Protein Info for BPHYT_RS33535 in Burkholderia phytofirmans PsJN

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 50 100 150 200 250 300 350 400 450 500 550 600 650 681 PF03979: Sigma70_r1_1" amino acids 62 to 141 (80 residues), 96.7 bits, see alignment E=1.9e-31 PF00140: Sigma70_r1_2" amino acids 158 to 189 (32 residues), 49 bits, see alignment (E = 1.4e-16) PF04546: Sigma70_ner" amino acids 199 to 415 (217 residues), 215.7 bits, see alignment E=2.1e-67 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 442 to 678 (237 residues), 394 bits, see alignment E=2.4e-122 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 442 to 667 (226 residues), 132.3 bits, see alignment E=1.3e-42 PF04542: Sigma70_r2" amino acids 448 to 516 (69 residues), 80.4 bits, see alignment E=2.1e-26 PF04539: Sigma70_r3" amino acids 525 to 601 (77 residues), 88.1 bits, see alignment E=1e-28 PF04545: Sigma70_r4" amino acids 614 to 667 (54 residues), 67.1 bits, see alignment 2.3e-22

Best Hits

Swiss-Prot: 60% identical to RPOD_NEIGO: RNA polymerase sigma factor RpoD (rpoD) from Neisseria gonorrhoeae

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 100% identity to bpy:Bphyt_6774)

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 B2T9G6 at UniProt or InterPro

Protein Sequence (681 amino acids)

>BPHYT_RS33535 RNA polymerase sigma factor RpoD (Burkholderia phytofirmans PsJN)
MTKKLNEVPVDDDATQSEESPAAAAPAKVEKAKARDRRAKEKALLKDAFASSQPGTVEEL
EERRSKLRALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIISTFNDMGVAVYEQAPDA
ETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIE
IAKRIEDGLKHMVMAISACPTTIADILAMAERVANEEIRIDELVDGLIDANAEDADGFSA
QEAEAIESEDEEVEEDSEEDEEEDDGTAQATANAAQMEALKRASLEKFAMISEWFDKMRR
AFEKEGYKSKSYLKAQETIQNELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHTVVD
KCGMPRAEFIARFPGSETDLEWADKIVGEGHAYSAILTRNIPAIREQQQRLLDLQARVVL
PLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM
KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQE
TGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPAD
AALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK
ALRKLRHPSRSDKLKSFLEGN