Exercises: Genome and Module Evolution in terms of Gene Content.

1. Phyletic patterns of pathways in COG

   1. Go to the STRING website at http://string.embl.de/. Press the search button. In the left panel change select protein families ("COGS"), and under there select "...by multiple protein names". Paste the following COGs into the query field.

      COG0763
      COG1044
      COG1043
      COG1519
      COG1663
      COG0774
      COG2877
      COG1212
      

      In the results go to the evidence view and and press co-occurrence. Fold the tree open by clicking on the "expand all" button. These COGs represent the "lipid A biosyntehsis pathway". Does this look like a nicely co-evolving pathway?
   
   
   2. Look at some of the exceptions to the "cohesiveness" (i.e. discordant phylogenetic profiels, disrupted co-occurrence). We want to inspect these weird presences, specifically in the animals. For example the presence of COG1043 in the honey bee. Go to the bottom of the page. Click on COG1043. Click on the button/tab for alignment and within that click on the "unaligned sequences". In the popup window look for the honey bee (Apis) sequence. Go to BLAST or PHMMER and search homologs of this sequence. What is the best hit and what is the lifestyle of the organism here. Speculate on the presence of COG1043 in Apis.
   
   
   3. Go to STRING home and as for the for the lipid A biosyntehsis pathway retrieve the phyletic patterns of the following set of subunits from the F0F1-type ATP synthase complex.

      COG0055
      COG0056
      COG0224
      COG0355
      COG0356
      COG0636
      COG0711
      COG0712
      

      How does this compare to the lipid A biosyntehsis pathway? Which COG stands out as the exception, especially with regards to the Archaea?
   
   
   4. Now do the same for the Archael ATP synthase complex.

      COG0636
      COG1155
      COG1156
      COG1269
      COG1394
      COG1436
      COG1527
      

      How does this pattern of help you to explain the outlier COG in the phyletic patterns of the F0F1-type ATP synthase COGs in the previous question? You can paste both gene lists together in STRING to see the total picture.