Table S4. Selected protein kinase- phosphoprotein pairs suggesting functional
roles for uncharacterized proteins
Substrate
protein
Ncb2p
Function *
Transcriptional
regulation
Protein kinase
(unknown
Akl1p
function)
Pma1p,
Proton pump,
Pma2p
regulation of pH
Pheromone alpha
Ste2p
factor receptor
Phosphatidylserin
Cho1p
e synthase
Phospholipid
binding, cell
Boi2p
polarity
Trehalose
phosphate
synthase
(carbohydrate
metabolism, stress
Tsl1p
response)
Polyamine
Ypr156cp transport
Protein kinase
(unknown
Ksp1p
function)
Protein kinase
(unknown
Ydr466wp function)
Protein kinase
(unknown
Ydr466wp function)
Pyruvate
dehydrogenase
component
(pyruvate
Pda1p
metabolism)
Protein kinase
Sgv1p
(transcription)
Chitin synthase
(cytokinesis,
osmotic stress
Chs2p
response)
Phospholuconolac
Sol2p
tonase (tRNA
Predicted
protein
kinase
Function *
Protein kinase (unknown
Akl1p
function)
Cellular morphogenesis,
cytokinesis, endocytosis,
DNA repair, cell growth,
chromosome segregation,
CK1 group meiosis, mitosis, nuclear
*****
division
Phosphopeptide
**
Scansite
score
***
Estimated
probability
****
HHNSVSD
0.256
0.1
DKDSNSSITI
0.124, 0.144
0.75, 0.6
— *******
Kin4p
Unknown
RVSTQHE
Kns1p
DMYTPDTAAD 0.207
0.2
Ksp1p
Unknown
Protein kinase (unknown
function)
GTLSRRA
0.143
0.6
Ksp1p
Protein kinase (unknown
function)
PSPTRNS
0.121
0.75
RSATRSPSA
0.146
0.6
RTSTAISRTR
0.144
0.6
NESSSTSPDE
0.144, 0.062
0.6, 0.9
SKASSEP
0.082
0.85
Cdc28p
Meiosis
Cyclin-dependent protein
kinase, regulation of mitosis
and meiosis
EPSSPPP
0.02
0.99
Ygl179cp
Unknown
GGHSMSD
0.143
0.6
Yjl057wp
Unknown
AKYTSVV
0.255
0.1
Ypr106wp Unknown
YRDSAHN
0.143
0.6
Ypr106wp Unknown
CKSTASAAE
0.187
0.33
Protein kinase (unknown
function)
Protein kinase (unknown
Ksp1p
function)
Cellular morphogenesis,
cytokinesis, endocytosis,
DNA repair, cell growth,
chromosome segregation,
meiosis, mitosis, nuclear
CK1 group division
Ksp1p
Mek1p
processing)
Bre5p
Unknown
Bre5p
Unknown
Mlf3p
Unknown
Mlf3p
Unknown
Mrh1p
Unknown
Mrh1p
Unknown
Ycr023cp Unknown
Ycr023cp Unknown
Ydl189wp Unknown
Ydl189wp Unknown
Ydr090cp Unknown
Yfr016cp
Yfr017cp
Unknown
Unknown
Yfr017cp
Unknown
Yfr024cp
Unknown
Yfr024cp Unknown
Yhr097cp Unknown
Yhr097cp Unknown
Yhr132wp Unknown
Cyclin-dependent protein
kinase, regulation of mitosis
Cdc28p
and meiosis
Axial budding, septin ring
Kcc4p
assembly
Cyclin-dependent protein
kinase, meiosis, regulation of
Ume5p
transcription (Pol II promoter)
Cyclin-dependent protein
kinase, meiosis, regulation of
Ume5p
transcription (Pol II promoter)
Protein kinase (transcriptional
Ctk1p
regulation (Pol II promoter))
Cyclin-dependent protein
kinase, regulation of mitosis
Cdc28p
and meiosis
Actin filament organization,
cell wall organization and
Pkc1p
biogenesis
Cellular morphogenesis,
cytokinesis, endocytosis,
DNA repair, cell growth,
chromosome segregation,
