Subject: TAK-1 mapping
I am a bit puzzled as to the mapping of a protein kinase, TAK-1.
I the general information a genbe encoding this kinase is mapped at 71B5,
however a personal communication from M. O'Connon puts (in the TAK-1 file)
places it at 19E1-4. It would be good if this was sorted out and
corrected.
In GADFly and at 19E there is a protein kinase with homology to TAK-1.
I hope that this is helpful
Alfonso Martinez Arias
Subject: Re: TAK-1 mapping
Dear Alfonso,
Nice to hear from you. Hope all is well.
The sequence accession in the Tak-1 file indeed comes from
19E.
There is a gene at 71, CG6890, which has been annotated as Tak1
as well. However, the translated product of CG6890 (GenBank
protein accession AAF06815) has no significant similarity to the
19E Tak1 protein in pairwise BLAST. Hence, I don't know if it
is an annotation glitch from the jamboree or some other problem.
Here are the proteins from the two genes.
Tak1 19E
MATASLDALQAAYVDFSEITLREKVGHGSYGVVCKAVWRDKLVAVKEFFASAEQKDIEKEVKQLSRVKHP
NIIALHGISSYQQATYLIMEFAEGGSLHNFLHGKVKPAYSLAHAMSWARQCAEGLAYLHAMTPKPLIHRD
VKPLNLLLTNKGRNLKICDFGTVADKSTMMTNNRGSAAWMAPEVFEGSKYTEKCDIFSWAIVLWEVLSRK
QPFKGIDNAYTIQWKIYKGERPPLLTTCPKRIEDLMTACWKTVPEDRPSMQYIVGVMHEIVKDYTGADKA
LEYTFVNQQIVTKESDGTVAAQPDSLSSQEGELSPSSTQLTPTTAANANVNAIAISKTTTSSMTENTSST
SSDITPTNSGQLDNNPLFYMVTNRWDAIPEEESNESRNDSFNLTSSAEATQRLETIRNGMILMACKPMEQ
LTLDVEANGFDLSPSESSSSSTNAKSDGRERLTVTDTKPVMMTTDLSNNNGGIHAHSNGLLSHANGWQAR
DEELQEQEHEQEIVNSLDVDVDPDEDENDGTEQSLAEILDPELQPEPPIPNDAESQLIYRDHRHMAKEYL
SVDTNLYYAQDFKDKLIVQMDRTEREQKQELLRKMKDKEGLQSLYNNLQQQYASRQLAAGHHPQPHPHPH
PNQLQHPHSHPPMHFLQDEGCGLLPGSVCGGSESVEEGWVVIPPHHNA
CG6890 'Tak1' 71B
MLATTHMLYVLIATCVIPIFGAALSKTVLYQAPDECRWSGGGEHDITLVCHLRTINSELENTNFSVIQPQ
NTVRLRLECNDALFFQSSLSPDSFRSLVELRDLTIEYCKLGNLTDGSFRGLQELRNLTIRTHNGDWSTMS
LEMASNSFVEFRQLERLDLSLNNIWLIPDGMVCPLKSLQHLNASYNKIQDISNFYFSASLSSRKARVCGS
TLQSLDLSANKMVSLPTAMLSALGRLTHLNMAKNSMSFLADRAFEGLLSLRVVDLSANRLTSLPPELFAE
TKQLQEIYLRNNSINVLAPGIFGELAELLVLDLASNELNSQWINAATFVGLKRLMMLDLSANKISRLEAH
IFRPLASLQILKLEDNYIDQLPGGIFADLTNLHTLILSRNRISVIEQRTLQGLKNLLVLSLDFNRISRMD
QRSLVNCSQLQDLHLNDNKLQAVPEALAHVQLLKTLDVGENMISQIENTSITQLESLYGLRMTENSLTHI
RRGVFDRMSSLQILNLSQNKLKSIEAGSLQRNSQLQAIRLDGNQLKSIAGLFTELPNLVWLNISGNRLEK
FDYSHIPIGLQWLDVRANRITQLGNYFEIESELSLSTFDASYNLLTEITASSIPNSVEVLYLNDNQISKI
QPYTFFKKPNLTRVDLVRNRLTTLEPNALRLSPIAEDREIPEFYIGHNAYECDCNLDWLQKVNRESRTQP
QLMDLDQIHCRLAYARGSSHVSLIEAKSDDFLCKYASHCFALCHCCDFQACDCKMECPDRCSCYHDQSWT
SNVVDCSRASYEQTLPSHIPMDSTQLYLDGNNFRELQSHAFIGRKRLKVLHLNHSRIEVLHNRTFYGLLE
LEVLQLQSNQLKALNGNEFQGLDNLQELYLQHNAIATIDTLTFTHLYHLKILRLDHNAITSFAVWNFLPS
YLNELRLASNPWTCSCEFIDKLRDYINRHEYVVDKLKMKCDVISGNSTQQMVIYPGSGEPASLPVVQCSQ
TLPLGLDNNFNYAEQAGGENASNATSTKMILNQPPKLDYIPILVAILTAFIFVMICISLVFIFRQEMRVW
CHSRFGVRLFYNAQKDVDKNEREKLFDAFVSYSSKDELFVNEELAPMLEMGEHRYKLCLHQRDFPVGGYL
PETIVQAIDSSRRTIMVVSENFIKSEWCRFEFKSAHQSVLRDRRRRLIVIVLGEVPQKELDPDLRLYLKT
NTYLQWGDKLFWQKLRFALPDVSSSQRSNVAGQSCHVPINHASYHHHHHVHQQAMPLPHSVHHHQQQFML
PPPPQQPGSFRRQPSLHQQQQQQQQIRGNNNTTQQQQQQQAALLMGGGSVGGPAPQMIPLAGGIQQQSLP
LPPNQQPTPASRNLHM
This message is being cc'd to the rest of the flybase-help group
in case they can help resolve this.
Best wishes,
Bill
Subject: Re: TAK-1 mapping
Dear Bill
Thank you for your reply.
Yes, I agree, that is why I was surprised that the location given for tak1
is 71B5 rather than 19E2.
I take this opportunity to tell you and your colleagues over there what a
great thing FlyBase is and how useful and interesting we find it in my
lab. The genome, of course, has added a new (or maybe many a) dimension to
it.
With best wishes
Alfonso
Subject: Re: TAK-1 mapping
Hi Alfonso,
.
As Bill said, the basic problem is that the wrong predicted gene (CG6890)
has been attached to the 'Tak1' gene (FBgn0026323) which we already had
in FlyBase (from the literature before the genome sequence came out).
I'd like to record your e-mail as a personal communication from you to
FlyBase so that people can see how we knew there was a problem with the
data for these genes.
I did a BLAST using the sequence for the Tak1 gene at 19E (AF199466)
and from the results its clear that the Tak1 gene at 19E corresponds to
the predicted gene CG1388.
I will fix all this in the database (although it will probably take a
few weeks for this to filter through to the public view).
.
Gillian