274826
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0.373487
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0.334367
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0.299465
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0.368991
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0.404158
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0.325743
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0.348612
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STM3415
STM3418
STM3420
STM3421
STM3426
STM3427
STM3428
STM3429
STM3430
STM3431
STM3433
STM3434
STM3435
STM3436
STM3437
STM3438
STM3439
STM3440
STM3441
STM3446
STM3447
STM3448
STM3453
STM3468
STM3483
STM3485
STM3487
STM3493
STM3494
STM3505
STM3506
STM3507
STM3529
STM3545
STM3554
STM3559
STM3560
STM3562
STM3563
STM3564
STM3565
STM3566
STM3569
STM3579
STM3581
STM3582
STM3583
STM3588
STM3589
STM3591
STM3593
STM3596
STM3605
STM3622
STM3644
STM3646
STM3647
STM3649
STM3655
STM3656
STM3665
STM3666
STM3679
STM3683
STM3696
STM3700
STM3701
STM3703
STM3713
STM3723
STM3727
STM3728
STM3730
STM3731
STM3732
STM3733
STM3734
STM3738
STM3740
STM3741
STM3742
STM3743
STM3746
STM3762
STM3767
STM3773
STM3780
STM3790
STM3796
STM3797
STM3803
STM3808
STM3828
STM3839
STM3840
STM3851
STM3862
STM3864
STM3865
STM3866
STM3867
STM3868
STM3869
STM3870
STM3871
STM3875
STM3877
STM3885
STM3900
STM3901
STM3902
STM3903
STM3904
STM3905
STM3909
STM3919
STM3921
STM3922
STM3927
STM3928
STM3936
STM3946
STM3949
STM3952
STM3965
STM3970
STM3972
STM3973
STM3974
STM3978
STM3986
STM3987
STM3996
STM3999
STM4002
STM4006
STM4007
STM4062
RNA polymerase, alpha subunit
rpoA
30S ribosomal subunit protein S13
rpsM
preprotein translocase of IISP family, membrane subunit
secY
50S ribosomal subunit protein L15
rplO
30S ribosomal subunit protein S8, and regulator
rpsH
30S ribosomal subunit protein S14
rpsN
50S ribosomal subunit protein L5
rplE
50S ribosomal subunit protein L24
rplX
50S ribosomal subunit protein L14
rplN
30S ribosomal subunit protein S17
rpsQ
50S ribosomal subunit protein L16
rplP
30S ribosomal subunit protein S3
rpsC
50S ribosomal subunit protein L22
rplV
30S ribosomal subunit protein S19
rpsS
50S ribosomal subunit protein L2
rplB
50S ribosomal subunit protein L23
rplW
50S ribosomal subunit protein L4, regulates expression
rplD
50S ribosomal subunit protein L3
rplC
30S ribosomal subunit protein S10
rpsJ
protein chain elongation factor EF‐G, GTP‐binding
fusA
30S ribosomal subunit protein S7, initiates assembly
rpsG
30S ribosomal subunit protein S12
rpsL
FKBP‐type peptidyl‐prolyl cis‐trans isomerase (rotamase)
fkpA
acetylornithine transaminase (NAcOATase and DapATase)
argD
D‐ribulose‐5‐phosphate 3‐epimerase
rpe
membrane protein
damX
shikimate kinase I
aroK
transpeptidase of penicillin‐binding protein 1a (peptidoglycan synthetase)
mrcA
putative NTP pyrophosphohydrolase
yrfE
ferrous iron transport protein A
feoA
FeoB family, ferrous iron transport protein B
feoB
putative cytoplasmic protein
yhgG
putative glycerol dehydrogenase
putative oxidoreductase
yhhX
ABC superfamily (atp_bind), sn‐glycerol 3‐phosphate transport protein
ugpC
putative cytoplasmic protein
yhhV
ABC superfamily (atp_bind), branched‐chain amino acid transporter
livF
ABC superfamily (membrane), branched‐chain amino acid transporter
livM
ABC superfamily (membrane), branched‐chain amino acid transporter
livH
ABC superfamily (bind_prot), branched‐chain amino acid transporter
livK
putative acetyltransferase
yhhK
putative cytoplasmic protein
putative integral membrane cell division protein
ftsX
putative integral membrane protein
yhhQ
putative MFS family transport protein
yhhS
putative PerM family permease
yhhT
putative Phosphopantetheinyl transferase
acpT
putative periplasmic protein
yhiN
PiT family, low‐affinity phosphate transporter
pitA
universal stress protein A
uspA
putative SAM‐dependent methyltransferase
