Protein Info for Shew_1268 in Shewanella loihica PV-4

Name: smpB
Annotation: SsrA-binding 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 50 100 163 PF01668: SmpB" amino acids 16 to 160 (145 residues), 193.5 bits, see alignment E=8.9e-62 TIGR00086: SsrA-binding protein" amino acids 16 to 159 (144 residues), 182.7 bits, see alignment E=2e-58

Best Hits

Swiss-Prot: 100% identical to SSRP_SHELP: SsrA-binding protein (smpB) from Shewanella loihica (strain ATCC BAA-1088 / PV-4)

KEGG orthology group: K03664, SsrA-binding protein (inferred from 100% identity to slo:Shew_1268)

Predicted SEED Role

"tmRNA-binding protein SmpB" in subsystem Heat shock dnaK gene cluster extended or Staphylococcal pathogenicity islands SaPI or Trans-translation by stalled ribosomes

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 A3QCE0 at UniProt or InterPro

Protein Sequence (163 amino acids)

>Shew_1268 SsrA-binding protein (RefSeq) (Shewanella loihica PV-4)
MAKKNAKKSKNPPATIARNKRANFDYKFEEKFEAGLSLMGWEVKSIRVGKVNLSESYVFL
RDGEAYLFGCTITPLNTASTHVVCDPMRDRKLLLNRRELDKLQGLVERQGYSIVPISMYW
RKNAWVKLEIGLGKGKKEHDKRDDTKEREWKIEKSRTMKHAAR