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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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NTR:N-acetylmuramate catabolic process #8684

Closed gocentral closed 9 years ago

gocentral commented 13 years ago

Hi,

I will require the following new term for the UniPathway2GO mapping UPA00342 describing N-acetylmuramate degradation:

GO:0046348 amino sugar catabolic process --< GO:NEW N-acetylmuramate catabolic process [defn: The chemical reactions and pathways resulting in the breakdown of N-acetylmuramate. N-acetylmuramate (MurNAc) is a monosaccharide derivative of N-acetylglucosamine and has a chemical formula C11H19NO8 and is part of a biopolymer in the bacterial cell wall built from alternating units of N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc), cross-linked with oligopeptides at the lactic acid residue of MurNAc. This layered structure is called peptidoglycan. Synonym: N-acetylmuramate degradation] [Xrefs: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=5676].

Thanks, Yasmin

Reported by: yafaruque

Original Ticket: geneontology/ontology-requests/8472

gocentral commented 13 years ago

Actually to be consistent with previous request #3306873 (https://sourceforge.net/tracker/?func=detail&atid=440764&aid=3306873&group\_id=36855) perhaps this GO term should be named N-acetylmuramic acid catabolic process with N-acetylmuramate catabolic process as a synonym.

Original comment by: yafaruque

gocentral commented 13 years ago

(Also applies to preceding two term requests). The definitions make the term specific to bacteria - here, explicitly; in the preceding requests implicitly by specifying an exact path / fate. Is this intended, or needed? Peter

Original comment by: deustp01

gocentral commented 13 years ago

Hi Peter,

This was just going on from information I found doing a google search for each of the products N-acetylmuramic acid and 1,6-anhydro-N-acetylmuramate and it looks like they are both specific to bacteria. Also all the UniProtKB entries identified by the UniPathway2GO mapping team are all bacterial. Obviously then these terms will require a taxon restriction to applied to them?

Yasmin

Original comment by: yafaruque

gocentral commented 13 years ago

If you're sure that this process only ever happens in bacteria, then I guess a taxon restriction is needed (not sure about that). I was actually being lazier, and thinking that, in case some other organisms can do this - maybe a fungus or a macrophage breaking down bacteria? - a less restrictive definition might be handy.

Original comment by: deustp01

gocentral commented 13 years ago

Original comment by: paolaroncaglia

gocentral commented 12 years ago

Original comment by: paolaroncaglia

gocentral commented 12 years ago

Note for self: xref to N-acetylmuramate (CHEBI:47978)

Original comment by: paolaroncaglia

gocentral commented 12 years ago

Hi Yasmin and Peter,

It seems that N-acetylmuramate may be present in plants as well (see PMID: 9271197), so I won't add a taxon constrain to the term that I'm going to create, and I'll make its definition less restrictive. To be on the conservative side, I'll do the same for Yasmin's related request for 1,6-anhydro-N-acetylmuramic acid metabolic terms.

Paola

Original comment by: paolaroncaglia

gocentral commented 12 years ago

Hi Yasmin, this is done at last:

Added new terms: GO:0097172 N-acetylmuramic acid metabolic process GO:0097173 N-acetylmuramic acid catabolic process

Added them in goche and in go_xp_chebi as well.

Thanks, Paola

Original comment by: paolaroncaglia

gocentral commented 12 years ago

Original comment by: paolaroncaglia