yhiQ
putative cytoplasmic protein
yhiR
putative phage endolysin
putative cytoplasmic protein
yhjS
biotin sulfoxide reductase
bisC
2‐keto‐D‐gluconate reductase
yiaE
putative outer membrane lipoprotein
yiaF
major cold shock protein 7.4, transcriptional activator
cspA
glycine tRNA synthetase, beta subunit
glyS
glycine tRNA synthetase, alpha subunit
glyQ
valine‐pyruvate aminotransferase
avtA
paral putative oxidoreductase
ysaA
putative cytoplasmic protein
selenocysteine synthase (with SelD)
selA
putative transcriptional regulator
glycerol‐3‐phosphate dehydrogenase (NAD )
gpsA
molecular chaperone in protein export
secB
putative Rhodanese‐related sulfurtransferases
yibN
O‐antigen ligase
rfaL
lipopolysaccharide core biosynthesis modification of heptose region
rfaQ
50S ribosomal subunit protein L33
rpmG
50S ribosomal subunit protein L28
rpmB
flavoprotein affecting synthesis of DNA and pantothenate
dfp
deoxyuridinetriphosphatase
dut
putative transcriptional regulator (TetR/ArcR family)
ttk
orotate phosphoribosyltransferase
pyrE
RNase PH
rph
putative inner membrane protein
yigC
guanylate kinase
gmk
RNA polymerase, omega subunit
rpoZ
bifunctional : (p)ppGpp synthetase II also guanosine‐3,5‐bis
spoT
putative tRNA/rRNA methyltransferase
spoU
GltS family, glutamate transport protein
gltS
putative inner membrane protein
cigR
putative cytoplasmic protein
putative NtrC family transcriptional regulators, ATPase domain
putative fructose‐bisphosphate aldolase class‐II
response regulator (repressor) in two‐component regulatory system
uhpA
acetolactate synthase I, large subunit, valine sensitive
ilvB
ilvB operon leader peptide
ivbL
putative cytoplasmic protein
yidF
small heat shock protein
ibpB
galactonate dehydratase in bifunctional: 2‐oxo‐3‐deoxygalactonate 6‐phosphate aldolase
dgoA
50S ribosomal subunit protein L34
rpmH
RNase P, protein component (protein C5), processes
rnpA
putative xanthine/uracil permeases family
yieG
N‐acetyl glucosamine‐1‐phosphate uridyltransferase and glucosamine‐1‐phosphate acetyl traglmU
membrane‐bound ATP synthase, F1 sector, epsilon‐subunit
atpC
membrane‐bound ATP synthase, F1 sector, beta‐subunit
atpD
membrane‐bound ATP synthase, F1 sector, gamma‐subunit
atpG
membrane‐bound ATP synthase, F1 sector, alpha‐subunit
atpA
membrane‐bound ATP synthase, F1 sector, delta‐subunit
atpH
membrane‐bound ATP synthase, F0 sector, subunit b
atpF
membrane‐bound ATP synthase, F0 sector, subunit c
atpE
membrane‐bound ATP synthase, F0 sector, subunit a
atpB
initiation of chromosome replication
mioC
asparagine synthetase A
asnA
ribokinase
rbsK
ilvGEDA operon leader peptide
ilvL
acetolactate synthase II, large subunit, fragment 1
ilvG
acetolactate synthase II, small subunit
ilvM
branched‐chain amino‐acid aminotransferase
ilvE
dihydroxyacid dehydratase
ilvD
threonine deaminase
ilvA
ketol‐acid reductoisomerase
ilvC
modulator of enterobacterial common antigen (ECA) polysaccharide
wzzE
UDP‐N‐acetyl‐D‐mannosaminuronic acid dehydrogenase
wecC
dTDP‐glucose 4,6‐dehydratase
rffG
putative inner membrane protein
wecF
TDP‐Fuc4NAc:lipidII transferase
uroporphyrinogen III methylase
hemX
putative outer membrane lipoprotein
yifL
putative integrase/recombinase, site‐specific
xerC
MIT family, Mg2 /Ni2 /Co2 transport protein (Mg transport
corA
5‐methyltetrahydropteroyltriglutamate‐homocysteine S‐methyltransferase
metE
S‐adenosylmethionine : 2‐DMK methyltransferase and 2‐octaprenyl‐6‐methoxy‐1,4‐benzoqui ubiE
putative regulator in ubiquinone biosynthesis
aarF
component of Sec‐independent protein secretion pathway
tatA
component of Sec‐independent protein secretion pathway
tatB
putative oxidoreductase
yigC
Trk family, potassium transport protein, requires TrkE
trkH
protoporphyrin oxidase
hemG
putative homoserine kinase type II, protein kinase
yihE
DNA polymerase I, 3 ‐‐ 5 polymerase
polA
putative cytoplasmic protein
