Protein Info for Sama_2209 in Shewanella amazonensis SB2B

Updated annotation (from data): alpha-ketoglutarate TRAP transporter, solute receptor component
Rationale: specific phenotype on a-ketoglutarate. A putrescine ABC transporter (Sama_2642:Sama_2638) is also important in this condition, which is not explained. This organism can also utilize succinate or fumarate (but not L-malate), which we do not have fitness data for these under aerobic conditions. This could also transport some C4 compounds.
Original annotation: C4-dicarboxylate-binding periplasmic protein (RefSeq)

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 50 100 150 200 250 300 339 signal peptide" amino acids 1 to 34 (34 residues), see Phobius details TIGR00787: TRAP transporter solute receptor, DctP family" amino acids 40 to 289 (250 residues), 257.9 bits, see alignment E=4.9e-81 PF03480: DctP" amino acids 40 to 322 (283 residues), 337.3 bits, see alignment E=3.9e-105

Best Hits

Swiss-Prot: 79% identical to DCTP_SHELP: Solute-binding protein Shew_1446 (Shew_1446) from Shewanella loihica (strain ATCC BAA-1088 / PV-4)

KEGG orthology group: K11688, C4-dicarboxylate-binding protein DctP (inferred from 100% identity to saz:Sama_2209)

Predicted SEED Role

"TRAP-type C4-dicarboxylate transport system, periplasmic component"

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 A1S7Q8 at UniProt or InterPro

Protein Sequence (339 amino acids)

>Sama_2209 alpha-ketoglutarate TRAP transporter, solute receptor component (Shewanella amazonensis SB2B)
MKVSKPATLQSLFTLGKASLLATVLGFSFGAVAEPVEIKFSHVVAENTPKGQMALKFKEL
VESRLPGEYKVSVFPNSQLFGDNNELAALLLNDVQLVAPSLSKFERYTKKLQVFDLPFLF
EDMDAVDRFQQSEAGQQLLNSMSRKGLVGLGYLHNGMKQFSANNALSLPGDAAGKKFRIM
PSDVIAAQFEAVGAIPVKKPFSEVFTLLQTRAIDGQENTWSNIYSKKFYEVQTHITESNH
GVLDYMLVTSETFWKSLPKDKREIIKQSMDEAVALGNKLALEKANEDRQLILDSKRVELV
TLTPEQRQAWVNAMRPVWSQFEDKIGKDLIEAAESANKP