Protein Info for GFF3177 in Salmonella enterica subsp. enterica serovar Typhimurium str. MS1868

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 50 100 150 200 250 300 350 400 450 500 550 615 PF03979: Sigma70_r1_1" amino acids 5 to 81 (77 residues), 104.1 bits, see alignment E=8.9e-34 PF00140: Sigma70_r1_2" amino acids 98 to 128 (31 residues), 46 bits, see alignment (E = 1.2e-15) PF04546: Sigma70_ner" amino acids 139 to 350 (212 residues), 255.8 bits, see alignment E=1.1e-79 TIGR02393: RNA polymerase sigma factor RpoD" amino acids 377 to 613 (237 residues), 399.2 bits, see alignment E=6.4e-124 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 377 to 602 (226 residues), 129.2 bits, see alignment E=1.2e-41 PF04542: Sigma70_r2" amino acids 381 to 451 (71 residues), 82.9 bits, see alignment E=3.3e-27 PF04539: Sigma70_r3" amino acids 460 to 535 (76 residues), 96.8 bits, see alignment E=2e-31 PF04545: Sigma70_r4" amino acids 549 to 602 (54 residues), 65.1 bits, see alignment 1e-21

Best Hits

Swiss-Prot: 100% identical to RPOD_SALTI: RNA polymerase sigma factor RpoD (rpoD) from Salmonella typhi

KEGG orthology group: K03086, RNA polymerase primary sigma factor (inferred from 97% identity to enc:ECL_04399)

MetaCyc: 97% 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 (615 amino acids)

>GFF3177 RNA polymerase sigma factor RpoD (Salmonella enterica subsp. enterica serovar Typhimurium str. MS1868)
MEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAP
DADDLLLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEID
IAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTA
THVGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAK
GRSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMP
KKNFITLFTGNETSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQV
KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK
FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP
TPEELAERMLMPEDKIRKVPKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTE
SLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL
RHPSRSEVLRSFLDD