Hello!

I am re-posting this question with updated info as I am still having difficulty with just question 2 and 3 after attempting to answer them myself. I've attached the group A and B sequences. I've also attached my reasoning showing that these groups are homologs as well as the phylogeny.fr phylogentic tree of A and B sequences. They are in the document: "extras." This can help with questions 2 and 3:

Question 2: Do groups A and B have the same function? Are any of these sequences paralogs? - Explain. Again, I'm confused. I know what paralogs are. Am I supposed to look at the function of each protein sequence individually and then compare? That can't be right as it would be grossly inefficient. I did this species/protein tree superimposition once. The species tree looks completely different, and I used this site to create the species tree: http://itol.embl.de/tree/21316591127478961509489746

I used the general species IDs, not any specific strains. How am I supposed to know what specific strains to use (if applicable) when all these sequences are hypothetical and not well annotated?

Question 3: Find the structure of one member of this family and post the PDB number. -I've run blast with multiple different databases, cross-referenced multiple databases and searched PDB in many ways to find the PDB ID of many of these hypothetical proteins. It seems impossible to retrieve a PDB ID as requested.

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