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InterPro:IPR016130 inc mapping #549

Closed gocentral closed 9 years ago

gocentral commented 16 years ago

ssesm to be lipid phosphatases in pombe

see O13819 & O94526

Reported by: ValWood

Original Ticket: "geneontology/annotation-issues/549":https://sourceforge.net/p/geneontology/annotation-issues/549

gocentral commented 16 years ago

Original comment by: mah11

gocentral commented 16 years ago

Logged In: YES user_id=1549231 Originator: NO

Hi Val, could you be a bit more specific. The signature in IPR006130 identifies the Tyrosine specific protein phosphatases active site; see http://www.expasy.org/prosite/PDOC00323. As far as I can see there are no known exceptions -- if there are can you reactivate and divert any further comments to Swiss-Prot. Thanks david

Original comment by: dmlonsdale

gocentral commented 16 years ago

Original comment by: dmlonsdale

gocentral commented 16 years ago

Logged In: YES user_id=516865 Originator: YES

O13819 & are O94526

phosphatidylinositol-3-phosphatase activity Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 3-phosphate + H2O = 1-phosphatidyl-1D-myo-inositol + phosphate.

Midor, can you switch to Uniprot?

Thanks

Val

Original comment by: ValWood

gocentral commented 16 years ago

Original comment by: mah11

gocentral commented 16 years ago

Logged In: YES user_id=1549231 Originator: NO

The two proteins below are very different in terms of the signatures mapping too them - that is other than the protein tyrosine kinase active site. You can view the mapping by using InterproScan.

O13819 maps to IPR010569 Myotubularin-related 094526 maps to IPR014019 Phosphatase tensin type

I guess if you are saying they exhibit phosphatidylinositol-3-phosphatase activity there must be a publication to support?

cheers

David

Original comment by: dmlonsdale

gocentral commented 16 years ago

Logged In: YES user_id=516865 Originator: YES

Oh sorry yes, I only checked one of them (I assumed they were pombe / S. cerevisiae orthologs but they are 2 distince proteins.

O94526 is phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity Ptn1 in pombe A novel phosphatidylinositol(3,4,5)P3 pathway in fission yeast. PMID: 15249580

It seems that the prosite signature PS00383 is also hitting these.....

for the other one, there is a publication for the S. cerevisiae ortholog.

I think there are also lots publications for the Pten family in higher eukaryotes, but maybe they haven't been curated yet by Uniprot.... Theres an IDA for mouse MGI:109583 and an IGI for Drosopila FBgn0026379

Original comment by: ValWood

gocentral commented 16 years ago

Logged In: YES user_id=1549231 Originator: NO

Yes, If they had been Swiss_Prot records they should be marked up as status F (false positive) for the PROSITE pattern. Unfortunately, they are TrEMBL records and they do not have status's and so this will also be the case in InterPro - as all true matches are taken as status T (True)! Might still be worth reporting to Swiss-Prot - so if they become reviewed they will be given status F for the PROSITE.

Original comment by: dmlonsdale

gocentral commented 13 years ago

I'm not sure if there is an issue here so clodsing will open a new item if necessary

Original comment by: ValWood

gocentral commented 13 years ago

Original comment by: ValWood