Protein Info for SO0897 in Shewanella oneidensis MR-1

Name: dbpA
Annotation: ATP-dependent RNA helicase DbpA (NCBI ptt file)

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 50 100 150 200 250 300 350 400 458 PF00270: DEAD" amino acids 25 to 191 (167 residues), 168.9 bits, see alignment E=1.6e-53 PF04851: ResIII" amino acids 42 to 186 (145 residues), 30.3 bits, see alignment E=7.5e-11 PF00271: Helicase_C" amino acids 228 to 335 (108 residues), 96.8 bits, see alignment E=1.9e-31 PF03880: DbpA" amino acids 385 to 454 (70 residues), 73.6 bits, see alignment E=2.2e-24

Best Hits

Swiss-Prot: 54% 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 son:SO_0897)

MetaCyc: 54% 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 Q8EIE5 at UniProt or InterPro

Protein Sequence (458 amino acids)

>SO0897 ATP-dependent RNA helicase DbpA (NCBI ptt file) (Shewanella oneidensis MR-1)
MAFSTLKLKTELLENLSSMGYNEMTPIQAQSLPAILAGEDVIGQGKTGSGKTAAFGLGLL
NKLDVKRFRIQTLVLCPTRELADQVAQEIRTLARGIHNVKVLTLCGGVPMGPQIGSLEHG
AHIIVGTPGRIVDHLDRNRLDLSNLNMLVLDEADRMLEMGFQPQLDAIIEQSPRERQTLL
FSATFPEQIQSIAKQIMYNPVMVKAAVTHEKNTIEQHFYQLDDDKSRMQALQLLLLEHKP
ESAVVFCNTKRETQKVADELEGLGFSVLALHGDLEQRDRDETLLQFANKSACVLVATDVA
ARGLDIDALDAVFNYHVAYDTEVHIHRIGRTGRAGSKGAAYTFYNDQDGYKIALLEEYLD
REITSESLPSLSLLGSAPNAPTMITLQIDGGKKEKLRPGDILGALTGDNGIEGTQVGKIL
VTDYRAYVAVNRKVAKKALSKITSGRIKGKSYRAWLMK