Protein Info for GFF3068 in Hydrogenophaga sp. GW460-11-11-14-LB1

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 50 100 150 200 250 300 350 400 450 500 542 PF00309: Sigma54_AID" amino acids 5 to 48 (44 residues), 63.7 bits, see alignment 1.7e-21 TIGR02395: RNA polymerase sigma-54 factor" amino acids 10 to 540 (531 residues), 435.4 bits, see alignment E=1.4e-134 PF04963: Sigma54_CBD" amino acids 157 to 363 (207 residues), 175.8 bits, see alignment E=1.2e-55 PF04552: Sigma54_DBD" amino acids 384 to 540 (157 residues), 211.4 bits, see alignment E=1e-66

Best Hits

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 (542 amino acids)

>GFF3068 RNA polymerase sigma-54 factor RpoN (Hydrogenophaga sp. GW460-11-11-14-LB1)
VKQGLSLRVSQHLALTPQLQQSIRLLQLSTLEMAQEVEQMLDENPFLERSEEIAERETFG
LEQTDVPVSAGEQIAEAAVPDAPAPLSSSPESTSASTDSGDGDGLEGKLDGATPVEESWE
GDGTVEMSPDDSEWGGDAPARNSGSGDSDETASAADLARAPVSLQDHLHDQARCLRLSDE
DRAALYFLIESLNDDGYLEENLSDLADAWLHLSGMPQLAGDPNEALEAREALEQRLAVAL
QLLQHMEPSGVGARDLGECLRLQILELRNTAEARAALAICNQPLELMAKRDVKRLCNLCG
LDDETVRAALGLIARLEPKPGRRFVDVERNVVVPDVIVTRAGRGFKVILNPDVMPRLRVH
DVYANAMRQNRGGRDSGGEAGHAAMQQRLQEARWFIKNIQQRFDTILRVSSAIVERQRNF
FMHGELAMRPLVLREIADELGLHESTISRVTTAKYMATPFGTYELKYFFGSSLGTETGGN
ASSTAVRALLKQFIASEEPAKPLSDNQLSDLLREQGIECARRTVAKYREALRIAPANLRK
AL