Protein Info for SO1284 in Shewanella oneidensis MR-1

Name: rpoD
Annotation: RNA polymerase sigma-70 factor (NCBI ptt file)

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 50 100 150 200 250 300 350 400 450 500 550 616 PF03979: Sigma70_r1_1" amino acids 5 to 81 (77 residues), 104 bits, see alignment E=9.7e-34 PF00140: Sigma70_r1_2" amino acids 96 to 126 (31 residues), 45.7 bits, see alignment (E = 1.6e-15) PF04546: Sigma70_ner" amino acids 137 to 351 (215 residues), 252.7 bits, see alignment E=1e-78 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 378 to 614 (237 residues), 400.5 bits, see alignment E=2.5e-124 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 378 to 603 (226 residues), 125.5 bits, see alignment E=1.6e-40 PF04542: Sigma70_r2" amino acids 382 to 452 (71 residues), 82.9 bits, see alignment E=3.5e-27 PF04539: Sigma70_r3" amino acids 461 to 536 (76 residues), 101.2 bits, see alignment E=8.4e-33 PF04545: Sigma70_r4" amino acids 550 to 603 (54 residues), 66.5 bits, see alignment 3.6e-22

Best Hits

Swiss-Prot: 84% identical to RPOD_SHEVD: RNA polymerase sigma factor RpoD (rpoD) from Shewanella violacea (strain JCM 10179 / CIP 106290 / LMG 19151 / DSS12)

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 99% identity to shn:Shewana3_3087)

MetaCyc: 79% identical to RNA polymerase sigma factor RpoD (Escherichia coli K-12 substr. MG1655)

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 Q8EHE1 at UniProt or InterPro

Protein Sequence (616 amino acids)

>SO1284 RNA polymerase sigma-70 factor (NCBI ptt file) (Shewanella oneidensis MR-1)
MDHTPQSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAP
DADDMMMSEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIA
KRIEEGINTVQSSVAEYPQAIAMILEQYDQYEADELRLSDIISGFVNPDEEDLGPTATHI
GSELSEEDLEDEDDEEDDEDEDGDGDGDDDGNKGPDPEEARERFSQLRTAYESALKIIDA
KGREHPESIQALFEIGEIFKEFRLVPKQFDRLVKSMRSMMDRVRVQERLLMKLCVEQAKM
PKKNFVKFFTGNETNLDWFEAEKTSNKPYAEGLRMVEEDVQRCRSKLAAIEEETGLVIAA
IKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD
KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE
PSPEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATS
ESLKSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK
LRHPSRSEILKSFLDE