Protein Info for ABIE53_004960 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 50 100 150 200 250 300 350 400 450 500 550 600 664 PF03979: Sigma70_r1_1" amino acids 47 to 126 (80 residues), 81.9 bits, see alignment E=8.2e-27 PF00140: Sigma70_r1_2" amino acids 143 to 175 (33 residues), 45 bits, see alignment (E = 2.6e-15) PF04546: Sigma70_ner" amino acids 184 to 399 (216 residues), 188.3 bits, see alignment E=5e-59 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 426 to 649 (224 residues), 126.8 bits, see alignment E=6.3e-41 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 426 to 662 (237 residues), 370.5 bits, see alignment E=3.8e-115 PF04542: Sigma70_r2" amino acids 430 to 500 (71 residues), 75.1 bits, see alignment E=9e-25 PF04539: Sigma70_r3" amino acids 509 to 585 (77 residues), 86.8 bits, see alignment E=2.6e-28 PF04545: Sigma70_r4" amino acids 598 to 649 (52 residues), 64.6 bits, see alignment 1.4e-21

Best Hits

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 98% identity to bgf:BC1003_4397)

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 (664 amino acids)

>ABIE53_004960 RNA polymerase primary sigma factor (Paraburkholderia graminis OAS925)
MNPFDREDSQHETAAYTKAPSGRTPKGKGAGKAIPVAAELPPQQAEERQRQMRALIQLGK
EQGYLTHAQINDHLPDNFAQTAAIDSIVSAFNDMGVQVYEQAPDAETLLLNSNAPAVVSD
DQADEETEVALSTVDSEFGRTTDPVRMYMREMGATELLTRAGEIAIAKRIEDGLHEMVQA
IAACPLAISAILASAQQVADGELRIDELVDGLNEDNVPAEEETASADAAADVDADADEDD
DSDSDDDVGPADSSAADEARLKQLTSDCLEIFAQVGILYDQMNASHTRGDVSSKAYQKAR
EEIQQHLAKIRFTARTIDRLCGDVQHQVAQVRAIERNILQIVVTKSGMPREKFIESFSGH
EADLGWTERAARGNTPYGAALERHLPAIQSEQQKLIDIEATVSLPLKHLKEINRQMVAAE
SKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKFST
YATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISREILQQTGQEAHPSVLAERMDL
SEEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAASSPADAAMQADLRAAIDDALD
SLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQIESKAMRKLMHPSRADRLKS
FLDR