Due February 6 2014 MCB 432 Assignment 2 Using Entrez Too Name key 35 pt total We continue our exploration of some of the data and links available in the NCBI Entrez system 1a MJ1555 was the locus tag given to a protein encoding genes during the sequencing of a microbial genome In a cross database search http www ncbi nlm nih gov sites gquery for MJ1555 which three of the Entrez databases show matches the one word names are fine Nucleotide Gene and Protein 2 pt for all 1 pt for any 1b How many Protein entries were found 9 1 pt Follow the link to the Protein search results page Each title shown is the DEFINITION for the entry In all but one case the DEFINITION is the name or presumed function of the protein followed by the organism name in square brackets 1 Follow the link to the one that is different 2a What is the source database for this Entrez entry 2 UniProtKB Swiss Prot 1 pt 2b What is the DEFINITION of this sequence entry sorry about the lack of space my goof 1 pt RecName Full Aspartate tRNA ligase AltName Full Aspartyl tRNA synthetase Short AspRS 2c What is the accession number with version of this sequence entry Q58950 or Q58950 1 1 pt 2d What is the GenInfo GI number of this sequence entry 3 2500972 1 pt 2e What is the ORGANISM for this sequence Methanocaldococcus jannaschii DSM 2661 1 pt 2f What is the organism name in the TITLE of REFERENCE 1 Methanococcus jannaschii 1 pt Further down the page are the FEATURES of the sequence entry Each feature has a type indented over five spaces followed by a location of the feature in the sequence4 and then one or more additional descriptive items call qualifiers 5 Look down the FEATURES to find the following information 3a What is the product Aspartate tRNA ligase 1 pt 3b What is the EC number 6 1 1 12 1 pt 6 3c What is the note immediately following the EC number Aspartyl tRNA synthetase AspRS 1 pt 7 3d There is one Site with site type active What is the location given order 220 222 228 229 361 364 409 412 1 pt Go back to the Protein search results page Based on the ORGANISM in 2e you should be able to spot the two other sequence entries from the same organism Follow the link to GI 1592183 4a What is the source database for this Entrez entry GenBank 1 pt 8 4b What is the DEFINITION of this sequence entry aspartyl tRNA synthetase aspS Methanocaldococcus jannaschii DSM 2661 1 pt 4c What is the accession number with version of this sequence entry AAB99575 1 1 pt 4d What is the product aspartyl tRNA synthetase aspS c f the DEFINITION 1 pt 1 Entrez entries are copies of data from other databases their presentations of data differ The source database and corresponding accession number with version are below the bold title need the top of the page 3 A GenInfo number is the NCBI ID not source database ID for the protein or nucleotide sequence same entry another ID 4 Usually a range of positions indicated by first residue number dot dot last residue number as in 11 118 5 Usually indicated by slash qualifier name equals value as in locus tag MJ1555 hm sounds familiar 6 In this case is the alternative name from the title giving you an synonym the might help text searches 7 Locations can be complex in this case a list of residues and ranges of residues characterized as forming the active site 8 Remember this is a protein name or function and the organism so if I ask for the function I do not want the organism 2 Page 2 Assignment 2 Name 4e What is the EC number There is none given here 1 pt 4f What is the locus tag MJ 1555 1 pt 4g What is the old locus tag MJ1555 1 pt Go back to the Protein search results page Follow the link to GI 15669750 5a What is the source database for this Entrez entry NCBI Reference Sequence 1 pt 5b What is the DEFINITION of this sequence entry aspartyl tRNA synthetase Methanocaldococcus jannaschii DSM 2661 1 pt 5c What is the accession number with version of this sequence entry NP 248563 1 1 pt 5d What is the product aspartyl tRNA synthetase c f the DEFINITION 1 pt 5e What is the EC number 6 1 1 12 1 pt 5f What is the locus tag MJ 1555 1 pt 5g What is the old locus tag MJ1555 1 pt This is all well and good but this protein actually has an additional enzymatic activity EC 6 1 1 23 not included in any of the above descriptions or EC numbers Go to the ExPASy ENZYME database query page http enzyme expasy org In the Access to ENZYME by EC number query boxes enter 6 1 1 and 23 and then return or click Search 6a What is the Accepted Name for EC 6 1 1 23 Aspartate tRNA Asn ligase 1 pt 6b What is the value of in tRNA given in the Accepted Name Asn 1 pt 9 10 6c What is the value of in tRNA given in the Reaction catalysed Asx 1 pt I would tend to say that the fact that 6b and 6c are different is a bug not a feature This highlights the difference between defining a reaction and an enzyme which might do more than one reaction 11 Read the comments on the ENZYME page for 6 1 1 23 They might seem cryptic but we will come back to these enzymes 7 Follow the link to the KEGG Ligand Database for Enzyme Nomenclature entry for 6 1 1 23 7a This page lists two Reaction KEGG numbers what are they R03647 R05577 1 pt 7b This page lists one Pathway what is it ec00970 Aminoacyl tRNA biosynthesis 1 pt Follow the link to the pathway it is a diagram Notice that EC 6 1 1 23 highlighted in red is seen in two places the two reaction catalyzed by the enzyme 8a What are the products note the directions of the arrows of the two reactions L Aspartyl tRNA Asp and L Aspartyl tRNA Asn 1 pt 12 8b What EC number connects one of the two products in 8a to L Asparaginyl tRNA Asn 6 3 5 6 1 pt 8c What is the other EC number in this diagram that leads to L Asparaginyl tRNA Asn 6 1 1 22 1 pt 9 European spelling makes sense for databases created in Switzerland See http www ncbi nlm nih gov Class MLACourse Modules MolBioReview iupac aa abbreviations html for find out what this means You should become familiar with these abbreviations they are essential for dealing with data in the field 11 In this case I would say that the nomenclature is backwards the enzyme name defines one particular reaction one specific tRNA the reaction defines two reactions more than one …