Protein Info for GFF5724 in Hydrogenophaga sp. GW460-11-11-14-LB1

Annotation: Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)

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 50 100 150 223 transmembrane" amino acids 17 to 42 (26 residues), see Phobius details amino acids 54 to 78 (25 residues), see Phobius details amino acids 85 to 104 (20 residues), see Phobius details amino acids 139 to 156 (18 residues), see Phobius details amino acids 185 to 205 (21 residues), see Phobius details TIGR01726: amino ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family" amino acids 12 to 108 (97 residues), 90.9 bits, see alignment E=3e-30 PF00528: BPD_transp_1" amino acids 34 to 213 (180 residues), 63.9 bits, see alignment E=8.6e-22

Best Hits

Swiss-Prot: 35% identical to YCKA_BACSU: Probable amino-acid ABC transporter permease protein YckA (yckA) from Bacillus subtilis (strain 168)

KEGG orthology group: K02029, polar amino acid transport system permease protein (inferred from 66% identity to ara:Arad_8415)

Predicted SEED Role

"Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)" in subsystem D-ribose utilization (TC 3.A.1.2.1)

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 (223 amino acids)

>GFF5724 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1) (Hydrogenophaga sp. GW460-11-11-14-LB1)
MIEGGLNLYHVQLLGVGVLWTVCLSVIAFIGGGLVGGAVALCRISPVRAVRWAAIAWIQL
IQGTPLLVVLFVCYFGLSIMGLELPGLVAASIAMVIYVSAYLGEIWRGCIESVPRTQWEA
AECLALSRSQRMRLVVLPQALRIATPPTVGFMVQIVKNTSLASIVGFVELVRAGQLINNS
IFQPFLIYLIIAALYFAMCFPLSVWSRRLEQRLHFGNRIPSET