sensory kinase (phosphatase) in two‐component regulatory system
glnL
glutamine synthetase
glnA
6‐phosphofructokinase I
pfkA
156
‐0.17111461
‐0.066201754
‐0.029094636
0.023761628
0.156887
0.14298563
0.27224478
0.1746039
0.13766943
‐0.0887727
0.0771694
‐0.04383161
0.02788896
0.13707714
0.2131876
0.16592273
0.16622669
0.067706786
‐0.08544141
0.18110873
‐0.078892924
‐0.15138279
0.13268282
‐1.0901717
0.22289732
0.40057707
0.23728496
0.027661547
0.3264107
‐0.8980078
‐0.8008093
‐0.65874517
‐0.018010184
0.3654765
‐0.04468284
‐0.51195174
‐0.16427407
‐0.33340865
‐0.00253958
‐0.010174342
‐0.008102455
‐0.12003672
‐0.121858135
‐0.26206633
‐0.23966552
‐0.17338857
‐0.23017658
0.09012696
0.22636662
0.100602835
0.047663294
0.201224
0.1079073
0.47895348
0.14470662
0.24432333
0.26586452
0.18005908
0.30582297
0.36266342
0.1534823
‐0.3849482
‐0.29648966
‐0.15914151
‐0.13165651
0.3124642
0.037450768
0.12468472
0.36301234
0.19400369
0.6258041
0.5031419
0.06676046
‐0.04612479
0.05935783
0.22934297
0.019597685
0.24687901
0.15725826
0.14028324
‐0.056992415
‐0.16272414
‐0.027708873
0.1902197
‐0.3511006
0.15289244
0.20207778
‐0.20300399
1.5609252
0.30770418
0.18201616
‐0.28224045
0.21327987
‐0.31835505
‐0.1544575
‐0.14575565
0.36955515
‐0.011487707
0.01870176
0.54671985
0.10773366
0.22998466
0.048203807
0.009046757
0.24357018
0.21495241
‐1.8288294
0.3601816
‐0.23719585
0.6425514
1.0454634
0.79254895
0.775312
0.5118394
‐0.25719902
0.38888365
0.20276114
0.2537869
0.04580798
0.14082524
‐0.21156333
0.1862601
0.13264139
‐0.06012455
2.0208678
0.5451342
0.38699812
0.39415374
0.3267777
0.25310853
0.43091
0.4650082
0.36842012
0.37616727
1.8951077
‐0.6108326
‐0.53651893
0.23692147
‐0.32143748
0.001316099
‐0.40166813
‐0.003743239
‐0.07459578
0.044006325
0.408246
0.17433919
0.12731695
‐0.040331673
0.11529771
‐0.18462062
0.09586572
‐0.00233156
0.26937285
0.06168102
‐0.07109449
0.12034215
0.024410091
0.117635965
‐0.043607447
‐0.20287304
0.2703331
‐1.1069815
0.2771398
0.2942246
0.50706136
0.026157668
0.48532274
‐0.8358187
‐0.7850094
‐0.65858203
0.1032425
0.456926
‐0.26788393
‐0.36480522
‐0.3524308
‐0.43975687
‐0.16058128
‐0.028692126
0.07012291
‐0.18484004
‐0.13931735
‐0.28131464
‐0.15919942
‐0.06607158
‐0.21891128
0.17638624
0.075264834
0.2301181
0.05877624
0.28259528
0.1118315
0.5198404
0.19645415
0.18313937
0.36045036
0.46725303
0.17720874
0.41440406
0.13930215
‐0.3260673
‐0.65751076
‐0.19465336
‐0.2929532
0.18166745
0.085822046
0.07792352
0.49145386
0.34150213
0.38240027
0.37100726
0.10776893
‐0.030110795
0.2986477
0.43212935
0.077178694
0.47976634
0.3728713
0.18378332
‐0.25012997
‐0.015153673
0.10655096
0.071109936
‐0.57912034
0.35352457
0.57365334
‐0.23561907
1.3317875
0.0621715
0.007583045
‐0.41326177
0.3637907
‐0.10970761
‐0.16499291
‐0.21347322
0.5402315
‐0.029106656
0.13035516
0.3996228
0.061710186
0.44132522
0.19851294
0.11437796
0.1995768
0.17961408
‐2.0108335
0.39282104
‐0.3070986
0.59973615
0.92444766
0.75233585
0.45393547
0.3958778
‐0.60160685
0.4176267
0.18865238
0.19174887
0.24182725
0.40528783
0.12881263
0.26797107
‐0.00340049
0.373126
2.130202
0.7330351
0.4446431
0.21388204
0.4204216
‐0.06369869
0.36631954
0.2570255
0.5877408
0.5917273
1.6498793
‐0.4447654
‐0.5801261
0.23283237
‐0.239364
‐0.13031937
‐0.46753326
0.030900303
0.027831098
0.07243931
0.21400793
0.002341535
0.1843003
0.05516144
‐0.016960746
‐0.18147409
‐0.05151192
0.024264153
0.072163686
0.04589028
‐0.038105242
0.005215909
‐0.003385578
0.08852364
‐0.08896896
‐0.18437465
0.2590825
‐1.0186319
0.25279966
0.14190911
0.38406584
‐0.034723267
0.37126324
‐0.78202707
‐0.80909026
‐0.5766391
0.2209399
0.22306515
‐0.097273536
‐0.3218064
‐0.2516342
‐0.4066767
‐0.09113365
0.011515966
‐0.008915209
‐0.29097027
‐0.19150385
‐0.31972826
‐0.26792803
‐0.23319583
‐0.23699446
0.12930581
0.08798218
0.1864977
‐0.048142686
0.19151321
0.2380045
0.45286873
0.1428582
0.22066365
0.25343433
