Protein Info for HSERO_RS19855 in Herbaspirillum seropedicae SmR1

Annotation: RNA polymerase subunit 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 50 100 150 200 250 300 350 400 450 496 PF00309: Sigma54_AID" amino acids 4 to 48 (45 residues), 58.4 bits, see alignment 7.7e-20 TIGR02395: RNA polymerase sigma-54 factor" amino acids 10 to 494 (485 residues), 461.5 bits, see alignment E=1.6e-142 PF04963: Sigma54_CBD" amino acids 134 to 326 (193 residues), 197.8 bits, see alignment E=2.2e-62 PF04552: Sigma54_DBD" amino acids 339 to 494 (156 residues), 220.3 bits, see alignment E=1.7e-69

Best Hits

Swiss-Prot: 60% identical to RP54_CUPNH: RNA polymerase sigma-54 factor (rpoN) from Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337)

KEGG orthology group: K03092, RNA polymerase sigma-54 factor (inferred from 100% identity to hse:Hsero_3973)

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

See D8ISM8 at UniProt or InterPro

Protein Sequence (496 amino acids)

>HSERO_RS19855 RNA polymerase subunit sigma-54 (Herbaspirillum seropedicae SmR1)
MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQILTDNPLLERLDDALDNSVRL
LADGAVSAAPSSGVSETTGSEASSEAAPAAADGESSFEYQDTAPEGVSGDSDWSFDDVAR
SGKSPDDEDARPQLEAHEITLREHLLEQIRVTARTQRDRALLELLTDALDDSGYLEEPLE
DILARLPEELGVDLEELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKVPFVTRRLAL
KIVEDYLPLFAQRDFNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDVI
VKQTKNGWQVMLNHEVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDTI
LRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELK
YFFGSHVATETGGEASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVAK
YREVLKIPPVNLRKSL