Protein Info for OHPLBJKB_00498 in Escherichia coli HS(pFamp)R (ATCC 700891)

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 50 100 150 200 250 300 350 400 450 477 PF00309: Sigma54_AID" amino acids 5 to 48 (44 residues), 58.8 bits, see alignment 5.7e-20 TIGR02395: RNA polymerase sigma-54 factor" amino acids 9 to 474 (466 residues), 550.3 bits, see alignment E=1.8e-169 PF04963: Sigma54_CBD" amino acids 116 to 303 (188 residues), 215.6 bits, see alignment E=7.2e-68 PF04552: Sigma54_DBD" amino acids 317 to 475 (159 residues), 235.6 bits, see alignment E=3.4e-74

Best Hits

Swiss-Prot: 100% identical to RP54_ECOLI: RNA polymerase sigma-54 factor (rpoN) from Escherichia coli (strain K12)

KEGG orthology group: K03092, RNA polymerase sigma-54 factor (inferred from 100% identity to eoh:ECO103_3949)

MetaCyc: 100% 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)

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

Find the best match in UniProt

Protein Sequence (477 amino acids)

>OHPLBJKB_00498 RNA polymerase sigma-54 factor (Escherichia coli HS(pFamp)R (ATCC 700891))
MKQGLQLRLSQQLAMTPQLQQAIRLLQLSTLELQQELQQALESNPLLEQIDTHEEIDTRE
TQDSETLDTADALEQKEMPEELPLDASWDTIYTAGTPSGTSGDYIDDELPVYQGETTQTL
QDYLMWQVELTPFSDTDRAIATSIVDAVDDTGYLTVPLEDILESMGDEEIDIDEVEAVLK
RIQRFDPVGVAAKDLRDCLLIQLSQFDKTTPWLEEARLIISDHLDLLANHDFRTLMRVTR
LKEDVLKEAVNLIQSLDPRPGQSIQTGEPEYVIPDVLVRKHNGHWTVELNSDSIPRLQIN
QHYASMCNNARNDGDSQFIRSNLQDAKWLIKSLESRNDTLLRVSRCIVEQQQAFFEQGEE
YMKPMVLADIAQAVEMHESTISRVTTQKYLHSPRGIFELKYFFSSHVNTEGGGEASSTAI
RALVKKLIAAENPAKPLSDSKLTSLLSEQGIMVARRTVAKYRESLSIPPSNQRKQLV