0.35170114
0.02626356
0.12351569
0.18358889
‐0.4641717
‐0.54979634
‐0.29391286
‐0.263262
0.082764484
0.023267388
0.092866965
0.43890908
0.23618971
0.33417016
0.459275
0.15122965
‐0.15081427
0.09886001
0.260425
0.23095728
0.24572635
0.22955245
0.28171414
‐0.2844884
‐0.18987694
‐0.12550037
0.25572044
‐0.62720615
0.30111754
0.4473668
‐0.084135115
1.3896406
0.2673648
‐0.23177125
‐0.2579473
0.2827768
‐0.13283214
‐0.27050206
‐0.031739704
0.4510921
‐0.07965923
‐0.06819548
0.33254293
0.08329395
0.17325944
0.0882226
0.021699624
0.04752768
0.21395944
‐1.9725355
0.15744178
0.0417315
0.58618224
0.91379493
0.7646743
0.49352932
0.5679266
‐0.39823884
0.29808593
0.19314767
0.2785799
0.14677499
0.3006426
‐0.006796745
0.4029051
0.04418981
0.18432376
2.026502
0.5664514
0.40212184
0.36006528
0.35949153
‐0.00989898
0.36982083
0.34211197
0.24637876
0.34549972
2.0633426
‐0.4580785
‐0.66090095
0.19542523
0.40389606
0.43502557
0.56648
0.4057411
0.38986868
1.017614
0.55655867
0.58207536
0.37834528
0.33699328
0.8118268
0.7072566
0.8675472
0.47191405
1.2741129
0.88793
0.6980796
0.5133172
0.4772821
1.3127447
0.7281382
0.56427264
0.96936053
‐0.5776001
1.1238592
0.82500184
1.4653877
1.0460325
1.1182879
‐1.9934821
‐1.6182702
‐0.78440833
‐0.60592294
1.4265004
0.40960887
‐0.8147165
1.2833763
1.1676672
0.5935828
1.2721968
0.71416783
0.92943585
0.5935469
0.8972435
0.6503621
1.1769857
0.6221992
1.6446699
0.5316787
‐0.9589353
1.3996212
0.76100385
‐0.6818135
1.1361014
1.5618557
0.29687464
0.39822218
1.7636927
0.7584689
0.6817451
0.5673434
‐0.42707002
‐0.6548299
1.0289332
‐0.46893784
1.5715777
0.57160187
1.2429237
1.906771
1.0832036
1.5091441
0.8283098
0.64047354
0.88178676
0.8049446
1.0674946
0.5203567
‐0.44474292
0.8462617
0.7753145
0.5152583
0.4675559
0.7002074
‐0.59304273
0.43108487
0.540291
0.43595454
0.63575506
1.216307
‐0.5445204
‐0.53644156
‐0.46361297
0.54554945
1.121832
1.3615233
0.8828982
1.0702175
1.0321796
0.7332065
1.437102
0.89879
1.1519117
0.961933
0.65336937
1.5409764
1.5702454
‐0.7493705
0.5545818
‐0.71283674
0.6117585
0.80081606
0.65603364
1.5322919
1.3083211
0.7675543
0.90911055
1.0837299
0.7698976
0.4962595
0.57902503
0.8144221
0.6939396
1.0018001
0.5917475
1.3302777
1.9925156
0.6121604
0.49250725
1.2409211
0.7984362
0.42558333
0.7979541
0.4794375
0.86111623
‐3.046172
1.014649
‐0.8614913
‐0.8576517
0.540604
0.5317855
0.38486713
0.5109895
0.5357284
0.7627185
0.5555049
0.46410722
0.36636478
0.468183
0.866603
0.6380355
0.82554907
0.5576356
1.0043688
0.925726
0.44608715
0.5191262
0.5419155
1.2558875
0.7104598
0.39691463
0.8613894
‐0.8472112
1.5802953
0.9361938
1.4609106
1.0722368
1.1681563
‐1.9092382
‐1.514517
‐0.9887308
‐0.6886082
1.4592677
0.4329138
‐0.6967587
1.3266482
0.695106
0.61582816
1.210193
0.8418233
0.6644095
0.5677569
0.9045855
0.670634
1.239285
1.0144118
1.6807184
0.8371307
‐1.1389306
1.6575541
0.87566894
‐0.85911566
0.71533597
1.4502966
0.8787694
0.4916266
1.7109131
0.5775694
0.52612275
0.6090645
‐0.54028434
‐0.61710554
0.80916214
‐0.48872402
1.1473793
0.6174447
0.89182585
1.6350414
0.6196684
1.1095043
0.82460684
0.32047513
1.0015429
0.93363255
0.70575684
0.5639603
‐0.5762905
0.83134234
0.56308615
0.35582075
0.54671586
0.6240892
‐0.77539563
0.4718336
0.48780385
0.43045422
0.85417336
1.1003712
‐0.60196054
‐0.74233145
‐0.44752392
0.53348064
1.1214676
1.405014
0.96764827
0.9851888
0.99560744
0.8959317
1.0038995
0.8716521
1.0365077
0.96212155
0.7971888
1.056537
1.2295758
‐1.1015068
0.41455597
‐0.38508698
0.62401396
0.38492376
0.3946524
1.1240008
1.0906904
0.856862
0.9141631
1.0751495
0.623928
0.62923944
0.7906797
0.5928944
0.5428045
0.7039443
0.5367442
1.5007643
1.8771598
0.6710387
0.6424895
0.96708983
0.25809354
0.49539125
0.6967339
0.736238
0.68715334
‐3.429997
0.8775167
‐1.0806694
‐0.88586307
0.564277
0.48192284
0.5876388
0.47595713
0.5916262
0.7287779
0.57440585
0.3929964
0.48344076
0.49178082
