Protein Info for GFF213 in Variovorax sp. SCN45

Annotation: tmRNA-binding protein SmpB

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 50 100 158 TIGR00086: SsrA-binding protein" amino acids 12 to 154 (143 residues), 180.1 bits, see alignment E=1.2e-57 PF01668: SmpB" amino acids 12 to 154 (143 residues), 199.3 bits, see alignment E=1.4e-63

Best Hits

Swiss-Prot: 87% identical to SSRP_RHOFT: SsrA-binding protein (smpB) from Rhodoferax ferrireducens (strain ATCC BAA-621 / DSM 15236 / T118)

KEGG orthology group: K03664, SsrA-binding protein (inferred from 94% identity to vpe:Varpa_2859)

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)

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 (158 amino acids)

>GFF213 tmRNA-binding protein SmpB (Variovorax sp. SCN45)
MATKKQDTSSRIADNKKAAYNYFFEERFEAGMVLEGWEVKSLREGKVQLTDGYVVIRNGE
LFVVGCQINPLKSASTHVNPDSVRTKKLLLKKDEIRRLIGKVEQKGYTLVPLNLHWKAGK
VKCEIALAKGKAEHDKRDTIKDREGKREVERAMKSRNR