Protein Info for Shew_0339 in Shewanella loihica PV-4

Annotation: ATP-dependent RNA helicase RhlB (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 50 100 150 200 250 300 350 400 435 PF00270: DEAD" amino acids 33 to 207 (175 residues), 146.3 bits, see alignment E=7.5e-47 PF00271: Helicase_C" amino acids 243 to 351 (109 residues), 106.4 bits, see alignment E=1e-34

Best Hits

Swiss-Prot: 100% identical to RHLB_SHELP: ATP-dependent RNA helicase RhlB (rhlB) from Shewanella loihica (strain ATCC BAA-1088 / PV-4)

KEGG orthology group: K03732, ATP-dependent RNA helicase RhlB [EC: 3.6.4.13] (inferred from 100% identity to slo:Shew_0339)

MetaCyc: 68% identical to ATP-dependent RNA helicase RhlB (Escherichia coli K-12 substr. MG1655)
5.6.2.e [EC: 5.6.2.e]

Predicted SEED Role

"ATP-dependent RNA helicase RhlB" in subsystem ATP-dependent RNA helicases, bacterial

Isozymes

Compare fitness of predicted isozymes for: 3.6.4.13

Use Curated BLAST to search for 3.6.4.13 or 5.6.2.e

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 A3Q9R3 at UniProt or InterPro

Protein Sequence (435 amino acids)

>Shew_0339 ATP-dependent RNA helicase RhlB (RefSeq) (Shewanella loihica PV-4)
MSETHLTNQKFADFSLHPEIQQALVESGFEYCTPIQALSLPILLEHKDIAGQAQTGTGKT
LAFLVATFNHLLTTPIPDGRQLNQPRAIVMAPTRELAIQIAKDGELLAKHTGLKVGIVYG
GESYEVQRKVLDKGVDILIGTTGRIIDYVRQGVINLSAIQAVVLDEADRMFDLGFIKDIR
FLFRRMPDANERLNMLFSATLSMKVQELAYDHMNDPEKVEIAPSEKTSKNITEEIFYPSM
EDKMRLLLTLIEEDWPEKAIVFSNTKHSCENLWAHLEGDGHRVGLLTGDVPQKKRIRILE
QFTKGELDILVATDVAARGLHISDVSHVYNYDLPDDCEDYVHRIGRTGRAGQKGVSVSFA
CEEYALNLPAIEHYIQHSIPVTNYDSEALLDDIPPPVRIHRKHSPRPTGRSGGGKPQGGR
PGARPRRHDRTRRHS