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geneontology / go-annotation

This repository hosts the tracker for issues pertaining to GO annotations.
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IPR006329 and IPR001365 #955

Closed gocentral closed 9 years ago

gocentral commented 12 years ago

Hi,

It looks like these InterPro domains (IPR006329 and IPR001365), or their application of the S. cerevisiae genes YJL070C & YBR284W, should be reexamined.

This Saint-Marc C, et al (2009) paper indicates that "both proteins lack several residues (Figure S1) conserved in all described purine deaminases (Ribard et al. 2003)." and shows that they can not rescue a null mutation of the known AMP deaminase (AMD1).

However, these GO annots are coming via the InterPro domains:

DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms. MF AMP deaminase activity IEA: with EBI:IPR006329 MF deaminase activity IEA: with EBI:IPR001365 BP IMP biosynthetic process IEA: with EBI:IPR006329 BP purine ribonucleoside IEA: with EBI:IPR001365 monophosphate biosynthetic process

Saint-Marc C, Pinson B, Coulpier F, Jourdren L, Lisova O, Daignan-Fornier B (2009) Phenotypic consequences of purine nucleotide imbalance in Saccharomyces cerevisiae. Genetics 183(2):529-38, 1SI-7SI PMID: 19635936

Ribard C, Rochet M, Labedan B, Daignan-Fornier B, Alzari P, Scazzocchio C, Oestreicher N. Sub-families of alpha/beta barrel enzymes: a new adenine deaminase family. J Mol Biol. 2003 Dec 12;334(5):1117-31. PMID: 14643670.

Thanks,

-Karen

Reported by: krchristie

Original Ticket: geneontology/annotation-issues/956

gocentral commented 12 years ago

Hi Karen, Thanks for spotting this. Looking at the several thousand sequences matched by these InterPro entries, only the 2 that you've spotted seem to be have been experimentally characterised as as inactive. I'd therefore suggest keeping the GO terms for these InterPro entries and to filtering out the incorrect GO mappings at the protein level. To this end, I've asked the GOA team to add a NOT-qualified annotation to the proteins in UniProt. Would it be possible for you do do something similar at SGD using the IKR code? Alex

Original comment by: almitchell

gocentral commented 12 years ago

Hi Alex,

Thanks for looking into this. I have added NOT annotations, by both IKR & IGI, for these 2 genes.

thanks.

-Karen

Original comment by: krchristie

gocentral commented 12 years ago

Original comment by: syong