0.74783975
0.71248406
0.73800594
0.6335334
0.8330089
0.6928181
0.58348465
0.5149952
0.6356286
1.236176
0.63126135
0.43030784
0.81345856
‐0.9248754
0.8778368
1.1599814
1.3644738
0.61331016
0.9867609
‐1.8104979
‐1.5827016
‐0.9772643
‐0.55081296
1.38696
0.33226907
‐0.6396708
1.5995159
0.74952626
0.6754202
1.286044
0.926609
0.73091805
0.3352809
1.2626444
0.49067158
0.96768475
0.95787734
1.11275
0.96918947
‐1.3391746
1.3547417
0.6427716
‐0.45678973
0.33328858
1.095863
0.5413387
0.46281114
1.7175866
0.30078572
0.30909896
0.49966124
‐0.6653222
‐0.7088889
0.7335391
‐0.37355036
0.7342488
0.39696622
0.7405136
1.0828239
0.46239242
1.1165243
0.77496606
0.54447114
0.955422
0.7464978
0.77110326
0.637919
‐0.37029564
0.9367947
0.6088408
0.52016604
0.2914016
0.3462079
‐0.6598723
0.60070896
0.4386067
0.32178733
0.37672183
0.9060913
‐0.59754527
‐0.4259721
‐0.4528699
0.3950154
1.1418061
1.1863526
0.95135605
0.66823614
0.9898409
0.5588629
0.9538133
0.8813822
0.91901296
0.88443506
0.6472277
1.4860215
1.2453265
‐1.0090463
0.5954437
‐0.57018745
0.6385095
0.60558546
0.4817307
1.3032608
1.2207458
1.0445279
0.60147023
0.87831944
0.33736098
0.5452565
0.73144406
0.272307
0.53333163
0.65936977
0.34873492
1.636712
1.2903749
0.8239563
0.9343452
0.6855373
0.6248028
0.6512143
0.5071127
0.29896173
0.30518755
‐3.3333795
0.7090234
‐1.1501278
‐0.8942313
0.502926
0.482911
0.512995
0.464229
0.505741
0.83637
0.562156
0.479726
0.409384
0.432319
0.808757
0.685925
0.810367
0.554361
1.037164
0.835491
0.575884
0.515813
0.551609
1.268269
0.689953
0.463832
0.881403
‐0.78323
1.193997
0.973726
1.430257
0.910526
1.091068
‐1.90441
‐1.57183
‐0.9168
‐0.61511
1.424243
0.391597
‐0.71705
1.40318
0.870766
0.628277
1.256145
0.827533
0.774921
0.498862
1.021491
0.603889
1.127985
0.864829
1.479379
0.779333
‐1.14568
1.470639
0.759815
‐0.66591
0.728242
1.369338
0.572328
0.450887
1.730731
0.545608
0.505656
0.55869
‐0.54423
‐0.66027
0.857211
‐0.44374
1.151069
0.528671
0.958421
1.541545
0.721755
1.245058
0.809294
0.501807
0.946251
0.828358
0.848118
0.574079
‐0.46378
0.871466
0.64908
0.463748
0.435224
0.556835
‐0.6761
0.501209
0.488901
0.396065
0.622217
1.074257
‐0.58134
‐0.56825
‐0.45467
0.491348
1.128369
1.31763
0.933968
0.907881
1.005876
0.729334
1.131605
0.883941
1.035811
0.936163
0.699262
1.361178
1.348383
‐0.95331
0.521527
‐0.55604
0.624761
0.597108
0.510806
1.319851
1.206586
0.889648
0.808248
1.0124
0.577062
0.556918
0.700383
0.559875
0.590025
0.788371
0.492409
1.489251
1.720017
0.702385
0.689781
0.964516
0.560444
0.524063
0.667267
0.504879
0.617819
‐3.26985
0.867063
‐1.03076
‐0.87925
1.417084
1.397561
1.42701
1.37958
1.419853
1.785552
1.476475
1.394479
1.328118
1.349401
1.751701
1.608734
1.753658
1.468518
2.052189
1.784465
1.49059
1.4298
1.465719
2.408725
1.613231
1.3792
1.842166
0.581065
2.287857
1.963906
2.694948
1.879731
2.130317
0.267126
0.336382
0.529682
0.652878
2.683736
1.311845
0.608341
2.644839
1.828634
1.545718
2.388566
1.774649
1.711097
1.413098
2.030016
1.519808
2.185533
1.821124
2.788288
1.716337
0.451977
2.771446
1.693273
0.630293
1.656619
2.583521
1.486921
1.36688
3.318959
1.459635
1.419768
1.472931
0.685759
0.632758
1.811533
0.735227
2.220783
1.4426
1.943182
2.911062
1.649187
2.37028
1.752354
1.415986
1.926858
1.775664
1.800151
1.488726
0.725086
1.829521
1.568168
1.37912
1.352121
1.471038
0.625853
1.415399
1.403375
1.315914
1.539238
2.105637
0.668342
0.674435
0.729678
1.405758
2.186114
2.492563
1.910523
1.876287
2.008162
1.657873
2.191023
1.84541
2.050266
1.913433
1.623674
2.568949
2.546265
0.516447
1.435474
0.680168
1.541955
1.512682
1.424846
2.496404
2.307908
1.852724
1.751084
2.017264
1.491808
1.471124
1.624936
1.474141
1.505273
1.727124
1.406792
2.807432
3.294402
1.627193
1.613038
1.951409
1.474723
1.437999
1.588062
1.419004
1.534554
0.103676
1.823946
0.489451
0.54365
0.665133
0.315353
0.263122
‐0.64166
‐2.35785
‐0.56292
0.552608
‐0.2497
