Protein Info for Shew_0566 in Shewanella loihica PV-4

Annotation: RNA chaperone Hfq (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 25 50 75 92 TIGR02383: RNA chaperone Hfq" amino acids 5 to 64 (60 residues), 99.1 bits, see alignment E=4.8e-33 PF17209: Hfq" amino acids 7 to 68 (62 residues), 101.7 bits, see alignment E=6.9e-34

Best Hits

Swiss-Prot: 100% identical to HFQ_SHELP: RNA-binding protein Hfq (hfq) from Shewanella loihica (strain ATCC BAA-1088 / PV-4)

KEGG orthology group: K03666, host factor-I protein (inferred from 100% identity to slo:Shew_0566)

Predicted SEED Role

"RNA-binding protein Hfq" in subsystem Hfl operon or Polyadenylation bacterial

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 A3QAE0 at UniProt or InterPro

Protein Sequence (92 amino acids)

>Shew_0566 RNA chaperone Hfq (RefSeq) (Shewanella loihica PV-4)
MAKGQSLQDPFLNALRRERVPVSIYLVNGIKLQGQVESFDQFVILLKNTVSQMVYKHAIS
TVVPARPFNVSSHHNTPNQAAGYNASHDDSAE