IMG Find Functions Exercises Answers
Note: For some of these exercises, there is more than one way to find the answer.
1. How many genes in img belong to COG1679? Which organisms in img have a
member of COG1679?
Go to Function Search under the Find Functions tab. In the box labeled Keyword,
write COG1679. In the Filters menu, select COG (list), then press Go. The number of
genes with the COG assigned are listed in the table. For the organisms, click on the
number in the Genome Count column.
2. How many members of the Major Facilitator Superfamily are in E. coli K12?
Go to Function Search under the Find Functions tab. In the Filters box select
Transporter Classification (list). In the Keyword box type “Major Facilitator”. In the
organism menu, select one of the E. coli K12 genomes, then click Go.
3. How many types of aminotransferases (EC 2.6.1.) are in Escherichia coli K12?
Go to Function Search under the Find Functions tab. In the box labeled Keyword
enter 2.6.1. In the Filters, select EC number or enzyme name (inexact). In the organism
list, select one of the Escherichia coli K12. Press go to see the list of aminotransferases.
4. Do any Archaea have homogentisate 1,2-dioxygenase (EC 1.13.11.5)?
Use the Function Search under the Find Functions tab. In the Keyword box enter
1.13.11.5. In the Filters box select EC Number (list). In the Genome Filter section, in
the Domain menu, select Archaea. Click on Go to find the result.
5. In the COG category signal transduction mechanisms, what COG is the most
prevalent in Saccharomyces cerevisiae? Escherichia coli K12? Methanocaldococcus
jannaschii?
Go to the COG Browser under the Find Functions tab. Click on Signal transduction
mechanisms [T]. Press Select All, then Add Selected to Function Cart. You are now in
the Function Cart. Click on the Profile & Alignment tab. In the list of organisms select
M. jannaschii, E. coli, and S. cerevisiae (You have to use control-click to select more
than one organism). Then click on View Functions vs. Genomes. To see the COG with
the highest number of genes for each organism, click on the organism name in the
column heading.
After doing this, empty the function cart by going to the Function cart and clicking on
Remove selected, the blue button close to the top of the page.
6A. View histidine biosynthesis in four Bacillus anthracis genomes – A2012, Ames,
Ames ancestor, and Sterne.
This can be done either with IMG Terms or with COGs. For COGs, go to the COG
Browser subtab of the Find Functions tab. Click on Histidine biosynthesis under Amino
acid transport and metabolism [E]. Click Select All then Add Selected to Function Cart.
You are now in the Function Cart. Click on the tab for Profile & Alignment. Select
the four B. anthracis in the organism list and click on View Functions vs. Genomes.
6B. Compare the organisms with respect to the given pathway (Do they miss
enzymes?)
Two B. anthracis genomes lack phosphoribosyl-ATP pyrophosphatase,
phosphoribosyl-AMP cyclohydrolase, and histidinol phosphatase.
6C. Determine if they really miss or there are problems in the ORF calls..
We will do two things here: 1) check the neighborhood surrounding these genes, and
2) use tblastn to see if the enzymes are present.
1) Select one of the enzymes that is present in all four genomes. You should now be
on a Gene Detail page. Go to the bottom of the page and select Top IMG Homolog Hits
in the Homolog Selection menu. Select the genes from the other three B. anthracis
genomes, then click on Add Selections to Gene Cart. You are now in the Gene Cart.
Select the Gene Neighborhoods tab and click on Show Neighborhoods. In B. anthracis
Ames and Ames ancestor there is a gap where the two enzymes should be found.
2) Do the function profile again (as in 6A). Select one of the phosphoribosyl-ATP
pyrophosphohydrolase genes from one of the two genomes that have this gene called.
You should now be on a Gene Detail page. Get the amino acid sequence by clicking on
the Amino Acid Sequence Length, selecting the sequence and selecting Edit -> Copy
from the browser tab. Go to the BLAST subtab under Find Genes. Paste the amino acid
sequence into the box. Select tblastn and select B. anthracis Ames and Ames ancestor in
the organism selection box. Click on Run BLAST. You will see that there is a 100%
match in both of these strains, but the gene was not called by the gene finder.
7. Do all finished Sphingomonadales have the Embden-Meyerhof pathway? EntnerDoudoroff pathway?.
Under the Find Genomes tab, select Genome Browser. Click on the View
Phylogenetically button near the top of the page. Select all of the finished
Sphingomonadales genomes (Finished genomes have “[F]” after the name.
Sphingomonadales are in alpha-proteobacteria), then click on Add Selected to Genome
Cart at the top of the page. Go to the IMG Pathway “Standard Embden-Meyerhof
pathway”. On the IMG Pathway Details page, click Select All, then unselect “Add this
pathway to the function cart.” Click on Add Selected to Function Cart. In the Function
Cart, click on the Profile & Alignment tab. Select all the Sphingomonadales and click on
View Functions vs. Genomes. Only one of the genomes has a phosphofructokinase.
Do the same with the IMG Pathway “Standard Entner-Doudoroff pathway”. Seven of
the genomes have this pathway. Remember to go back to the Genome Browser and click
Select All, then Add Selected to Genome Cart.
8. How many proteins in E. coli K12 have both GGDEF and EAL domains? How
many have GGDEF but not EAL domain?
Go to the Gene Search under the Find Genes tab. Enter “GGDEF, EAL” in the
Keyword box and select Pfam Domain Search (list) as the filter. Select E. coli K12 in the
organism box, then click on Go.
To find GGDEF but not EAL, follow the same steps but enter “GGDEF, !EAL” in the
Keyword box.