Protein Info for ABIE53_004866 in Paraburkholderia graminis OAS925

Annotation: RNA polymerase primary sigma factor

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 50 100 150 200 250 300 350 400 450 500 550 600 650 680 PF03979: Sigma70_r1_1" amino acids 61 to 140 (80 residues), 96.7 bits, see alignment E=1.9e-31 PF00140: Sigma70_r1_2" amino acids 157 to 188 (32 residues), 49 bits, see alignment (E = 1.4e-16) PF04546: Sigma70_ner" amino acids 198 to 414 (217 residues), 219.1 bits, see alignment E=1.9e-68 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 441 to 677 (237 residues), 394.1 bits, see alignment E=2.3e-122 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 441 to 666 (226 residues), 132.3 bits, see alignment E=1.3e-42 PF04542: Sigma70_r2" amino acids 447 to 515 (69 residues), 80.4 bits, see alignment E=2e-26 PF04539: Sigma70_r3" amino acids 524 to 600 (77 residues), 89.7 bits, see alignment E=3.3e-29 PF04545: Sigma70_r4" amino acids 613 to 666 (54 residues), 67.1 bits, see alignment 2.3e-22

Best Hits

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 99% identity to bgf:BC1003_4533)

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 (680 amino acids)

>ABIE53_004866 RNA polymerase primary sigma factor (Paraburkholderia graminis OAS925)
MTKKLNEVPVDDDATQSEETPVAAPGKVEKAKARDRRAKEKALLKDAFSSSQPGTVEELE
ERRSKLRALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIISTFNDMGVAVYEQAPDAE
TLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEI
AKRIEDGLKHMVMAISACPTTIADILAMAERVANEEIRIDELVDGLIDADAEDADGFSVQ
EAEAIESEDEEEEEEDEEDEEEDDGTAQATANAAQMEALKRASLEKFALISEWFDKMRRA
FEKEGYKSKSYLKAQETIQNELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHTVVDK
CGMPRAEFIARFPGSETDLEWADKIVSEGHPYSAILTRNIPAIREQQQRLLDLQARVVLP
LKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK
AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQET
GLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADA
ALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKA
LRKLRHPSRSDKLKSFLEGN