Protein Info for RS_RS11120 in Ralstonia solanacearum GMI1000

Annotation: RNA polymerase sigma factor RpoD

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 828 PF03979: Sigma70_r1_1" amino acids 209 to 288 (80 residues), 96.5 bits, see alignment E=2.2e-31 PF00140: Sigma70_r1_2" amino acids 305 to 337 (33 residues), 49.9 bits, see alignment (E = 7.6e-17) PF04546: Sigma70_ner" amino acids 346 to 562 (217 residues), 220.1 bits, see alignment E=9.5e-69 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 589 to 825 (237 residues), 392.5 bits, see alignment E=7.2e-122 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 589 to 814 (226 residues), 129.6 bits, see alignment E=8.5e-42 PF04542: Sigma70_r2" amino acids 595 to 663 (69 residues), 80 bits, see alignment E=2.7e-26 PF04539: Sigma70_r3" amino acids 672 to 748 (77 residues), 89.1 bits, see alignment E=4.8e-29 PF04545: Sigma70_r4" amino acids 761 to 814 (54 residues), 66.8 bits, see alignment 3e-22

Best Hits

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 95% identity to rsl:RPSI07_1208)

Predicted SEED Role

"RNA polymerase sigma factor RpoD" in subsystem Flagellum or Macromolecular synthesis operon or Transcription factors cyanobacterial RpoD-like sigma factors 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 Q8XXA1 at UniProt or InterPro

Protein Sequence (828 amino acids)

>RS_RS11120 RNA polymerase sigma factor RpoD (Ralstonia solanacearum GMI1000)
MGQAGGKAAVPAKTGKAQPSKTAEISAAAKPAPRVKGAIQSSTSGKVSTSMSTSARPGGK
EAASVALKGKTTTVAKSKITEVESKESAASARAAKTGTARTSTAKPNKAADADTKRTVRE
AEAIPTPTSPAPRAEAAAEPKKRGRKPRAGAQADDESSTDVTEEFDEAPAAPAPKSDKQK
ARDRKAKEKALLKEFAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDM
VDAESMDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEF
GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMGERV
ANDEAKIDEYIDGLIDPNADAAEAAQAGDEDEDFEDEDADESGDEEEDEDDDGSGSSAAS
ARQLEELKQAALAKFAIIGDQFEKMRRAFEKEGYKSKPYLKAQEAIQNELMTIRFTARNV
ERLCDTLRGQVDEVRKLERAILNIVVDKCGMSRGDFVSRFPGNETNLGWINTVVADGKPY
SAIVERNIPAVHELQQKLIDLQARVVLPLAELKDVNKKMSEGERRAREAKREMTEANLRL
VISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ
ARTIRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPIS
METPIGDDDDSHLGDFIEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRFGIE
MSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEGS