Protein Info for GFF5506 in Hydrogenophaga sp. GW460-11-11-14-LB1

Annotation: TRAP-type C4-dicarboxylate transport system, large permease component

These analyses and tools can help you predict a protein's function, but be skeptical. For enzymes, over 10% of annotations from KEGG or SEED are probably incorrect. For other types of proteins, the error rates may be much higher. MetaCyc and Swiss-Prot have low error rates, but the best hits in these databases are often quite distant, so this protein's function may not be the same. TIGRFam has low error rates. Finally, many experimentally-characterized proteins are not in any of these databases. To find relevant papers, use PaperBLAST.

Protein Families and Features

1 50 100 150 200 250 300 350 400 430 transmembrane" amino acids 6 to 38 (33 residues), see Phobius details amino acids 51 to 71 (21 residues), see Phobius details amino acids 99 to 128 (30 residues), see Phobius details amino acids 140 to 165 (26 residues), see Phobius details amino acids 172 to 197 (26 residues), see Phobius details amino acids 217 to 235 (19 residues), see Phobius details amino acids 239 to 239 (1 residues), see Phobius details amino acids 242 to 260 (19 residues), see Phobius details amino acids 273 to 299 (27 residues), see Phobius details amino acids 319 to 348 (30 residues), see Phobius details amino acids 360 to 385 (26 residues), see Phobius details amino acids 405 to 428 (24 residues), see Phobius details PF06808: DctM" amino acids 13 to 421 (409 residues), 398.6 bits, see alignment E=1.5e-123 TIGR00786: TRAP transporter, DctM subunit" amino acids 22 to 424 (403 residues), 444.9 bits, see alignment E=1.2e-137

Best Hits

Swiss-Prot: 43% identical to SIAM_VIBCH: Sialic acid TRAP transporter large permease protein SiaM (siaM) from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)

KEGG orthology group: None (inferred from 78% identity to pna:Pnap_0044)

Predicted SEED Role

"TRAP-type C4-dicarboxylate transport system, large permease component"

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search structures

Predict protein localization: PSORTb (Gram-negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the current SEED with FIGfam search

Find homologs in fast.genomics or the ENIGMA genome browser

Find the best match in UniProt

Protein Sequence (430 amino acids)

>GFF5506 TRAP-type C4-dicarboxylate transport system, large permease component (Hydrogenophaga sp. GW460-11-11-14-LB1)
MSVEALAFVVFIAGMLVLMGIGMNMAFALLLTGAAMAWVMDFWDTQLLAQNMVAGIDSFP
LLAVPFFILAGELMNSGGISKRIIDMAQAWVGHVRGGLGYVAIGAAVLLSAMSGSALADA
AAMSAILLPMMRKHGYPVASSAGLIAAGSVIGPIIPPSMAFVIYGVTTNTSISALFISGI
VPGLVMGVALVVAWRVVLRKMTLTSSPPVPMAERLRLTGRAVWALVMPVIIIGGMKSGIF
TPTEAAVVAAFYALVIALFVHREMRLPELYSALVRAASTTSVVMFLCAGAAVASYMITLA
DLPSTLTGWLGPLVEHPRVLMVVMMLVLVAIGTALDLTPTILIFAPVMLPIAVKAGIDPV
YFGLMFVLNGAIGLVTPPVGTVLNVVAGVGRLPMHQVIKGVNPFLITYLIVLGLFIVFPQ
IVTAPVAWMR