How to convert gene names to EC numbers?
Hi there!!! I have curated thousands of genes from different bacteria from IMG database. Now I want to get their respective E.C. numbers so that I can get map them with MetaCyc pathways. Can anyone please tell me how can I map the gene name s to E.C. numbers? Here are some examples of my genes:
phenylalanyl-tRNA synthetase beta subunit
phenylalanyl-tRNA synthetase, alpha subunit
transketolase subunit A
transketolase subunit B (EC 2.2.1.1)
GTP pyrophosphokinase
fructose-bisphosphate aldolase, class II
PTS system, mannose-specific IIB component
ribokinase
purine nucleosidase
histidinol phosphate aminotransferase apoenzyme (EC 2.6.1.9)
imidazoleglycerol-phosphate dehydratase
1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
phosphoribosyl-AMP cyclohydrolase
phosphoribosyl-ATP pyrophosphatase
histidinol-phosphatase (PHP family)
arsenate reductase
enolase
exopolyphosphatase / guanosine-5'-triphosphate,3'-diphosphate pyrophosphatase
PTS system IIB component, Gat family
NADH-quinone oxidoreductase subunit G
myo-inositol 2-dehydrogenase (EC 1.1.1.18)
Adenine deaminase
Many thanks, dpc
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lieven.sterck
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dpc
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dpc
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Not an easy thing to do, but there are options to do it anyway.
- you can either look them up one by one on the Expasy website , you can enter the description you have like you posted them en continue from there
- alternatively you can run the interpro analysis on your protein dataset and activate the EC option for it. It will then apart from the domains also report the ECnumbers if available
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ok, it has been a while apparently :)
it is a two-step procedure, first get the GO-labels from interpro and 'convert' those to EC numbers (on the expasy or ebi webiste there is a GO2EC conversion list (EC2GO more likley).
I came across this (old) post as well: EC number assignment tools
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Use BRENDA (LINK) or download ENZYME database from SwissProt (LINK). Map your enzyme names to the EC numbers.