Protein Info for GFF4237 in Sphingobium sp. HT1-2

Annotation: Capsular polysaccharide ABC transporter, permease protein KpsM

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 50 100 150 200 268 transmembrane" amino acids 41 to 63 (23 residues), see Phobius details amino acids 69 to 87 (19 residues), see Phobius details amino acids 120 to 145 (26 residues), see Phobius details amino acids 152 to 175 (24 residues), see Phobius details amino acids 186 to 205 (20 residues), see Phobius details amino acids 241 to 259 (19 residues), see Phobius details PF01061: ABC2_membrane" amino acids 23 to 230 (208 residues), 39.7 bits, see alignment E=2e-14

Best Hits

Swiss-Prot: 44% identical to CTRC_NEIMB: Capsule polysaccharide export inner-membrane protein CtrC (ctrC) from Neisseria meningitidis serogroup B (strain MC58)

KEGG orthology group: K09688, capsular polysaccharide transport system permease protein (inferred from 62% identity to glo:Glov_1523)

Predicted SEED Role

"Capsular polysaccharide ABC transporter, permease protein KpsM" in subsystem Capsular Polysaccharide (CPS) of Campylobacter or Rhamnose containing glycans

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

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

Compare to protein 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 (268 amino acids)

>GFF4237 Capsular polysaccharide ABC transporter, permease protein KpsM (Sphingobium sp. HT1-2)
MSTQSGFSLRGLLDSFAIQRRVIGALLMREVLTRYGRHNIGFFWLFVEPMLFTLGVTALW
TALKAVHGSEIPITAFALTGYSTVLLWRNMPNRCVGAVQPNLALMYHRNVRIIDIFMSRL
ILEAAGATISFIVLSIFFMALGWIVYPEDLLKVIVGWFLLAWFGCALAILLASYAEEYDM
VEKLWHPASYLLFPLSGAGFMVSALPEEFRQFVLYLPMVHSVECIRDGFFGSHIKTFYDL
EYMSTINAVLTFAALSQMMRISRKVIPE