‐0.90794
‐1.38255
‐0.37111
‐0.62802
‐0.37363
0.96709
‐0.11816
‐0.5448
‐0.46067
‐0.56479
‐1.10013
‐0.8103
‐0.47413
‐0.13652
‐0.72674
‐0.71901
‐0.61861
0.441179
0.410167
‐0.45119
‐0.33358
0.263943
0.435592
‐0.90625
‐1.19641
0.250595
‐0.93936
0.579981
0.062796
0.942842
‐0.43392
‐0.55502
0.848555
0.679647
‐0.58275
0.660554
0.294078
0.021029
0.104247
‐0.4713
‐0.41172
‐0.30336
‐0.47301
‐0.25311
‐0.70119
‐0.57059
‐0.61357
1.033219
0.0312
0.42765
‐0.41665
‐0.36326
‐0.67193
0.045402
0.639963
‐0.45086
0.126095
‐0.4197
0.035514
‐0.29628
‐0.46753
‐0.05103
0.206924
‐0.44367
0.266171
0.224551
0.29266
‐0.05172
0.858425
0.321095
0.315924
0.52061
0.993629
0.273153
‐0.0039
‐1.61551
0.727759
‐0.12718
0.654424
‐0.81989
‐0.39007
0.885319
‐0.6246
‐0.96994
‐0.05931
0.316915
0.279636
0.742813
‐0.30482
0.48811
‐0.60933
‐0.41275
‐0.89217
‐0.22183
‐0.20944
0.159499
0.282757
‐0.55737
‐0.27829
0.178185
‐2.25206
‐1.88097
0.892174
0.459504
‐0.59117
‐0.70605
‐1.75215
‐0.26617
‐0.21073
‐0.44457
0.515429
0.027061
‐0.181
‐0.50861
0.065893
0.430821
0.656237
‐0.57998
0.854953
‐0.59043
‐0.02541
0.006476
0.363257
‐0.66513
0.344184
‐0.40397
‐0.72065
0.33435
‐0.10893
0.245833
1.644979
1.702273
1.602588
1.619256
1.600999
2.410986
2.146603
1.543085
1.397503
1.422585
2.788162
2.451992
2.757218
1.833
2.699985
2.547884
1.752576
2.003346
1.828235
4.550601
2.416344
1.511409
2.919967
‐2.16973
2.586974
2.748666
4.954701
2.250713
3.521238
‐6.17056
‐5.49226
‐2.84695
‐2.07955
5.148109
1.368422
‐2.33346
3.955862
2.149887
2.242403
4.501173
2.606479
2.310736
1.476454
2.714242
1.931456
3.338294
2.286955
3.367128
2.022602
‐3.13398
4.200615
2.352485
‐1.78929
1.493549
3.455931
1.348426
1.59119
6.354972
1.403189
1.389893
1.942413
‐1.67683
‐2.33821
2.489417
‐1.52327
2.313833
1.637165
2.369068
3.094522
1.632598
3.210497
2.965024
1.431458
3.255938
2.66332
2.310646
1.979159
‐1.46778
3.018624
2.026896
1.497257
1.314066
1.532583
‐2.18795
1.633288
1.714788
1.352116
1.580257
3.102563
‐2.1201
‐1.63079
‐1.7455
1.616055
4.299051
4.084684
3.315306
2.401418
3.739228
2.065678
2.765537
3.352232
3.207017
3.324281
2.29458
3.328926
3.676329
‐2.63962
1.679526
‐1.58584
2.371179
1.588552
1.535835
3.529914
3.782734
2.637024
2.250454
3.135962
1.507509
1.890564
2.196991
1.355257
1.917044
2.170405
1.495227
4.324233
3.635352
2.202754
1.789451
2.318101
1.35041
1.62529
1.956845
1.319532
1.471229
‐8.81328
2.519574
‐3.00752
‐3.29535
0.502926
0.482911
0.512995
0.464229
0.505741
0.83637
0.562157
0.479726
0.409384
0.432319
0.808757
0.685925
0.810367
0.554361
1.037164
0.835491
0.575884
0.515813
0.551609
1.268269
0.689953
0.463832
0.881403
‐0.78323
1.193997
0.973726
1.430257
0.910527
1.091068
‐1.90441
‐1.57183
‐0.9168
‐0.61511
1.424243
0.391597
‐0.71705
1.40318
0.870766
0.628277
1.256145
0.827533
0.774921
0.498862
1.021491
0.603889
1.127985
0.864829
1.479379
0.779333
‐1.14568
1.470639
0.759815
‐0.66591
0.728242
1.369338
0.572328
0.450887
1.730731
0.545608
0.505656
0.55869
‐0.54423
‐0.66027
0.857212
‐0.44374
1.151069
0.528671
0.958421
1.541545
0.721755
1.245058
0.809294
0.501807
0.946251
0.828358
0.848118
0.574079
‐0.46378
0.871466
0.649081
0.463748
0.435224
0.556835
‐0.6761
0.501209
0.488901
0.396065
0.622217
1.074257
‐0.58134
‐0.56825
‐0.45467
0.491349
1.128369
1.31763
0.933968
0.907881
1.005876
0.729334
1.131605
0.883942
1.035811
0.936163
0.699262
1.361178
1.348383
‐0.95331
0.521527
‐0.55604
0.624761
0.597108
0.510806
1.319851
1.206586
0.889648
0.808248
1.0124
0.577062
0.556919
0.700383
0.559875
0.590025
0.788371
0.492409
1.489251
1.720017
0.702385
0.689781
0.964516
0.560444
0.524063
0.667267
0.504879
0.617819
‐3.26985
0.867063
‐1.03076
‐0.87925
0.305734
0.283686
0.320104
0.286693
0.315891
0.3469
0.261882
0.310888
0.292939
0.303897
0.290068
0.279742
0.293908
0.302434
0.384137
0.327916
0.328593
0.257476
0.301717
0.278704
0.285536
0.306887
0.301854
0.36098
0.461542
0.354254
0.288667
0.40455
