Due noon May 13 2014 MCB 432 Assignment 10 Key Name key There are two options for turning in this assignment i email and ii the box outside 383 Morrill Hall If you drop it in the box keep a copy in case something happens This assignment has a separate instruction sheet on the course WWW site you need to go there for the data anyway Some questions include additional or alternative instructions Scoring Unless noted otherwise the scoring is A Function is 2 points partial credit for close EC numbers are an overall score for the assignment B Organism is 1 point Strains are an overall assessment for the assignment C Explanation is 1 point I am pretty generous but there are limits This is 55 points In addition over the assignment as a whole Up to 5 points for organism strains one point for each genome identified correctly to the strain level There were 5 genomes for which this was trivial so this should have been an easy 5 points There were two others that were harder Thermus aquaticus YT 1 and Wohlfahrtiimonas chitiniclastica DSM 18708 In these latter two cases I actually accepted a very similar alternative strain Up to 5 points for EC numbers one point for an EC number associated with a reasonable function Four were very straightforward so only one of the remaining 3 possible was required for full credit Up to 5 points for PubMed IDs with a maximum of two awarded for any given problem A table at the end of the key gives the PMIDs that were accepted or not accepted for each problem As pointed out in the instructions The complete genome sequence of is generally not an acceptable answer for justifying a particular function assignment This makes a total of 70 points about 19 of the total points in the course Individual problems 1 gi 378949564 this is an NCBI GenInfo number for a protein sequence GenInfo numbers are the Entrez identifier for a copy of a sequence from some other database In addition to the usual parts of the answer what is the original database that the sequence is from and what is the accession number of the protein in that database A 3 demethylubiquinone n 3 methyltransferase 3 pt for both of these 2 pt for one 2 polyprenyl 6 hydroxyphenol methylase protein UbiG this is named for the gene not the enzyme activity or 1 pt EC 2 1 1 64 and EC 2 1 1 222 the second EC requires following link to Swiss Prot entry B Pseudomonas fluorescens F113 C The GenInfo number takes you straight to the Entrez entry This gives the organism and a not very good function The Related Sequences link or BLASTP give you many alternatives that are less jargonish However finding the 2 polyprenyl 6 hydroxyphenol methylase is harder and the second EC number take some rooting around such as looking at a Swiss Prot entry among the related sequences D RefSeq immediately below the large print title at the top of the page 1 pt YP 005207052 1 not NC 016830 1 which is the DNA sequence 1 pt Page 2 Assignment 10 Name key 2 gb ADE02987 1 this is a GenBank protein accession number There is only one useful annotation among the 20 or so best matching sequences A Dolichyl monophosphomannose protein mannosyltransferase AglS 2 pt membrane protein putative this is pretty bad or 1 pt EC 2 4 1 109 I had missed this one but some students found it B Haloferax volcanii DS2 C The Accession number takes you straight to the Entrez entry This gives the organism and a very vague function The Related Sequences link or the Identical Sequences link take you to a list of similar sequences of which the entry for sp D4GYH0 1 leaps out as having a much more descriptive name It is also possible to get there with BLASTP but NCBI lists the RefSeq entry first for 5 identical proteins so it is hard to see the Swiss Prot title in the Descriptions hypothetical protein HVO 1526 Haloferax volcanii DS2 ref WP 004041404 1 hypothetical protein Haloferax volcanii sp D4GYH0 1 AGLS HALVD RecName Full Dolichyl monophosphomannose protein mannosyltransferase AglS AltName Full Archaeal glycosylation protein S gb ADE02987 1 membrane protein putative Haloferax volcanii DS2 gb ELY35751 1 hypothetical protein C498 02985 Haloferax volcanii DS2 You can also see it scrolling down to the alignments and expanding the See 4 more title s Once you see it you might notice that there are a few similar titles among the insignificant BLAST matches The Swiss Prot entry also includes a PubMed links for this protein 22730124 23086206 Page 3 Assignment 10 Name key 3 ref NP 294020 this is an NCBI RefSeq protein accession number The correct answer to this has been biologically known for a long time but it is nowhere among the matching sequences this enzyme adds the third amino acid to the stem peptide involved in cell wall cross linking but the amino acid added is not 2 6 diaminopimelate UDP Nacetylmuramyl peptide synthase and UDP N acetylmuramyl tripeptide synthetase are true but only because they do not specify the amino acid being added the first of these descriptions does not even tell us that it is the third amino acid Since most of the top matches are from Deinococcus try searching PubMed for Deinococcus sp nov peptidoglycan no quotes and looking at some of the abstracts In addition to the usual parts of the answer what is the genus name of the best matching sequence in the NCBI BLAST nr protein database that does not come from a Deinococcus A UDP N acetylmuramoylalanyl D glutamate L ornithine ligase 2 pt UDP N acetylmuramoylalanyl D glutamate 2 6 diaminopimelate ligase or 1 pt UDP N acetylmuramoylalanyl D glutamate L lysine ligase or 1 pt I gave credit for EC 6 3 1 13 or 6 3 1 7 even though the function is wrong B Deinococcus radiodurans R1 C Okay the accession takes you to the protein which gives you the organism and a function that I tell you is wrong because it says that it uses 2 6 diaminopimelate So if the enzyme does not use 2 6 diaminopimelate what does it use In searching PubMed Deinococcus gets related organisms sp nov gets organism descriptions and peptidoglycan must be relevant or I would not have included it in the query So here is the text in the first 10 abstracts related to peptidoglycan peptidoglycan contained D alanine L glutamic acid glycine and L ornithine di amino acid L ornithine was detected in its peptidoglycan ornithine was found to be the diamino acid in the cell wall peptidoglycan ornithine as the diamino acid in the cell wall peptidoglycan The peptidoglycan of strain TM 1 T contained ornithine alanine glycine and glutamic acid The