Protein Info for GFF1690 in Salmonella enterica subsp. enterica serovar Typhimurium str. MS1868

Annotation: RNA polymerase sigma factor for flagellar operon

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 50 100 150 200 239 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 15 to 236 (222 residues), 112.7 bits, see alignment E=1.4e-36 PF04542: Sigma70_r2" amino acids 16 to 88 (73 residues), 60.5 bits, see alignment E=2.2e-20 TIGR02479: RNA polymerase sigma factor, FliA/WhiG family" amino acids 16 to 236 (221 residues), 288.4 bits, see alignment E=4e-90 PF04539: Sigma70_r3" amino acids 97 to 167 (71 residues), 66.5 bits, see alignment E=3.9e-22 PF08281: Sigma70_r4_2" amino acids 179 to 232 (54 residues), 37.6 bits, see alignment E=2.8e-13 PF04545: Sigma70_r4" amino acids 185 to 233 (49 residues), 59.9 bits, see alignment 2.8e-20

Best Hits

Swiss-Prot: 100% identical to FLIA_SALTI: RNA polymerase sigma factor FliA (fliA) from Salmonella typhi

KEGG orthology group: K02405, RNA polymerase sigma factor for flagellar operon FliA (inferred from 99% identity to seg:SG1098)

MetaCyc: 93% identical to RNA polymerase sigma factor FliA (Escherichia coli K-12 substr. MG1655)

Predicted SEED Role

"RNA polymerase sigma factor for flagellar operon" in subsystem Flagellar motility or Flagellum 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)

Search 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 (239 amino acids)

>GFF1690 RNA polymerase sigma factor for flagellar operon (Salmonella enterica subsp. enterica serovar Typhimurium str. MS1868)
VNSLYTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYD
ALQGTAFTTYAVQRIRGAMLDELRSRDWVPRSVRRNAREVAQAMGQLEQELGRNATETEV
AERLGIPVAEYRQMLLDTNNSQLFSYDEWREEHGDSIELVTEEHQQENPLHQLLEGDLRQ
RVMDAIESLPEREQLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGKL