Protein Info for GFF6984 in Variovorax sp. SCN45

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 50 100 150 200 228 PF04542: Sigma70_r2" amino acids 7 to 61 (55 residues), 38.2 bits, see alignment E=1.5e-13 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 9 to 218 (210 residues), 85.5 bits, see alignment E=1.6e-28 PF08281: Sigma70_r4_2" amino acids 164 to 214 (51 residues), 30.4 bits, see alignment E=3.7e-11 PF04545: Sigma70_r4" amino acids 169 to 216 (48 residues), 51.7 bits, see alignment 7.3e-18

Best Hits

KEGG orthology group: None (inferred from 66% identity to vap:Vapar_2283)

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 (228 amino acids)

>GFF6984 RNA polymerase sigma factor for flagellar operon (Variovorax sp. SCN45)
MMAATLYGRRTHNDVEFEDYLQFARIGLIEAIDRFDPLRGAQFKTFATKRVQGAILNGLA
RFTEKNQQIALSMRLRRERLEAVKDAAAQAAPGAAQGTDSPPSGRQPEELFRYLAEVGIG
LALSVMLEDTGMIDSGAPGDTGQLPSPEVSYFRQSEIAQLRSVLRNLVDRLGEQQRMVIH
QHYLQEVPFEEIARRVGLTRGRVSQLHRQALGRLRELLGKDARFDVSW