Protein Info for DVU1788 in Desulfovibrio vulgaris Hildenborough JW710

Name: rpoD
Annotation: RNA polymerase sigma-70 factor (TIGR)

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 75 (70 residues), 73.2 bits, see alignment E=3.5e-24 PF00140: Sigma70_r1_2" amino acids 100 to 132 (33 residues), 47.2 bits, see alignment (E = 4.3e-16) TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 352 to 577 (226 residues), 133 bits, see alignment E=8e-43 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 352 to 588 (237 residues), 404.4 bits, see alignment E=1.6e-125 PF04542: Sigma70_r2" amino acids 356 to 426 (71 residues), 84 bits, see alignment E=1.2e-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), 61.4 bits, see alignment 1.2e-20

Best Hits

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 100% identity to dvu:DVU1788)

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 Q72B50 at UniProt or InterPro

Protein Sequence (590 amino acids)

>DVU1788 RNA polymerase sigma-70 factor (TIGR) (Desulfovibrio vulgaris Hildenborough JW710)
MSNIKEIQQIKSLIAKGKVSGFLTFDEVNKALPAEVNTPEQIEEIIGIFDQLDIAIVDSE
KDGKKISMSPGESEEEAPSEGGLDLSDDEETVDYSSRSTDPVRMYLREMGSVPLLDRDGE
VVIAKKIEMGEQDVLYALVEVPVAVEELVNVGEDLKQNRIKLKDVVKTIEEDDPSEDEMN
QRQRVILLLEEIRTTFKKKRKVYSKLDECCTLERRVASVQREIMNYKEDIVSRLRDIKLE
KTLIDRIIETVEDYVRQMHNCQRDLSAYILSTGKTQAEIQALFSGLEAREVSPVAASAAL
NMTVEELFSFKEMILGKIEILSRLQDKCCHNVNDLEEVLWRIKRGNSIAMRAKQELIRSN
LRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAI
ADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPTPEEIAERMDYPIDKVKKVLKIAKE
PISLETPIGDEEDSSLGDFIEDKKAVAPAEEVVNTKLGEQIASVLADLTPREEQVLRKRF
GIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQTLRSYYES