Protein Info for Psest_2125 in Pseudomonas stutzeri RCH2

Updated annotation (from data): D-gluconate TRAP transporter, periplasmic component
Rationale: specific phenotype on D-gluconate and no other transporter is apparent in the fitness data
Original annotation: tripartite ATP-independent periplasmic transporter solute receptor, DctP family

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 50 100 150 200 250 300 338 signal peptide" amino acids 1 to 26 (26 residues), see Phobius details TIGR00787: TRAP transporter solute receptor, DctP family" amino acids 36 to 291 (256 residues), 276.7 bits, see alignment E=8.8e-87 PF03480: DctP" amino acids 36 to 316 (281 residues), 316 bits, see alignment E=1.2e-98

Best Hits

Swiss-Prot: 38% identical to YIAO_ECOLI: 2,3-diketo-L-gulonate-binding periplasmic protein YiaO (yiaO) from Escherichia coli (strain K12)

KEGG orthology group: None (inferred from 93% identity to psa:PST_2199)

MetaCyc: 38% identical to 2,3-diketo-L-gulonate:Na+ symporter - periplasmic binding protein (Escherichia coli K-12 substr. MG1655)
TRANS-RXN0-235

Predicted SEED Role

"TRAP-type transport system, periplasmic component, predicted N-acetylneuraminate-binding protein" in subsystem Sialic Acid Metabolism

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 L0GMV7 at UniProt or InterPro

Protein Sequence (338 amino acids)

>Psest_2125 D-gluconate TRAP transporter, periplasmic component (Pseudomonas stutzeri RCH2)
MKRLLISTLAAALLGSTLSLGYAQAADDIRPRMIRFGYGLNEDSNQGRAAKLLAEEVAKA
SGGKLKVRTFASASLGSDDQMQNALIGGAQEMMVGSTATLVGISKEMAVWDTPFLFTDPR
QADQVLDGPVGRQVMDKLEEKGLVGLVYWENGFRNVTNSARPIEKLEDFNGVKLRVMPNP
VFIDTFKRMGANAVPLPFSELFTALETKAVDGQENPFNTILSSKFYEVQKYLSVTNHVYS
PWIVTVSKRWWDGLSATEQGILMEAAEKARDAEREDTRREASQALAALKERGMQINEVSP
DEIQRMREKAQPAIQTVIDAVGQELFDQVQAEVEKAAP