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Group discussion

Group discussion . Name this protein. Protein sequence, from Aedes aegypti automated annotation. >25558.m01330 MIHVQQMQVSSPVSSADGFIGQLFRVILKRQGSPDKGLICKIPPLSAARREQFDASLMFE REPWFYERILPEFEAYQRAKGVGERDGFVAYAKSYVAYYKSMDQGTVLVMEDLGRRGFRM

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Group discussion

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  1. Group discussion Name this protein

  2. Protein sequence, from Aedes aegypti automated annotation >25558.m01330 MIHVQQMQVSSPVSSADGFIGQLFRVILKRQGSPDKGLICKIPPLSAARREQFDASLMFE REPWFYERILPEFEAYQRAKGVGERDGFVAYAKSYVAYYKSMDQGTVLVMEDLGRRGFRM YNKLLPLDYNHVKLAMVQLGRFHAVSFAMKRDRQKVYESLKVSNPIVEMFRKNRYCRFLV SESLKLALEIPGLTEMERTVLNQLKDNVLAEFEACLDIGQAEPYTAIVHNDCWINNCMFS YEEDGLHPKELILIDWQLGCCAAPAVELIYLFYLCTDTQFRAKHFEEMVQLYHQSFGILL RKLGGDSDVDYPYEVLKKQLRRLGRYGVMMGSFLVPTMCIPSEDLPNLDESAARQKSTDQ YELPYKLDEKSLPVYQERMLGVIRDAIKFGCFDL Name this protein.

  3. The output of BLASTP against NR • Lots of full-length hits

  4. Top hits Here is a good illustration of the danger of the transitive proliferation of names from annotations to future annotations. In this case, the Aedes aegypti protein sequences, recently released by TIGR, are in Genbank. Our query sequence is one of them. Therefore, many of the hits we first encounter in our Blast output belong to this release. The top hit is our sequence to itself.

  5. Searching for a characterized hit • We go through all of the hits to find a characterized match. Here it is: (next page)

  6. First characterized match

  7. Exploring the best characterized match

  8. HMM Hit is to PF02958, Domain of unknown function (DUF227) • Total score: 256.6 • Trusted cutoff: -117.60 • Noise cutoff: -118.00 • Total expect: 7e-74 The alignment looks good…

  9. HMM details

  10. Interpro

  11. SMART protein signature

  12. SignalP There is no signal peptide in our sequence.

  13. TargetP • No clear targeting sequence

  14. TmHMM

  15. Results • Blast: • HMM: • Interpro: • SignalP • TargetP • TmHMM: How would you name this protein? Why?

  16. Discussion • Blast: 42% similarity over 72% of length to a studied protein, Juvenile hormone-inducible protein 26 from Drosophila melanogaster, another Diptera (insect). Its function is not known. • HMM: very strong hit to PF02958, Domain of unknown function (DUF227), a domain found in insects and C. elegans. A member of the Protein kinase superfamily. • Interpro: IPR004119 Protein of unknown function DUF227. This family includes proteins of unknown function. All known members of this group are proteins from drosophila and Caenorhabditis elegans. • SMART: SM00587 CHK. ZnF_C4 abd HLH domain containing kinases domain. A subfamily of choline kinases. • SignalP: No signal peptide. • TargetP: No clear targeting sequence. • TmHMM: None. Discussion: The 42% similarity over 72% of the length of this protein is marginal. It is not definitive enough to name the protein “Juvenile hormone-inducible protein” by our standards. However, depending on the standards of your project, you might append the word “putative” to it: “Juvenile hormone-inducible protein, putative”—but a conservative call would be “conserved hypothetical protein.” Another option is to call it protein kinase, putative. Discuss which of these you believe is most supported.

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