meiosis, mitosis, nuclear
CK1 group division
Mek1p
Meiosis
Cyclin-dependent protein
kinase, meiosis, regulation of
Ume5p
transcription (Pol II promoter)
Actin filament organization,
cell wall organization and
Pkc1p
biogenesis
Cyclin-dependent protein
kinase, meiosis, regulation of
Ume5p
transcription (Pol II promoter)
Mek1p
Meiosis
cAMP-dependent protein
kinase, Ras signal
transduction, pseudohyphal
Tpk1p
growth
Amino acid biosynthesis,
regulation of translational
Gcn2p
initiation
Amino acid biosynthesis,
regulation of translational
Gcn2p
initiation
Rck2p
Regulation of meiosis
Cellular morphogenesis,
cytokinesis, endocytosis,
DNA repair, cell growth,
chromosome segregation,
meiosis, mitosis, nuclear
CK1 group division
cAMP-dependent protein
kinase, Ras signal
transduction, pseudohyphal
Tpk1p
growth
NASTPSSSPE
0.165
0.5
NASTPSSSPE
0.1
0.75
PATSPYV
0.084
0.85
PYVSPQQ
0.099
0.8
PAATPNL
0.145
0.6
PVASPRP
0.063
0.9
HRSSLSSLSN
0.101
0.8
HRSSLSSLSN
RRASVEG
0.125
0.064
0.75
0.9
VEGSPSS
0.1
0.8
SRLSV--
— *******
TPESPKV
RRRSTNY
0.02
0.127
0.99
0.75
RRSSGPM
0.19
0.33
PTNSGGSGGK 0.233
0.05
PTNSGGSGGK 0.143
ANSSTTTLD
0.077
0.6
0.85
ANSSTTTLD
0.206
0.33
RRMSSSSG
0.101
0.75
Yhr132wp Unknown
*Yhr186cp Unknown
Yhr186cp Unknown
Yhr186cp Unknown
Yml029wp Unknown
Yml029wp Unknown
Yml072cp Unknown
Yml072cp Unknown
Ymr196wp Unknown
Ymr196wp Unknown
Ymr295cp Unknown
Ymr295cp Unknown
Ynl136wp Unknown
Ynl136wp Unknown
Ynl156cp Unknown
Ynl156cp Unknown
Ynl156cp Unknown
Ynl321wp Unknown
Yor042wp Unknown
Yor042wp Unknown
Calmodulin-dependent protein
kinase
RRMSSSSG
Actin filament organization,
Pbs2p
osmoregulation
KAGSIQTQSR
Actin filament organization,
Prk1p
cytokinesis
ANLSTMSLVN
MAPKKK, actin cytoskeleton
organization and biogenesis,
osmosensory signaling
Ssk2p
pathway
ANLSTMSLVN
Yak1p
Cell growth and maintenance RSQSPVSFAP
Cell wall organization and
biogenesis, cellular
Sps1p
morphogenesis
RSQSPVSFAP
Cyclin-dependent protein
kinase, regulation of mitosis
Cdc28p
and meiosis
TSVTPRA
Mitotic spindle checkpoint,
Mps1p
spindle pole body duplication RASSFAR
Double-strand break repair,
meiosis, mitotic chromosome
segregation, response to
Mck1p
stress, sporulation
SGLTPQS
Amino acid biosynthesis,
regulation of translational
Gcn2p
initiation
SISSDKA
Cellular morphogenesis,
cytokinesis, endocytosis,
DNA repair, cell growth,
chromosome segregation,
meiosis, mitosis, nuclear
CK1 group division
SSISNTSDHD
Regulation of DNA
replication, G1/S and G2/M
transition of mitotic cell cycle,
cell ion homeostasis, cell
polarity, flocculation,
regulation of transcription Pol
CK2 group I and Pol III promoters),
******
response to DNA damage
SSISNTSDHD
Actin filament organization,
Ark1p
cytokinesis
GNTSNET
Double-strand break repair,
meiosis, mitotic chromosome
segregation, response to
Mck1p
stress, sporulation
NETSPKR
