I have a list of thousands of NCBI-GIs of proteins. I want to determine;
1. how many of them are enzymes ?
2. what are their EC numbers ?
3. What is the reference database for this information ?
Input example:
197250412
198245186
383497501
378955480
194450450
194447589
.
.
My desired output is;
197250412 no
198245186 yes EC=2.1.1.80 UniProt (or BRENDA)
383497501 no
378955480 yes EC=2.1.1.80 UniProt
194450450 yes EC=1.10.3.- UniProt
194447589 no
.
.
I have applied KEGG by converting NCBI-GIs of proteins to respective KEGG-IDS and then looking them in KEGG Enzyme Brite Hierarchy files, but I am not sure of the obtained output, as it is mentioning "Succinate dehydrogenase cytochrome b556 large membrane subunit" as non-enzyme. I want to apply BRENDA (www.brenda-enzymes.info) or ExPASy ENZYME (enzyme.expasy.org), as they are also comprehensive database.
Kindly guide me in this issue.
you can find it using id conversion for eg. biomart . (online or via R package).
Are these human genes ?
using R , you can do it using via bio-conductor packages for eg . package org.Hs.eg.db
http://www.bioconductor.org/help/workflows/annotation/annotation/#sample-workflow-OrganismDb
here is sample :
library(org.Hs.eg.db)
columns(org.Hs.eg.db)
ids = c("NME1","CNR1","ACE","BACE1","LOC206456")
keys
All NCBI-GIs belong to different strains of Salmonella enterica. Can you guide me for that in Boconductor? My main issue is just to find out enzymes from the proteins. EC is my secondary aim.
N.B.: I have edited my post.
@Tobias Sikosek; I have already applied KEGG. I wanted to apply some other database/tool to get my desired output.
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