Protein Info for PFR28_02349 in Pseudomonas sp. RS175

Annotation: D-xylose-binding periplasmic protein

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 50 100 150 200 250 300 333 signal peptide" amino acids 1 to 23 (23 residues), see Phobius details TIGR02634: D-xylose ABC transporter, D-xylose-binding protein" amino acids 29 to 330 (302 residues), 525.8 bits, see alignment E=2e-162 PF13407: Peripla_BP_4" amino acids 29 to 287 (259 residues), 214.4 bits, see alignment E=2.1e-67 PF00532: Peripla_BP_1" amino acids 51 to 242 (192 residues), 36.7 bits, see alignment E=3.3e-13

Best Hits

Swiss-Prot: 60% identical to XYLF_ECOLI: D-xylose-binding periplasmic protein (xylF) from Escherichia coli (strain K12)

KEGG orthology group: K10543, D-xylose transport system substrate-binding protein (inferred from 98% identity to pba:PSEBR_a2596)

MetaCyc: 60% identical to xylose ABC transporter periplasmic binding protein (Escherichia coli K-12 substr. MG1655)
ABC-33-RXN [EC: 7.5.2.10, 7.5.2.13]

Predicted SEED Role

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

Isozymes

No predicted isozymes

Use Curated BLAST to search for 7.5.2.10 or 7.5.2.13

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 (333 amino acids)

>PFR28_02349 D-xylose-binding periplasmic protein (Pseudomonas sp. RS175)
MKTVKRTLLAGALALLSLPVMADATHPKIGFSIDDLRLERWSRDRDYFVAAAEKLDAKVY
VQSADANEQKQISQIENLISRGVDVIVIVPFNATVLTNAVAEAKKAGIKVVSYDRLILNA
DIDAYISFDNEKVGEMQASGVLKAAPKGNYFLLGGAPTDNNAKVLREGQMKVLQPAIDKG
DIKIVGQQWVKEWNPTEALSIVENALTRNNNKIDGIVASNDATAGGAIQALAAQKLAGKV
PISGQDADLAAVKRVIDGTQTMTVYKPLKLIASEAAKLSVQLARNEKPNFSSQYDNGSKK
VDTILLTPTPLTKDNIDLLEKDGFYTKAQIAGQ