Protein Info for CSW01_12815 in Vibrio cholerae E7946 ATCC 55056

Annotation: RNA polymerase sigma-54 factor

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 50 100 150 200 250 300 350 400 450 487 PF00309: Sigma54_AID" amino acids 4 to 49 (46 residues), 63.9 bits, see alignment 1.4e-21 TIGR02395: RNA polymerase sigma-54 factor" amino acids 10 to 484 (475 residues), 519.8 bits, see alignment E=3.2e-160 PF04963: Sigma54_CBD" amino acids 128 to 315 (188 residues), 206 bits, see alignment E=6.4e-65 PF04552: Sigma54_DBD" amino acids 327 to 485 (159 residues), 243.9 bits, see alignment E=1e-76

Best Hits

Swiss-Prot: 84% identical to RP54_VIBAN: RNA polymerase sigma-54 factor (rpoN) from Vibrio anguillarum

KEGG orthology group: K03092, RNA polymerase sigma-54 factor (inferred from 100% identity to vcm:VCM66_2450)

MetaCyc: 57% identical to RNA polymerase sigma factor RpoN (Escherichia coli K-12 substr. MG1655)

Predicted SEED Role

"RNA polymerase sigma-54 factor RpoN" in subsystem Flagellar motility or Flagellum or Transcription initiation, bacterial sigma factors

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

Find the best match in UniProt

Protein Sequence (487 amino acids)

>CSW01_12815 RNA polymerase sigma-54 factor (Vibrio cholerae E7946 ATCC 55056)
MKPSLQLKLGQQLAMTPQLQQAIRLLQLSTLDLQQEIQEALESNPLLEVEENQDEAPSLD
SVRMTEESPREPEELYEPEPQDSSDLIEKSEISAELEMDTTWDEVYSANTGSTGLALDDD
APIYQGETTQTLQDYLHWQLDLTPFSDVDRTIAVALIDAIDDYGYLTVSLEEIQESLRSD
DIELDEIEAVRKRIQQFDPFGVASLNLQDCLLLQLTTYPCDTPWLEEARLLLSQYIDDLG
NRDYKTILKETKLKEEDLREILQLIQQLDPRPGSRIAQDHAEYVIPDVSVYKEQGRWLVT
INPDSVPKLKINQQYADLMRGNNAESNYIRTNLQEAKWLIKSLESRNETLLKVAKCIVEH
QHDFFEYGEEAMKPMVLNDVAMAVEMHESTISRVTTQKYMHTPRGIFELKYFFSSHVSTD
NGGECSSTAIRALIKKLVAAENPAKPLSDSKIATLLADQGIQVARRTIAKYRESLGIAPS
SQRKRLL