Due Feb 27 2014 MCB 432 Name key Assignment 5 1 pt each 30 pt total Analyzing Sequences Using NCBI BLAST http blast ncbi nlm nih gov Blast cgi Readings important to this and future assignments include http www ncbi nlm nih gov blast about especially the entire section on BLAST Forms ftp ftp ncbi nlm nih gov pub factsheets HowTo NewBLAST pdf http www life illinois edu mcb 432 Glossary html especially GenInfo number The sequence data for this assignment are available from the class WWW server in the Assignment 05 directory http www life uiuc edu mcb 432 Assignments 05 or via the Schedule page on the course WWW site http www life uiuc edu mcb 432 Schedule html pep1 txt is a plain text file with a protein sequence in FASTA format 1 Using BLAST to Find Sequences Similar to a Protein Go to the NCBI BLAST Home page http blast ncbi nlm nih gov Blast cgi Follow the link from the BLAST Home page to protein blast Use your web browser s Copy and Paste functions to paste a copy of the pep1 definition and sequence into the Enter Query Sequence box Check that the following setting are set most but not all will be the default value Database Non redundant protein sequences nr 2 Algorithm blastp Max target sequences3 500 Short queries Automatically adjust Expect threshold 10 Word size 3 Matrix BLOSUM62 Gap Costs Existence 11 Extension 1 Compositional adjustments Conditional compositional score Filter unchecked and Mask both choices unchecked When this is all verified click one of the BLAST buttons Eventually you should get the Formatting Results page with the BLAST results It is a good idea to look at the page to see that it makes sense for what you thought you were trying to do 1a What is the RID Request ID for your search 4 Anything reasonable 1b What was the length of the query sequence 315 1c What is the number of sequences in the database searched 5 37 425 594 changes 1d What is the number of amino acids letters in the database searched 13 257 553 858 changes 1e Based on the above values what was the average length of the sequences in the database 13256553858 37425594 354 changes very little Some of the following questions cannot be answered from the summary table Sequences producing significant alignments you will need to go down to the Alignments portion of the report You might need to follow accession number links to get more details about any particular database sequence 2 For the best matching sequence unless I say otherwise I always mean the highest score answer the following 1 See the Glossary 2 Being non redundant in sequence a single entry can represent the same gene from one or more databases GenBank SwissProt Refseq PDB etc and can also represent identical sequences from multiple organisms 3 If you do not see this or the parameters that follow click the arrow next to Algorithm parameters to reveal these settings 4 Near the top for the results page to the right of NCBI BLAST blastp suite Formatting Results The RID allows you to access previous search results By default they are saved for 36 hours 5 Look at Other reports Search Summary just above Graphic Summary You might need to click on it Page 2 Assignment 5 2a 2b 2c 2d 2e 2f Name The first listed sequence entry is from RefSeq ref what is the accession number YP 007358325 1 What is the score in bits the parenthetical value is the raw score not bit score 630 What is the E value of the match Expect 0 0 What is the percent sequence identity of the query sequence and subject sequence 100 What is the percent positives6 is this match 100 From what organism does this sequence come include the strain Myxococcus stipitatus DSM 14675 2g What is the NCBI taxonomy ID of the organism 1278073 2i What function description is associated with this entry do not include the organism tRNA synthetase class I domain containing protein 2j I do not find this to be a very precise description If you have not done so expand the See 2 more title s What are the identifiers of the two additional sequence entries revealed ref WP 015346904 1 and gb AGC42641 1 1 pt each 2 pt total 2k Do either of these titles provide a more precise description of the protein function No they are exactly the same 3 For the second best matching sequence the first listed sequence entry is from RefSeq ref 3a What is the accession number associated with this entry YP 004663479 1 3b What is the E value of the match 0 0 3c What is the percent sequence identity of the query sequence and subject sequence 82 3d From what organism does this sequence come include the strain Myxococcus fulvus HW 1 3e What is the NCBI taxonomy ID of the organism 483219 3f What function description is associated with this entry tRNA synthetase class I domain containing protein 3g This sequence has a second entry title What function is associated with it it changed tRNA synthetase class I domain containing protein or glutamyl Q tRNA Asp ligase 4 Continue down to the match with accession number YP 002132677 1 4a What is the source database of this entry i e with the accession number ref or RefSeq 4b What function description is associated with this entry glutamate tRNA ligase 5 Continue down to the match with accession number WP 021297554 1 5a What is the source database of this entry ref or RefSeq 5b What function description is associated with this entry hypothetical protein 6 Continue down to the match with accession number WP 018977453 1 6a What is the source database of this entry ref or RefSeq 6b What function description is associated with this entry hypothetical protein So many choices but these proteins all have the same function which is best described in 3g 6 Aligned pairs of residues that have a positive score in the BLOSUM62 matrix