Calmodulin-dependent protein
Cmk2p
kinase
RSVSIDSTKY
Cytokinesis, regulation of exit
Cdc15p
from mitosis
RSVSIDSTKY
Calmodulin-dependent protein
Cmk2p
kinase
RILSASSIHE
Cytokinesis, regulation of exit
Cdc15p
from mitosis
ATPSSPK
MAPKKK, pseudohyphal
growth, conjugation with
Ste11p
cellular fusion
YIDTPDTETK
Bub1p
Mitotic spindle checkpoint
YIDTPDTETK
Cmk2p
0.1
0.8
0.104
0.8
0.167
0.5
0.038
0.084
0.95
0.85
0.145
0.6
0.101
0.8
0.128
0.75
0.102
0.8
0.124
0.75
0.082
0.85
0.168
0.5
0.122
0.75
0.081
0.85
0.099
0.8
0.146
0.6
0.119
0.75
0.165
0.5
0.058
0.149
0.9
0.6
Yor052cp Unknown
Yor052cp Unknown
Yor175cp Unknown
Yor175cp Unknown
Ypl247cp Unknown
Yro2p
Sec31p
Unknown (heat
shock protein
homologue)
Endoplasmic
reticulum-Golgi
transport,
autophagy
Receptor signalling, MAPK
cascade
RSSSNSSVTS
Cellular morphogenesis,
cytokinesis, endocytosis,
DNA repair, cell growth,
chromosome segregation,
meiosis, mitosis, nuclear
CK1 group division
RSSSNSSVTS
Amino acid biosynthesis,
regulation of translational
Gcn2p
initiation
MSFSGYSPKP
Double-strand break repair,
meiosis, mitotic chromosome
segregation, response to
Mck1p
stress, sporulation
MSFSGYSPKP
Endocytosis, sphingolipid
Ypk1p
metabolism
KRSSISF
Regulation of DNA
replication, G1/S and G2/M
transition of mitotic cell cycle,
cell ion homeostasis, cell
polarity, flocculation,
regulation of transcription Pol
I and Pol III promoters),
CK2 group response to DNA damage
DVATDSE-Ykl116cp
Atg1p
Vesicle organization and
biogenesis, autophagy
RVPSLVA
0.039
0.95
0.082
0.85
0.233
0.05
0.082
0.85
0.083
0.85
— *******
0.062
0.9
* Functional annotations based on RefSeq (Pruitt et al. 2003)
** The phosphorylated residues are underlined, and the residues not present in the
phosphopeptide sequences (Ficarro et al. 2002) are shown in italic. When there is more
than one phosphorylation site, the one discussed is shown in bold, unless the same protein
kinase is predicted for all sites in the peptide.
*** Scansite (Yaffe et al. 1999) scores were calculated as described in the Methods
section. When the same protein kinase is predicted for more than one site in the peptide,
the scores are given for the respective sites, starting at the N-terminus. If more than one
protein kinase yields a similar score, all the possible kinases are listed.
**** Probabilities were calculated as described in the Methods section (Figure 1). When
the same protein kinase is predicted for more than one site in the peptide, the values are
given for the respective sites, starting at the N-terminus.
***** Protein kinases Cka1p, Cka2p or Cdc7p. The predicted specificities are too similar
to be distinguished.
****** Protein kinases Yck1p, Yck2p, Yck3p or Hrr25p. The predicted specificities are
identical.
******* Scansite score could not be measured because the phosphorylation site is too
close to the C-terminus.