Protein Info for GFF4467 in Xanthobacter sp. DMC5

Annotation: RNA polymerase sigma-54 factor 2

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 50 100 150 200 250 300 350 400 450 521 PF00309: Sigma54_AID" amino acids 6 to 50 (45 residues), 65.4 bits, see alignment 4.8e-22 TIGR02395: RNA polymerase sigma-54 factor" amino acids 11 to 510 (500 residues), 417.5 bits, see alignment E=3.5e-129 PF04963: Sigma54_CBD" amino acids 150 to 337 (188 residues), 184.2 bits, see alignment E=3.2e-58 PF04552: Sigma54_DBD" amino acids 352 to 511 (160 residues), 231.4 bits, see alignment E=7e-73

Best Hits

Swiss-Prot: 80% identical to RP54_AZOC5: RNA polymerase sigma-54 factor (rpoN) from Azorhizobium caulinodans (strain ATCC 43989 / DSM 5975 / JCM 20966 / NBRC 14845 / NCIMB 13405 / ORS 571)

KEGG orthology group: K03092, RNA polymerase sigma-54 factor (inferred from 86% identity to xau:Xaut_0064)

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

Find the best match in UniProt

Protein Sequence (521 amino acids)

>GFF4467 RNA polymerase sigma-54 factor 2 (Xanthobacter sp. DMC5)
MAMSPKLEFRQSQSLVMTPQLMQAIKLLQLSNMELVAYVEAELERNPLLERITEGDTSGS
DPQPEVRETRGEEMARGGLDGEPPPASDWTGNDNEQSRAAMETRLDTDLGNVFPDDVPAD
RGVTGGGSTASSPSMGEWSGGGERGEDYNPEAFLTAETTLADHLEAQLSVAVSDPARRLI
GINVIGLIDETGYFTGDLDLLAGQFGVPRAEVEAVLKLIQTFEPSGVGARNLAECLAIQL
RERDRFDPAMQALVANLELLARHDRNALKRVCGVDNEDLADMIGEIRRLDPKPGLAFGSG
VVHPLVPDVYVRPGADGTWLVELNSETLPRVLVNQSYHATVVKHAKSQEEKSFLADCLQS
ASWLTRSLDQRARTILKVASEIVRQQDAFLLHGVRFLRPLNLRTVADAIGMHESTVSRVT
SNKYISTPRGVVEMKFFFSSAISASGGGEAHSAESVRHRIKMLIEAEAPKDVLSDDTLVQ
KLKDDGIDIARRTVAKYREGMNIPSSVQRRREKMAMRSEAS