Protein Info for PS417_04345 in Pseudomonas simiae WCS417

Annotation: RNA polymerase factor sigma-54

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 50 100 150 200 250 300 350 400 450 497 PF00309: Sigma54_AID" amino acids 5 to 48 (44 residues), 62.6 bits, see alignment 3.6e-21 TIGR02395: RNA polymerase sigma-54 factor" amino acids 10 to 494 (485 residues), 511.3 bits, see alignment E=1.2e-157 PF04963: Sigma54_CBD" amino acids 130 to 323 (194 residues), 219.8 bits, see alignment E=3.9e-69 PF04552: Sigma54_DBD" amino acids 337 to 495 (159 residues), 231.1 bits, see alignment E=8.2e-73

Best Hits

Swiss-Prot: 90% identical to RP54_PSEPU: RNA polymerase sigma-54 factor (rpoN) from Pseudomonas putida

KEGG orthology group: K03092, RNA polymerase sigma-54 factor (inferred from 99% identity to pfs:PFLU0882)

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 A0A1N7U256 at UniProt or InterPro

Protein Sequence (497 amino acids)

>PS417_04345 RNA polymerase factor sigma-54 (Pseudomonas simiae WCS417)
MKPSLVLRMGQQLTMTPQLQQAIRLLQLSTLDLQQEIQEALESNPMLERQEEGDDFDNAD
PLADNIEQKPNSDVQEPSYQETAPTVDNLEEGDWNERIPNELPVDTAWEDVYQTSASSLP
SNDDDEWDFTTRTSVGESLQSHLLWQLNLAPMSDTDRLIAVTLIDCINNQGYLDETLEEI
LEAFDPELDIELDEIEAVLHRIQQFEPAGIGARTLSECLLLQLRQLPAKTAWLTEAQRLV
TDYIDLLGSRDYSQLMRRMKLKEDDLRQVIELVQSLNPRPGSQIESSEAEYVVPDVIVRK
DNERWLVELNQESVPRLRVNPQYAGFVRRADTSADNTFMRNQLQEARWFIKSLQSRNETL
MKVATQIVEHQRGFLEYGDEAMKPLVLHDIAEAVGMHESTISRVTTQKFMHTPRGIYELK
YFFSSHVSTSEGGECSSTAIRAIIKKLVAAENQKKPLSDSKIAGLLEAQGIQVARRTVAK
YRESLGIAPSSERKRLM