0.309854
0.308628
0.28619
0.322029
0.295792
0.276654
0.286167
0.307289
0.354709
0.405029
0.28018
0.279071
0.317491
0.335357
0.337878
0.376345
0.31266
0.337893
0.378158
0.439359
0.385312
0.365567
0.350101
0.322984
0.372163
0.487592
0.396229
0.424441
0.283364
0.272343
0.388834
0.363809
0.287627
0.324555
0.282385
0.344342
0.291305
0.497473
0.322919
0.404556
0.498153
0.44209
0.387808
0.272947
0.350556
0.290623
0.311025
0.367048
0.290062
0.315972
0.288697
0.320234
0.309732
0.331205
0.363331
0.309012
0.306871
0.285108
0.292923
0.393744
0.346248
0.274205
0.348449
0.26048
0.304042
0.262469
0.322578
0.281714
0.37806
0.269006
0.353072
0.409181
0.263687
0.322983
0.281614
0.304745
0.408894
0.366774
0.361154
0.310521
0.350627
0.263481
0.375882
0.332592
0.373905
0.318972
0.337368
0.359149
0.322835
0.382792
0.294578
0.318792
0.413113
0.307779
0.363237
0.32932
0.344397
0.473136
0.318867
0.385471
0.41608
0.415018
0.322443
0.340991
0.38262
0.419934
0.371014
0.344131
0.342728
0.266815
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STM4068
STM4081
STM4088
STM4089
STM4096
STM4100
STM4101
STM4103
STM4110
STM4112
STM4118
STM4119
STM4125
STM4137
STM4138
STM4139
STM4147
STM4150
STM4152
STM4159
STM4160
STM4161
STM4162
STM4163
STM4172
STM4182
STM4188
STM4190
STM4199
STM4218
STM4222
STM4226
STM4233
STM4234
STM4237
STM4245
STM4256
STM4271
STM4282
STM4299
STM4330
STM4356
STM4358
STM4360
STM4362
STM4363
STM4378
STM4380
STM4385
STM4386
STM4391
STM4392
STM4394
STM4415
STM4436
STM4446
STM4450
STM4452
STM4459
STM4460
STM4466
STM4475
STM4480
STM4482
STM4490
STM4492
STM4509
STM4516
STM4545
STM4563
STM4581
STM4586
STY0070
STY0277
STY0402
STY0414
STY0586
STY0963
STY0968
STY1106
STY1228
STY1314
STY1431
STY1488
STY1505
STY1509
STY1567
STY1602
STY2099
STY2115
STY2194
STY2202
STY2261
STY2303
STY2703
STY2769
STY2867
STY2893
STY2897
STY2906
STY3050
STY3296
STY3467
STY3653
STY3709
STY3710
STY3724
STY3725
STY3804
STY3808
STY3827
STY3864
STY4175
STY4517
STY4627
STY4655
STY4846
putative regulatory protein, gntR family
triosephosphate isomerase
tpiA
putative cytoplasmic protein
yiiU
putative methyltransferase in menaquinone biosynthesis protein
menG
50S ribosomal subunit protein L31
rpmE
cystathionine gamma‐synthase
metB
aspartokinase II in bifunctional enxyme: aspartokinase II
metL
putative cytoplasmic protein
General PTS family, enzyme I
ptsA
PTS system fructose‐like IIC component
frwC
putative Integral membrane protein
yijP
phosphoenolpyruvate carboxylase
ppc
regulatory protein sensor for oxidative stress, regulates
oxyR
UDP‐N‐acetylenolpyruvoylglucosamine reductase
murB
bifunctional: biotin‐[acetylCoA carboxylase] holoenzyme synthetase biotin operon
birA
pantothenate kinase
coaA
preprotein translocase IISP family, membrane subunit
secE
50S ribosomal subunit protein L1, regulates synthesis
rplA
50S ribosomal subunit protein L7/L12
rplL
deoxyxylulose‐5‐P thi‐S‐COSH tyrosine
thiH
deoxyxylulose‐5‐P thi‐S‐COSH tyrosine
thiG
putative involved in thiamine biosynthesis
catalyzes the adenylation of thisS as part
thiF
thiamin phosphate synthase (thiamine phosphate pyrophosphorylase)
thiE
zinc‐resistance associated protein
zraP
homoserine transsuccinylase
metA
B12‐dependent homocysteine‐N5‐methyltetrahydrofolate transmethylase, repressor of metEmetH
(alpha)‐aspartyl dipeptidase
pepE
putative cytoplasmic protein
putative inner membrane protein
putative outer membrane protein
yjbE
putative inner membrane protein
yjbA
chorismate pyruvate lyase
ubiC
p‐hydroxybenzoate: octaprenyltransferase
ubiA
SOS response regulator, transcriptional repressor (LexA family)
lexA
quinone oxidoreductase, NADPH dependent
qor
ssDNA‐binding protein controls activity of RecBCD nuclease
ssb
putative inner membrane protein
part of formate‐dependent nitrite reductase complex involved
nrfG
GPH family, melibiose permease II
melB
chaperone Hsp60 with peptide‐dependent ATPase activity, affects
