search

geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
Creative Commons Attribution 4.0 International
222 stars 40 forks source link

nitrogenase activity has definition that is not precisely correct and deviates from source #22119

Closed cmungall closed 3 years ago

cmungall commented 3 years ago 
id: GO:0016163
name: nitrogenase activity
namespace: molecular_function
def: "Catalysis of the reaction: 8 reduced ferredoxin + 8 H+ + nitrogen + 16 ATP = 8 oxidized ferredoxin + 2 NH3 + 16 ADP + 16 phosphate." [EC:1.18.6.1]
synonym: "iron-iron nitrogenase activity" NARROW []
synonym: "molybdenum-iron nitrogenase activity" NARROW []
synonym: "reduced ferredoxin:dinitrogen oxidoreductase (ATP-hydrolysing) activity" RELATED [EC:1.18.6.1]
synonym: "vanadium-iron nitrogenase activity" NARROW []
xref: EC:1.18.6.1
xref: MetaCyc:NITROGENASE-RXN
xref: RHEA:21448
xref: UM-BBD_enzymeID:e0395
is_a: GO:0016732 ! oxidoreductase activity, acting on iron-sulfur proteins as donors, dinitrogen as acceptor

Where did this def come from? It says https://enzyme.expasy.org/EC/1.18.6.1 but it doesn't match. nitrogenase takes dinitrogen as input.

I think where we do cite EC as sole def xref we should auto-check the defs match

But in this case this would be superseded anyway - we have an equivalent rhea, so we should use rhea as the source (which also correctly has dinitrogen)

image

hdrabkin commented 3 years ago

I'm betting it came in via xref: UM-BBD_enzymeID:e0395 I imagine the RHEA:21448 got added because of the EC:1.18.6.1 The text def saying 'nitrogen' was probably implied to be N2. There is no free N. And in fact, the EC says 8 reduced ferredoxin + 8 H(+) + N(2) + 16 ATP + 16 H(2)O <=> 8 oxidized ferredoxin + H(2) + 2 NH(3) + 16 ADP + 16 phosphate N(2) is being used for N2 here like H(2)O for H20 I can fix the text def

hdrabkin commented 3 years ago

fixed (also added missing 16 H20 to def