Protein Info for GFF3822 in Hydrogenophaga sp. GW460-11-11-14-LB1

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 738 PF03979: Sigma70_r1_1" amino acids 132 to 211 (80 residues), 85.2 bits, see alignment E=7.6e-28 PF00140: Sigma70_r1_2" amino acids 228 to 258 (31 residues), 45.9 bits, see alignment (E = 1.3e-15) PF04546: Sigma70_ner" amino acids 270 to 472 (203 residues), 195.7 bits, see alignment E=2.8e-61 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 499 to 724 (226 residues), 136.1 bits, see alignment E=8.6e-44 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 499 to 735 (237 residues), 392.8 bits, see alignment E=5.6e-122 PF04542: Sigma70_r2" amino acids 503 to 573 (71 residues), 82.2 bits, see alignment E=5.6e-27 PF04539: Sigma70_r3" amino acids 582 to 657 (76 residues), 81.7 bits, see alignment E=1e-26 PF04545: Sigma70_r4" amino acids 672 to 724 (53 residues), 64.5 bits, see alignment 1.5e-21

Best Hits

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 82% identity to aaa:Acav_1445)

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

Find the best match in UniProt

Protein Sequence (738 amino acids)

>GFF3822 RNA polymerase sigma factor RpoD (Hydrogenophaga sp. GW460-11-11-14-LB1)
VTQKTPAAKAAPAKKSAAKSEAELLEEPAKKKAGRPAKADTGDKPAAKRGRKPKAAAKGG
KADADLDDADLSDIEDDLTGDETEVEAVDTTAAQTTEKVKPLRMKISKAKERALMKEFGL
DETVLSEEEARNRRERLKTLIKLGKTRGYLTHGEINDHLPDKLVEAETLEVVVSLLNDMG
VAVYEQTPDAETLLLNNTGPTAATEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTV
ELLTREGEIEIAKRIEGGLNDMMAAISESPATIAEILVMAEDIREGKVVISTVVDGFADA
DEADDYVAEEDFDDYDEADDDDGKGGSKALTRKLEELKREALSRFDNMRTLFEKLHKIYD
KEGYGTPGYLKTQTSITETLMSIRFTAKAIEKLCGTMRSQVDDVRKKERELRRIIVDKCG
MPQETFIKEFPPNLLNLKWVEKQAAAGKPWSVVIERNIPPVQELQQGLINIQASVVVPLT
HLKDIHKRMNQGESTSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV
DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGF
EPDASILAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDQANTAPIEAAM
QAGLREVVKEILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIESKAVR
KLKHPSRSDKLRSFIDTL