Protein Info for Psest_3313 in Pseudomonas stutzeri RCH2

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 50 100 150 200 250 300 350 400 450 502 PF00309: Sigma54_AID" amino acids 5 to 48 (44 residues), 62 bits, see alignment 5.6e-21 TIGR02395: RNA polymerase sigma-54 factor" amino acids 10 to 499 (490 residues), 516.3 bits, see alignment E=3.9e-159 PF04963: Sigma54_CBD" amino acids 134 to 328 (195 residues), 222.6 bits, see alignment E=5.4e-70 PF04552: Sigma54_DBD" amino acids 342 to 500 (159 residues), 233 bits, see alignment E=2.2e-73

Best Hits

Swiss-Prot: 85% identical to RP54_PSEPU: RNA polymerase sigma-54 factor (rpoN) from Pseudomonas putida

KEGG orthology group: K03092, RNA polymerase sigma-54 factor (inferred from 87% identity to pfv:Psefu_3675)

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 L0GR58 at UniProt or InterPro

Protein Sequence (502 amino acids)

>Psest_3313 RNA polymerase sigma-54 factor (Pseudomonas stutzeri RCH2)
MKPSLVLKMGQQLTMTPQLQQAIRLLQLSTLDLQQEIQEALDSNPMLEREEDGDDFDSSD
PMAEAADRPGDTGTEKSSSQESTYEEPSHSGESADDGDWGERIPSELPVDTAWEDIYQTS
ASSLPSNDDDEWDFTSRTSNGISLQSHLLWQLNLAPMSDTDRLIATTLIDCINDQGYLEE
TLQEIVDSFDPELEIELDEVEVVLRRIQQFEPAGIGARDLRECLLLQLRQLSERTPWLSE
AQRLVSDYLDILGSRDYSLLMRRMKLKEDELRQVIELIQSLNPRPGSQIEASEPEYVVPD
VIVRKHNDRWLVELNQEAMPRLRVNAQYAGFVKRADSSADNTFMRNQLQEARWFIKSLLS
RNETLMKVATQIVEHQRAFLEHGDEAMKPLVLHDIAEAVGMHESTISRVTTQKYMHTPRG
IYELKYFFSSHVSTAEGGECSSTAIRAIIKKLVAAENQKKPLSDSKIAGLLEAQGIQVAR
RTVAKYRESLGIAPSSERKRLL