mopA
putative sugar kinase
yjeF
N‐acetylmuramoyl‐l‐alanine amidase II, a murein hydrolase
amiB
delta(2)‐isopentenylpyrophosphate tRNA‐adenosine transferase
miaA
putative GTP‐ase, together with HflCK possibly involved
hflX
with HflC, part of modulator for protease
hflK
putative inner membrane protein
yjfN
putative hydrolase of the alpha/beta superfamily
yjfP
putative PTS enzyme IIsga subunit
ptxA
putative hexulose phosphate synthase (arabino hexulose phosphate
sgaH
30S ribosomal subunit protein S6
rpsF
primosomal replication protein N
priB
50S ribosomal subunit protein L9
rplI
fructose‐bisphosphatase
fbp
putative endonuclease
putative selenocysteine synthase [L‐seryl‐tRNA(Ser) selenium transferase
putative inner membrane protein
anaerobic ribonucleoside‐triphosphate reductase
nrdD
aspartate carbamoyltransferase, regulatory subunit (allosteric regulation)
pyrI
aspartate carbamoyltransferase, catalytic subunit
pyrB
putative carbamate kinase
valine tRNA synthetase
valS
putative permease
yjgQ
GntP family, L‐idonate transport protein
idnT
putative Mrr restriction endonuclease
putative cytoplasmic protein
putative cytoplasmic protein
putative inner membrane protein
yjiN
putative inner membrane protein
putative phosphoesterase
yjjU
putative ABC superfamily (atp_bind) transport protein
yjjK
transcriptional regulator (AraC/XylS family)
rob
citrate lyase alpha chain
citF2
hypothetical transcriptional regulator
yafC
PrpD protein
prpD
possible efflux pump
putative membrane protein
ybcI
anaerobic dimethyl sulfoxide reductase chain B
dmsB
pyruvate formate‐lyase 1 activating enzyme
pflA
putative transcriptional regulator (pseudogene)
conserved hypothetical protein
TonB protein
tonB
putative cytochrome
respiratory nitrate reductase 2 alpha chain
narZ
putative glycogen debranching protein
glgX
hypothetical protein
putative dimethyl sulphoxide reductase subunit
dmsB
hypothetical protein
high‐affinity zinc uptake system periplasmic binding protein
yebL
putative copper homeostasis protein
cutC
putative membrane protein
putative membrane protein
putative propanediol utilization protein PduV
pduV
putative reductase RfbI
rfbI
putative cobalamin adenosyltransferase
putative DNA‐binding protein
yfgA
hypothetical protein
putative exported protein
iroE
conserved hypothetical protein
putative exported protein
lipoprotein NlpD precursor
nlpD
hypothetical protein
protein chain initiation factor 2
infB
dihydroxyacid dehydratase
ilvD
phosphoribosylaminoimidazolecarboxamide formyltransferase and IMP cyclohydrolase (bifunpurH
phosphoribosylglycineamide synthetase
purD
thiamine biosynthesis protein
thiS
thiamine biosynthesis protein
thiG
putative carbohydrate kinase
periplasmic sulphate binding protein
sbp
L‐rhamnose isomerase
rhaA
hypothetical protein
hypothetical protein
conserved hypothetical protein
probable terminase subunit
Vi polysaccharide export protein
vexA
putative outer membrane protein
157
‐0.4316753
0.08820934
‐0.4223067
‐0.32543272
‐0.52524084
0.3551766
0.11339356
0.4829309
‐0.3237488
‐0.021079062
‐0.009622546
‐0.017977186
0.17255981
0.2412864
0.20755552
0.18044613
0.37733194
‐0.009967902
‐0.27338395
0.49387768
0.5696071
0.74364185
0.42741707
0.4782781
‐0.1561097
0.83211875
0.20014055
‐0.19743058
‐0.1392753
‐0.2195201
‐2.0814438
‐0.3906223
‐0.12871805
0.048525788
0.4908214
‐0.09936339
0.5871153
‐0.42716506
‐0.3483499
0.03857644
‐0.078556
‐0.26104313
0.084567875
0.21154094
0.7876796
0.8000094
‐0.08648893
0.15110746
‐0.17311272
‐0.09369197
0.2568282
0.16337097
0.17027046
0.31432876
‐0.07797606
‐0.42905918
‐0.013533389
‐0.015759228
‐0.15205932
‐0.1911988
‐0.2684855
‐0.13678817
0.063486755
0.07238632
0.3887054
0.5707446
0.03042349
‐0.00796756
‐0.036689278
‐0.24502057
0.26470044
0.18556161
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0.14265087
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