Protein Info for DvMF_0494 in Desulfovibrio vulgaris Miyazaki F

Annotation: RNA polymerase, sigma 70 subunit, RpoD subfamily (RefSeq)

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 50 100 150 200 250 300 350 400 450 500 550 590 PF03979: Sigma70_r1_1" amino acids 6 to 71 (66 residues), 68.6 bits, see alignment E=9.5e-23 PF00140: Sigma70_r1_2" amino acids 100 to 132 (33 residues), 46.8 bits, see alignment (E = 5.8e-16) TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 352 to 577 (226 residues), 135.1 bits, see alignment E=1.8e-43 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 352 to 588 (237 residues), 405.1 bits, see alignment E=9.6e-126 PF04542: Sigma70_r2" amino acids 356 to 426 (71 residues), 84 bits, see alignment E=1.3e-27 PF04539: Sigma70_r3" amino acids 435 to 511 (77 residues), 103.8 bits, see alignment E=1.1e-33 PF04545: Sigma70_r4" amino acids 524 to 577 (54 residues), 61.9 bits, see alignment 7.8e-21

Best Hits

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 100% identity to dvm:DvMF_0494)

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)

Compare to protein 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 B8DKM2 at UniProt or InterPro

Protein Sequence (590 amino acids)

>DvMF_0494 RNA polymerase, sigma 70 subunit, RpoD subfamily (RefSeq) (Desulfovibrio vulgaris Miyazaki F)
MGNIKDIQQIKSLIAKGKVSGFLTFDEVNKALPAEVNTPEQIEEIIGIFDQLEIAIVDTE
KDGKKISVSPGESEEEPSGEPGLDLVEDEESADYSSRSTDPVRMYLREMGAVPLLDRDGE
VQIAKKIELGEQDVLYALVEVPVAVEELINVGEDLKQNRIKLKDVVKTIEEDDPSEDEMN
QRSRVILLLDEIKHTYKKKRKVYAKLDDCCTLERRVTAIQKEILGFKEDIVNRLRDIKLE
KTLIDRIIETVEDYVRQMHNCQRDLSAYILSTGKTQVEIQDIFRMLEAREMNPVAASAAL
GMTVEELFSFKEMIIGKIEILNRLQDKCCHNVTDLEEVLWRIKRGNTHAMRAKQELIRSN
LRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAI
ADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPTPEEIAERMDYPIDKVKKVLKIAKE
PISLETPIGDEEDSSLGDFIEDKKAVAPAEEVVNTKLSEQIASVLADLTPREEQVLRKRF
GIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQMLRSYYES