Protein Info for Shew_0598 in Shewanella loihica PV-4

Annotation: ATP-dependent RNA helicase DbpA (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 50 100 150 200 250 300 350 400 468 PF00270: DEAD" amino acids 35 to 200 (166 residues), 165 bits, see alignment E=2.7e-52 PF04851: ResIII" amino acids 36 to 196 (161 residues), 28.4 bits, see alignment E=3e-10 PF00271: Helicase_C" amino acids 238 to 345 (108 residues), 100.2 bits, see alignment E=1.7e-32 PF03880: DbpA" amino acids 395 to 464 (70 residues), 73.8 bits, see alignment E=1.9e-24

Best Hits

Swiss-Prot: 53% identical to DBPA_ECOLI: ATP-dependent RNA helicase DbpA (dbpA) from Escherichia coli (strain K12)

KEGG orthology group: K05591, ATP-independent RNA helicase DbpA [EC: 3.6.4.13] (inferred from 100% identity to slo:Shew_0598)

MetaCyc: 53% identical to ATP-dependent RNA helicase DbpA (Escherichia coli K-12 substr. MG1655)
5.6.2.e [EC: 5.6.2.e]

Predicted SEED Role

"ATP-dependent 23S rRNA helicase DbpA"

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)

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 A3QAH2 at UniProt or InterPro

Protein Sequence (468 amino acids)

>Shew_0598 ATP-dependent RNA helicase DbpA (RefSeq) (Shewanella loihica PV-4)
MSQSDATTPSGAFDSLPLNPALLDTLKSIGFHQMTPIQAQSLPAILNGQDVIGQGKTGSG
KTAAFGLGLLNKLDVKRFRIQTLVLCPTRELADQVAAELRTLARGIHNIKILTLCGGVPM
GPQIGSLEHGAHIIVGTPGRIIDHLDRGRLDLDNVDTLVLDEADRMLEMGFQRELDAIMQ
EVPRERQTLLFSATFPEQIQGLSEQFMIDPLMVKVEVQHGGESIEQHFYECGNNNDRMKA
LQLLLLKHQPESAVVFCNTKRETKDVAAKLTNAGFSVVALHGDLEQRDRDQMLLKFANKS
ASVMVATDVAARGLDIDALDMVVNYHMAYDTEVHIHRIGRTGRAGSKGAAHTLFNHEDGY
KLSLLADALGREIDGEALPGEALLDTMPPQPRMVTIQIDGGKKQKVRPGDILGCLTGDNG
IEGSEVGKIKITEFRSYVAVDRKVLRKALNKIVKGKLKGKSYRAWELK