Protein Info for GFF6290 in Variovorax sp. SCN45

Annotation: RNA polymerase sigma-54 factor RpoN

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 50 100 150 200 250 300 350 400 450 500 533 PF00309: Sigma54_AID" amino acids 5 to 48 (44 residues), 65.8 bits, see alignment 3.6e-22 TIGR02395: RNA polymerase sigma-54 factor" amino acids 10 to 531 (522 residues), 416.7 bits, see alignment E=6.1e-129 PF04963: Sigma54_CBD" amino acids 152 to 361 (210 residues), 159.8 bits, see alignment E=1e-50 PF04552: Sigma54_DBD" amino acids 375 to 531 (157 residues), 207.5 bits, see alignment E=1.5e-65

Best Hits

KEGG orthology group: K03092, RNA polymerase sigma-54 factor (inferred from 94% identity to vpe:Varpa_0484)

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 (533 amino acids)

>GFF6290 RNA polymerase sigma-54 factor RpoN (Variovorax sp. SCN45)
MKQGLSLRVSQHLALTPQLQQSIRLLQLSTLELSQEVEQMLDENPFLERTAEEAAREEFG
LDAVDTPVQRDEVAEAGEGDFTPPSASTSTASTETSTTAADSDGPAAEIAEREPDWEGDG
TVDMAPDDSEWGSDAPARQNNLGDDERADATELARSQESLQSFLHRQALSLRLSENDSAA
LRFLIESLNDDGYLEDSLPALASGLAGDDNDQFDDLVHHFQVALGLLQSLEPVGVGARDL
GECLSIQLRALAAEDEDGEEEDRAQVYKTAIAICKQPMELLARRDFKRLATLTRSNEELV
RLALQVIARLEPKPGRRFVDVERNIVIPDVIVTKTGRGTNVKFRVMLNPEVMPRLRVHDI
YAGALKSHKGEGSQALSQRLQEARWFIKNIQQRFDTILRVSNAIVERQKSYFVHGELAMR
PLVLREIADELGLHESTISRVTTAKYMATPFGTVELKYFFGSALGTETGGNASSTAVRAL
IKQFVSSESIKKPLSDSQISEMLKEQGIECARRTVAKYREALRIAPANLRKAL