Getting Gene-Enzyme Annotations From A Genome

Question

[aarongaroutte]

Hello

I was wondering if anyone knew how to get a list of all of the annotated genes in a genome from NCBI? I'd like to compare the genes present in a list of different organisms. Ideally I'd like to have a list of the EC numbers of the annotated genes but RefSeq numbers or KOs would be great too!

Thanks for any help!

Answer 1

[Khader Shameer]

You can parse this data for your organism(s) of interest from ENZYME nomenclature database maintained by EXPASY team (Download enzyme.dat). You can get a list of Uniprot IDs with short organism names for each enzyme.

Here is an example:

ID   1.1.1.2
DE   Alcohol dehydrogenase (NADP(+)).
AN   Aldehyde reductase (NADPH).
CA   An alcohol + NADP(+) = an aldehyde + NADPH.
CF   Zinc.
CC   -!- Some members of this group oxidize only primary alcohols; others act
CC       also on secondary alcohols.
CC   -!- May be identical with EC 1.1.1.19, EC 1.1.1.33 and EC 1.1.1.55.
CC   -!- A-specific with respect to NADPH.
PR   PROSITE; PDOC00061;
DR   Q6AZW2, A1A1A_DANRE;  Q568L5, A1A1B_DANRE;  P35630, ADH1_ENTHI ;
DR   Q24857, ADH3_ENTHI ;  Q04894, ADH6_YEAST ;  P25377, ADH7_YEAST ;
DR   O57380, ADH8_PELPE ;  P0CH36, ADHC1_MYCS2;  P0CH37, ADHC2_MYCS2;
DR   P0A4X1, ADHC_MYCBO ;  P0A4X0, ADHC_MYCTU ;  P25984, ADH_CLOBE  ;
DR   P75214, ADH_MYCPN  ;  P14941, ADH_THEBR  ;  Q3ZCJ2, AK1A1_BOVIN;
DR   Q5ZK84, AK1A1_CHICK;  O70473, AK1A1_CRIGR;  P14550, AK1A1_HUMAN;
DR   Q9JII6, AK1A1_MOUSE;  P50578, AK1A1_PIG  ;  Q5R5D5, AK1A1_PONAB;
DR   P51635, AK1A1_RAT  ;  Q6GMC7, AK1A1_XENLA;  Q28FD1, AK1A1_XENTR;
DR   Q9UUN9, ALD2_SPOSA ;  P27800, ALDX_SPOSA ;
//

PS. I heard of this resource via BioStar, thanks to Lars !

If you need to look for overall similarity in the level of protein sequences between 3 genomes, you can use TaxPlot also - but the resource is not restricted to enzyme families, it consider all proteins.