Protein Info for PGA1_262p00430 in Phaeobacter inhibens DSM 17395

Updated annotation (from data): glucose transporter, periplasmic substrate-binding component
Rationale: specific phenotype on glucose and cofit with other nearby components. This is similar (65% identity) to gxyS (Atu3576) of Agrobacterium tumefaciens, which is involved in the transport of glucose, glucosamine, and xylose (PMCID: PMC4135649). It is not clear if the Phaeobacter system transports xylose, as it is not required for utilizing xylose, but no other xylose transport system was identified either.
Original annotation: D-xylose-binding periplasmic protein XylF

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 50 100 150 200 250 300 341 signal peptide" amino acids 1 to 22 (22 residues), see Phobius details TIGR02634: D-xylose ABC transporter, D-xylose-binding protein" amino acids 26 to 329 (304 residues), 479.7 bits, see alignment E=2.3e-148 PF13407: Peripla_BP_4" amino acids 26 to 280 (255 residues), 211.7 bits, see alignment E=2.1e-66 PF00532: Peripla_BP_1" amino acids 43 to 235 (193 residues), 24.5 bits, see alignment E=2.7e-09

Best Hits

Swiss-Prot: 41% identical to XYLF_HAEIN: D-xylose-binding periplasmic protein (xylF) from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)

KEGG orthology group: K10543, D-xylose transport system substrate-binding protein (inferred from 86% identity to sit:TM1040_3174)

Predicted SEED Role

"Xylose ABC transporter, periplasmic xylose-binding protein XylF" in subsystem Xylose utilization

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

See I7F4G1 at UniProt or InterPro

Protein Sequence (341 amino acids)

>PGA1_262p00430 glucose transporter, periplasmic substrate-binding component (Phaeobacter inhibens DSM 17395)
MKFLSGVSALAFAATASMAFAEDVTVGVSWSNFQEERWKTDEAAIKAALEAKGATYVSAD
AQSSSAKQLSDIESLIAQGVDALIVLAQDAQAIGPAVQAAADEGIPVVAYDRLIEDGRAF
YLTFDNVEVGRMQARAVLEAQPSGNYVMIKGSPTDPNADFLRGGQQEIIQAAIDSGDIKI
VGEAYTDGWLPANAQRNMEQILTANDNKVDAVVASNDGTAGGVVAALTAQGMEGIAVSGQ
DGDHAALNRVAKGTQTVSVWKDARDLGKAAANIAVEMAEGAVMGDVAGGAAWTSPAGTEL
TARFLEPIPVTADNLSVVVDAGWITKEALCQGVTNGPAPCN