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