Group discussion

1
Group discussion

• Name this protein

2
Protein sequence, from Aedes aegypti automated
annotation

• gt25558.m01330
• MIHVQQMQVSSPVSSADGFIGQLFRVILKRQGSPDKGLICKIPPLSAARR
  EQFDASLMFE
• REPWFYERILPEFEAYQRAKGVGERDGFVAYAKSYVAYYKSMDQGTVLVM
  EDLGRRGFRM
• YNKLLPLDYNHVKLAMVQLGRFHAVSFAMKRDRQKVYESLKVSNPIVEMF
  RKNRYCRFLV
• SESLKLALEIPGLTEMERTVLNQLKDNVLAEFEACLDIGQAEPYTAIVHN
  DCWINNCMFS
• YEEDGLHPKELILIDWQLGCCAAPAVELIYLFYLCTDTQFRAKHFEEMVQ
  LYHQSFGILL
• RKLGGDSDVDYPYEVLKKQLRRLGRYGVMMGSFLVPTMCIPSEDLPNLDE
  SAARQKSTDQ
• 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
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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
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SMART protein signature
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SignalP
There is no signal peptide in our sequence.
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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,
  putativebut 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.