Protein Info for GFF3646 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 50 100 150 200 250 300 350 400 474 PF00309: Sigma54_AID" amino acids 4 to 47 (44 residues), 41.5 bits, see alignment 1.4e-14 TIGR02395: RNA polymerase sigma-54 factor" amino acids 9 to 465 (457 residues), 394.4 bits, see alignment E=3.8e-122 PF04963: Sigma54_CBD" amino acids 105 to 295 (191 residues), 170.4 bits, see alignment E=5.6e-54 PF04552: Sigma54_DBD" amino acids 310 to 466 (157 residues), 193.9 bits, see alignment E=2.3e-61

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 (474 amino acids)

>GFF3646 RNA polymerase sigma-54 factor RpoN (Hydrogenophaga sp. GW460-11-11-14-LB1)
MMQLDARAEQRQTLSPRLQHAVRLLQMSSLDFGIVVRDVLGRNPFLEAEDEAAEEARDGG
PDTRPDEGRDAQAEPPAASDRDLWLADGLAPARQGHDGDVSALDFVMEEVPLNAHLHAQL
GTMALSPRDLALAGVVVESLDDDGYLRSPLTALCGVAAVTPAATLEDLQIALKLVQSLEP
VGVAARDVAECLSLQLGEIECPHLRAMARTIVHGHLHSLAARDVPAMARALGASAGEVEM
ACDRIRHLDPRPGWRQSSSQVNWIVPDVIVRKDRGVWDVQLNAAVVPRVRLNEVYAQLFQ
RHRGAENTEMGAHLQEARWTVRNVEQRFSTILDVSQAIVRRQRHFFEYGSMAMKPLGLRE
IADEVGVHESTVSRVTNNKYMATPTGVYELKHFFSRAMVSANGKACSGTAIRGLIQDIIE
SESTGQPLSDAEITRQLARQGLTVARRTVTKYRQMLRIDAVGRRKRHDGLAVEA