Protein Info for Shew_3311 in Shewanella loihica PV-4

Annotation: RNA polymerase factor sigma-54 (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 50 100 150 200 250 300 350 400 450 495 PF00309: Sigma54_AID" amino acids 4 to 49 (46 residues), 61.9 bits, see alignment 5.9e-21 TIGR02395: RNA polymerase sigma-54 factor" amino acids 10 to 493 (484 residues), 521.1 bits, see alignment E=1.3e-160 PF04963: Sigma54_CBD" amino acids 135 to 322 (188 residues), 214.9 bits, see alignment E=1.3e-67 PF04552: Sigma54_DBD" amino acids 336 to 493 (158 residues), 227.9 bits, see alignment E=7.8e-72

Best Hits

Swiss-Prot: 86% identical to RP54_SHEVD: RNA polymerase sigma-54 factor (rpoN) from Shewanella violacea (strain JCM 10179 / CIP 106290 / LMG 19151 / DSS12)

KEGG orthology group: K03092, RNA polymerase sigma-54 factor (inferred from 100% identity to slo:Shew_3311)

MetaCyc: 62% 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

See A3QI79 at UniProt or InterPro

Protein Sequence (495 amino acids)

>Shew_3311 RNA polymerase factor sigma-54 (RefSeq) (Shewanella loihica PV-4)
MKASLQLKMGQHLTMTPQLQQAIRLLQLSSLELQQEIQQALESNPLLELDEEQESASIEL
QDDGVTDSFDNKYDDKIELDSSQDNSGVETSDALTQDSMPDELPVDTTWDEVYTASPNSS
SGAMRDDDMPFQGETSEGLYEHLEWQKNLTPFSDNDLAIATAIIDAIDERGYLTQTCEDI
LEAMGDPEIELDEVEAVLKRVQHFDPIGVAARDLSECLTIQLAQYSDDTPHIANARMLIK
EHLDLIAGRDFRLLMRKTKLKEDELRDAIALIQTLNPRPGLAITASRDEYVIPDVTVTKK
KGRWVVELNPDSMPKINVNQQYAAMARSTKSQADGQFIRGHLQEAKWFLKSLESRNETLL
KVTNCIVDFQQGFFEFGEEAMKPMVLNDIAEAVEMHESTISRVTTQKYMHTPRGIFELKY
FFSSHVGTDDGGECSSTAIRAFIKKLVAAENQKKPLSDSKMAQLLAEQGIKVARRTIAKY
REAMLIPPSNQRKSL