Dear fellows, i have a set of list of ids (1:given below) which i extract from pathways (2:given below) i want the protein sequence of the ids , i have almost 400 enzymes/proteins for which i want the protein/AA sequences.
1: IDs A1S_2750 A1S_2287 A1S_2751 A1S_2138 A1S_2137 A1S_2141 A1S_2142 A1S_2140 A1S_2139 A1S_0001 A1S_0980 A1S_0140 A1S_0260 A1S_0261 A1S_0574 A1S_0111 A1S_1141 A1S_1474 A1S_1977 A1S_1978
2: Source of ids for eg: C 00627 Aminobenzoate degradation [PATH:00627] D A1S_1865 Glu-tRNA amidotransferase K01426 E3.5.1.4; amidase [EC:3.5.1.4] D A1S_1774 putative hydrolase K18541 mdlY; mandelamide amidase [EC:3.5.1.86] D A1S_1116 vanillate O-demethylase oxygenase subunit K03862 vanA; vanillate monooxygenase D A1S_1115 vanillate O-demethylase oxidoreductase K03863 vanB; vanillate monooxygenase D A1S_0106 putative enoyl-CoA hydratase/isomerase K01692 paaF; enoyl-CoA hydratase [EC:4.2.1.17] D A1S_2677 Twin-arginine translocation pathway signal K01113 phoD; alkaline phosphatase D C 00791 Atrazine degradation [PATH:00791] D A1S_1269 putative allophanate hydrolase subunit 1 and 2 K01457 atzF; allophanate hydrolase D A1S_1283 putative amidase K01457 atzF; allophanate hydrolase [EC:3.5.1.54] D A1S_1277 Allophanate hydrolase subunit 2 K01941 E6.3.4.6; urea carboxylase [EC:6.3.4.6] D A1S_1014 urease alpha subunit K01428 ureC; urease subunit alpha [EC:3.5.1.5]
I think in R biomaRt you can retrieve protein sequences as well (never needed it before), did you look at biomaRt already?
No, i will give you short briefing of work basically i retrieve unique metabolic pathways of pathogenic Bactria now i want the protein sequences than i will blast it with human proteome.