Due Apr 24 2014 MCB 432 Name key Assignment 9 30 pt total Introduction to the SEED http core theseed org FIG seedviewer cgi http core theseed org FIG index cgi This assignment requires information in the Assign 09 notes pdf file on the course WWW site Go to http core theseed org FIG seedviewer cgi the pretty interface to the Core SEED This is a generic search page for much of the content of the SEED 1 Enter fig 443906 9 peg 1877 without the quotation marks into the search box and press return Because this is the unique identifier of a genomic feature you should only get one match 1a What is the name of the Genome Clavibacter michiganensis subsp michiganensis NCPPB 382 1b What is the Function UDP N acetylmuramate glycine ligase 2 Click on the Feature ID to follow the link to the page with more details about this feature 2a What is the taxonomy id 443906 2b Click on the taxonomy id number to follow the link to the NCBI taxonomy What is the phylum of this organism Actinobacteria 2c What is the family of this organism Microbacteriaceae 2d Go back to the SEED feature page for fig 443906 9 peg 1877 How many alignments and trees include this protein 3 3 Click the show button for annotation history There should now be a table with three entries 3a When was the last most recent annotation made 4 7 2014 3b Who is listed as the Annotator for this change gjo Click the show button for data base cross references dbxref There should now be six entries showing links to related data in other databases 4a Follow the link to UniProt A5CS50 What is the Recommended name in UniProt UDP N acetylmuramate L alanine ligase hmm a little different than 1b 4b What EC number do they give for this protein 6 3 2 8 4c Go back to the SEED feature page and follow the link to RefSeq YP 001222600 1 What is the DEFINITION of the sequence do not include the organism name putative UDP N acetylmuramate alanine ligase 4d Is this function more like that in the answer to 1b or 4a 4a 4e What EC number do they give for this protein 6 3 2 8 Go back to the SEED feature page and flow the link to the trees as in alignments and trees Because the protein is in more than one tree we need to specify which we want Click the radio button for the first tree listed 00000078 and click Update 5 Use your browser s search function to find Clavibacter on the page it only occurs once 5a There is one other genome specifically related to the Clavibacter protein sequence that has been given the same function What is the genome name for that protein marine actinobacterium PHSC20C1 5b Looking at the branching order there are two more genomes with proteins that are specifically related to these two but which have been assigned a different function What are the genome names for these proteins Tropheryma whipplei TW08 27 and Tropheryma whipplei str Twist 1 pt for both Page 2 Assignment 9 Name key 5c The most common function in a tree is given the background color brown What is that function for this tree UDP N acetylmuramate alanine ligase EC 6 3 2 8 5d The organism name Erysipelothrix rhusiopathiae only occurs one place in this tree What is the function of the protein from this genome UDP N acetylmuramate L serine ligase 5e What two other genomes have proteins specifically related to this Erysipelothrix rhusiopathiae protein and have been assigned the same function 1 pt each Erysipelotrichaceae bacterium 5 2 54FAA Holdemania filiformis DSM 12042 5f The organism name Chlamydia muridarum only occurs one place in this tree What is the function of the protein from this genome UDP N acetylmuramate alanine ligase EC 6 3 2 8 D alanine D alanine ligase EC 6 3 2 4 this is a two domain protein with two functions 6 Go back to the SEED feature page for fig 443906 9 peg 1877 In the green menu bar near the top of the page select Feature Evidence vs FIG in the Feature menu On that page click the Tabular Protein Evidence tab This will show a table of the 50 most similar sequences in the SEED 6a What is the name of the genome Organism with the greatest similarity 1 Salinibacterium sp PAMC 21357 6b What is the E value of this match 3e 127 or 3 10 127 but not 3e 127 6c What is the identity of this match 70 36 seems to have an extra significant figure 6d What is the name of the genome Organism of the least similar protein that has been assigned the same function as fig 443906 9 peg 1877 Zimmermannella faecalis ATCC 13722 6e What is the identity of this match 61 90 6f What is the name of the genome Organism with most similar protein that has an assigned function that differs from that of fig 443906 9 peg 1877 Cellulomonas fimi ATCC 484 6h What is the identity of this match 49 89 quite similar protein but different function 6i What is the function assigned to this protein UDP N acetylmuramate alanine ligase EC 6 3 2 8 7 Go down to the matching protein in Cellulomonas flavigena DSM 20109 Note the background colors especially for the Aligned Positions of Hit This means that the query only matches that later part the blue color means a later part of the database sequence and that the beginning might have a different function Click on the protein ID fig 446466 7 peg 1598 to go the SEED feature page Note that the assigned function is split into two roles 7a Is the first role the same as 5f or 6i if so which No 7b Is the second role the same as 5f or 6i if so which Yes 6i The fusion in 5f is different than that in this question though one domain is in common 1 I mean the first one in the table with a primarily white background