Protein Info for CSW01_02745 in Vibrio cholerae E7946 ATCC 55056

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 50 100 150 200 250 300 350 400 450 500 550 600 625 PF03979: Sigma70_r1_1" amino acids 4 to 80 (77 residues), 99.7 bits, see alignment E=2.2e-32 PF00140: Sigma70_r1_2" amino acids 98 to 128 (31 residues), 46.5 bits, see alignment (E = 8.7e-16) PF04546: Sigma70_ner" amino acids 139 to 360 (222 residues), 228.9 bits, see alignment E=1.9e-71 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 387 to 612 (226 residues), 127 bits, see alignment E=5.4e-41 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 387 to 623 (237 residues), 398.3 bits, see alignment E=1.2e-123 PF04542: Sigma70_r2" amino acids 391 to 461 (71 residues), 82.8 bits, see alignment E=3.6e-27 PF04539: Sigma70_r3" amino acids 470 to 545 (76 residues), 99.1 bits, see alignment E=3.6e-32 PF04545: Sigma70_r4" amino acids 559 to 612 (54 residues), 68.8 bits, see alignment 6.9e-23

Best Hits

Swiss-Prot: 77% identical to RPOD_SALTY: RNA polymerase sigma factor RpoD (rpoD) from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 100% identity to vcj:VCD_001088)

MetaCyc: 76% 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

Find the best match in UniProt

Protein Sequence (625 amino acids)

>CSW01_02745 RNA polymerase sigma factor RpoD (Vibrio cholerae E7946 ATCC 55056)
MDQNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAP
DADDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEID
IAKRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMETEAPTA
THIGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNELRGKF
QNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLVM
KAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQKLQMIE
QETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG
NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR
QMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTL
ELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR
QIEAKALRKLRHPSRSEVLRSFLDE