Protein Info for GFF3116 in Sphingobium sp. HT1-2

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 50 100 160 PF01668: SmpB" amino acids 15 to 157 (143 residues), 198.8 bits, see alignment E=2e-63 TIGR00086: SsrA-binding protein" amino acids 15 to 157 (143 residues), 189.6 bits, see alignment E=1.5e-60

Best Hits

Swiss-Prot: 78% identical to SSRP_SPHWW: SsrA-binding protein (smpB) from Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273)

KEGG orthology group: K03664, SsrA-binding protein (inferred from 86% identity to sch:Sphch_1789)

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

Find the best match in UniProt

Protein Sequence (160 amino acids)

>GFF3116 tmRNA-binding protein SmpB (Sphingobium sp. HT1-2)
MARPRPATFDKKKIVAENRRARFDYFIEDVFEAGIALQGTEVKALRGGEGNIAESYAEVK
GNQVFLVNSNIPEYSHGNRENHEPKRVRKLLLHEREIEKMHSAVSRKGMTLVPLMVYFNS
QGRAKVELALAKGKQNHDKRDTIKERDWKRDQQRIMKAHS