Protein Info for HSERO_RS04365 in Herbaspirillum seropedicae SmR1

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 PF03979: Sigma70_r1_1" amino acids 231 to 308 (78 residues), 97.4 bits, see alignment E=1.1e-31 PF00140: Sigma70_r1_2" amino acids 326 to 358 (33 residues), 50 bits, see alignment (E = 6.9e-17) PF04546: Sigma70_ner" amino acids 367 to 584 (218 residues), 219.9 bits, see alignment E=1.1e-68 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 611 to 847 (237 residues), 389.5 bits, see alignment E=5.6e-121 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 611 to 836 (226 residues), 130.8 bits, see alignment E=3.8e-42 PF04542: Sigma70_r2" amino acids 617 to 685 (69 residues), 80 bits, see alignment E=2.8e-26 PF04539: Sigma70_r3" amino acids 694 to 770 (77 residues), 83.3 bits, see alignment E=3.2e-27 PF04545: Sigma70_r4" amino acids 784 to 836 (53 residues), 66.3 bits, see alignment 4.2e-22

Best Hits

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 96% identity to hse:Hsero_0870)

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 D8J051 at UniProt or InterPro

Protein Sequence (850 amino acids)

>HSERO_RS04365 RNA polymerase sigma factor RpoD (Herbaspirillum seropedicae SmR1)
MANAMKKPAKTPAASTKSSKTVTAAKPTAAARPTKAVAAKSPVKGTAKAADTVKTTAKTA
AAATPKKTAVKTTAAKPARAAAPKATATPANKLPQAAEQAVSVKATKTSVTTKKPETKTA
KTTKAAKVEGKDVSATAASSVSQTTDAAALAAIDTSGYVLPSVKVPGRRGRKPKEFQPES
DEVAALNTIERTELKAADKAKAKDRKAKEKALLKDAFSSDTEASEEELERRRQKLKTLIK
LGKERGFLTFSEINDHLPENIVDPEAIEGIIGTFSDMGISVYEHAPDAETLLLSDNVANV
ASDDDAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEIEIAKRIEDGLKDM
IQAISACPTTIAEILAAAERISKDEIKVDEIVDGLVDPNESEQQVEAASSDSDEDDEDEE
EEEEDEEEEESESTGSGAAGFSAEQLEQLKRDALGKFAVIGTQFENMRKAFEKEGYNSKP
YVKAQEIISNELLGIRFTAKIVEKLCDTLRAQVDEVRTVERQILDVAVNKCNMPRAHFIK
VFPGNEVNLDWVDGEVAANHDYSAVLSRNVPAIKELQQKLIDLQARVVLPLQDLRAINKK
MGAGEKKARMAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG
YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATLA
IKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHASMRNVV
KDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS
DKLKSFLEGN