IPR000722; incorrect mapping to nucleus

[gocentral]

Hi can you take a look of this?

Came in via Fiona. See emails below.

Val

Hi Val,

Since you are the prokaryote & IEA mapping expert in my world, I am contacting you about a user query I received.

Janet is working with Listeria monocytogenes. She downloaded her GO annotations and contacted me asking why there are annotations to nucleus when they have no nucleus. I asked her to send me an example and looking at the example she sent, this appears to be an IEA mapping (see below).

Is this common amongst the prokaryote IEAs?

thanks, Fiona The AgBase Databases Department of Basic Sciences Box 6100 MS 39762-6100 Mississippi State University USA Tel: (+ 1) 662 325 5859 Fax: (+ 1) 662 325 1031

Hi Fiona,

Just a real quick look at my dataset gave me this example for a bad info retrieval through Expasy:

On Expasy with this protein, when you get the info page up, you click on QuickGo View and it will place this in the nucleus:

Q724E9, DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) (RNAP subunit beta') (Transcriptase subunit beta') (RNA polymerase subunit beta')

Thanks for all of your help!

Janet

Assistant Professor Department of Biological Sciences

Reported by: ValWood

Original Ticket: "geneontology/annotation-issues/491":https://sourceforge.net/p/geneontology/annotation-issues/491

[gocentral]

• labels: --> InterPro mapping
• milestone: --> InterPro
• assigned_to: nobody --> orchard

Original comment by: mah11

[gocentral]

Logged In: YES user_id=1242047 Originator: NO

I checked the Listeria IEA annotations and found 13 gene products mapped to nuclues. They are all InterPro maapings to:

IPR000722 RNA polymerase, alpha subunit IPR001005 SANT, DNA-binding IPR004102 PARP_reg IPR010090 Phage tail tape measure protein TP901, core region

NOTE: that the IPR010090 InterPro entry is not linked to any GO terms in the Interpro database but it is the only InterPro domain that Q4ENL5 & Q4EJE4 are maaped to.

Doing a similar search with E.coli I found only 2 gene products mapped to nucleus:

Q83XC6 InterPro2GO mapping because of IPR002100: Transcription factor, MADS-box Q70Q81 InterPro2GO mapping to IPR006695: CENPB_N_term_bd

Fiona

Original comment by: fmccarthy

[gocentral]

Logged In: YES user_id=545117 Originator: NO

Cleaned a couple of errant entries which were left from the days before we had the taxonomy browser to immediately tell us if there were any bacterial entries. Q724E9 will behave once the update cycle is completed. IPR004102 I have not changed - I think the listeria protein hit to that is a false positive. Similarly I have not changed IPR002100.

Sandra

Original comment by: orchard

[gocentral]

• status: open --> closed

Original comment by: orchard