Protein Info for SO0947 in Shewanella oneidensis MR-1

Name: srmB
Annotation: ATP-dependent RNA helicase SrmB (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 50 100 150 200 250 300 350 420 PF00270: DEAD" amino acids 25 to 189 (165 residues), 143.7 bits, see alignment E=7.3e-46 PF04851: ResIII" amino acids 36 to 189 (154 residues), 35.4 bits, see alignment E=1.5e-12 PF00271: Helicase_C" amino acids 232 to 340 (109 residues), 113.4 bits, see alignment E=9.8e-37

Best Hits

Swiss-Prot: 54% identical to SRMB_ECOLI: ATP-dependent RNA helicase SrmB (srmB) from Escherichia coli (strain K12)

KEGG orthology group: K05590, ATP-dependent RNA helicase SrmB [EC: 2.7.7.-] (inferred from 100% identity to son:SO_0947)

MetaCyc: 54% identical to ATP-dependent RNA helicase SrmB (Escherichia coli K-12 substr. MG1655)
5.6.2.e [EC: 5.6.2.e]

Predicted SEED Role

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

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 2.7.7.-

Use Curated BLAST to search for 2.7.7.- 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 Q8EI96 at UniProt or InterPro

Protein Sequence (420 amino acids)

>SO0947 ATP-dependent RNA helicase SrmB (NCBI ptt file) (Shewanella oneidensis MR-1)
MQFEDFQLDPSLLESLKAMGHLSPTTIQQETLPHALEQRDILARAPTGTGKTASFLLPAL
QHLIDFPRRYSGQARVLILTPTRELASQIHRYACHLATDQGLNIAIITGGVPYAPQEEAL
KGNIDILVATPGRLMEYLDKGKFSAESVDILIIDEADRMLDMGFSAVVKAIALEAQGRKQ
NMLFSATLEGSGVIRFAREVLNDPIEIDVDAPRKEKAKIHQWIHLADDKDHKFALLCHLL
KQEDVKRAIVFVKTRDVVSSLEGQLLQAGIPCAFMRGDMEQKKRFQALSRFTKGEVNVLL
ATDVAARGIDIDDISHVINFDMPRSADTYIHRIGRTGRAGAKGTAISLAEAHDMRIVGKI
ERYIEQPLKRRIIEELRPKHKEARVPTKKKAKVKAKEAAKKTSKKEAAKKASKIARKKQS