Protein Info for Shew_0457 in Shewanella loihica PV-4

Annotation: ATP-dependent helicase HepA (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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 968 PF18339: Tudor_1_RapA" amino acids 3 to 53 (51 residues), 84 bits, see alignment 2e-27 PF18337: Tudor_RapA" amino acids 55 to 117 (63 residues), 93 bits, see alignment 3.5e-30 PF04851: ResIII" amino acids 157 to 315 (159 residues), 40 bits, see alignment E=1.4e-13 PF00270: DEAD" amino acids 171 to 315 (145 residues), 24.4 bits, see alignment E=7.5e-09 PF00176: SNF2-rel_dom" amino acids 172 to 345 (174 residues), 66.9 bits, see alignment E=5.9e-22 PF00271: Helicase_C" amino acids 492 to 602 (111 residues), 63.8 bits, see alignment E=6.1e-21 PF12137: RapA_C" amino acids 606 to 964 (359 residues), 485.9 bits, see alignment E=2.7e-149

Best Hits

Swiss-Prot: 59% identical to RAPA_ALIFM: RNA polymerase-associated protein RapA (rapA) from Aliivibrio fischeri (strain MJ11)

KEGG orthology group: K03580, ATP-dependent helicase HepA [EC: 3.6.4.-] (inferred from 59% identity to vsa:VSAL_I0352)

Predicted SEED Role

"RNA polymerase associated protein RapA (EC 3.6.1.-)" (EC 3.6.1.-)

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 3.6.1.-, 3.6.4.-

Use Curated BLAST to search for 3.6.1.- or 3.6.4.-

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 A3QA31 at UniProt or InterPro

Protein Sequence (968 amino acids)

>Shew_0457 ATP-dependent helicase HepA (RefSeq) (Shewanella loihica PV-4)
MPFSLGQRWISDTESELGLGTVIGLEGRMVTLMFPATDENRMFARDDAPLTRVIYNPGDI
IESHEGWSLKVSEIEEKNQLVIYHGIHTETGEEVSLRETLLNHNIRFNKPQDRLFAGQID
RLDRFGVRYQSQLLRHKLATSDLLGLQGPRVGLIPHQQWIAHEVGQRFAPRVLLADEVGL
GKTIEAGLIIHQQLLTGRAERILIIVPDTLRHQWLVEMLRRFNLRFSVFDEDRCVEAYAD
HDNPFYTEQLVICSLELLRKKKRLDQALDADWDLMVVDEAHHLEWTEEEPSRAYRVVEAL
SEVVPGVLLLTATPDQLGHQSHFARLRLLDPDRFYDYQAFLKEEESYKEVASAADALASG
KRLPDEAVASLTELLNEKDITPALRLIEDESVDNEQRDQARSELLQELLDRHGTGRVLYR
NSRASVKGFPTRIFNAHPQTMPAQYKTAARVSDMMGGQTDLTAKVKQALSPEKLYQAFES
DSASWWKFDPRVDWLIDFLKNHRSKKVLIIASQAETALSLEEALRTREGIQATVFHEGMS
IIERDKAGAYFAQESGGAQALICSEIGSEGRNFQFASHLVLFDLPLNPDLLEQRIGRLDR
IGQANDVEIHLPYLANTAQENLMNWYHKGLNAFEQTCPTGHILFNEFSEELLTQLVYRDE
DKFTQLLNHTQSRYKALKKAMEQGRDKLLEINSHGGDKAQKLVENLAARDQDTQLIGSVI
RLWDIIGVEQEDSGENAIVLHPSEHMMFPTYPGLPEDGITVTFDREMALSRDDIALITQE
HPLVQTGLDLITSSETGTTSVAVLKNKALPAGTIFLELIYMADASAPRSSQLYRYMPPTP
VRVLLDKNGNNLSQNVSYESFDKQLSAVNRHIASKLVNASQTLLHPLFAKGEEFAQAAMK
QLTEEASNKMTQQLTAELERLEALKAVNPNIRDEELEHLRNQMVELGNYLDACQLQLDAV
RLVLVSHA