Protein Info for HSERO_RS05260 in Herbaspirillum seropedicae SmR1

Updated annotation (from data): ABC transporter for L-fucose, substrate-binding component
Rationale: Specifically important for L-fucose utilization.
Original annotation: LacI family transcriptional regulator

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 50 100 150 200 250 312 signal peptide" amino acids 1 to 25 (25 residues), see Phobius details PF13407: Peripla_BP_4" amino acids 31 to 284 (254 residues), 197.2 bits, see alignment E=5.6e-62 PF00532: Peripla_BP_1" amino acids 32 to 235 (204 residues), 55 bits, see alignment E=1.3e-18

Best Hits

KEGG orthology group: K10439, ribose transport system substrate-binding protein (inferred from 100% identity to hse:Hsero_1051)

Predicted SEED Role

"Possible fucose ABC transporter, substrate-binding component" in subsystem L-fucose utilization

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

See D8J113 at UniProt or InterPro

Protein Sequence (312 amino acids)

>HSERO_RS05260 ABC transporter for L-fucose, substrate-binding component (Herbaspirillum seropedicae SmR1)
VFKNKLLGAALGLAFAMGASAAQAQEAYIPLISKGFQHQFWQAVKAGADQAGKDYKVKVT
FEGPETEAMVDKQIDMLSAALAKKPQAIGFAALDSKAAIPLLKKAQAAKIPVVAFDSGVD
SDIPVTTATTDNRAAAALAADKMAELVGKEGEVAVVAHDQTSRTGVDRRDGFLERIKSAY
PKIKVVSVQYGAGDQLKSTEVTKSILQAYPKIKGIFGTNEGSAIGVVNGVKEMKRKIIII
GYDSGKQQKDAIREGIMAGAITQNPVGIGYKTVEAAVKAIKGEKLPKVIDTGFYWYDKSN
IDDAKIAAVLYD