Protein Info for GFF5774 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 50 100 150 200 244 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 12 to 240 (229 residues), 109.6 bits, see alignment E=1.3e-35 PF04542: Sigma70_r2" amino acids 13 to 85 (73 residues), 62.1 bits, see alignment E=6.9e-21 TIGR02479: RNA polymerase sigma factor, FliA/WhiG family" amino acids 13 to 241 (229 residues), 272.5 bits, see alignment E=3e-85 PF04539: Sigma70_r3" amino acids 97 to 150 (54 residues), 33 bits, see alignment E=1.1e-11 PF08281: Sigma70_r4_2" amino acids 184 to 236 (53 residues), 27.4 bits, see alignment E=4.3e-10 PF04545: Sigma70_r4" amino acids 189 to 238 (50 residues), 54.8 bits, see alignment 1.1e-18

Best Hits

Swiss-Prot: 48% identical to FLIA_ECOLI: RNA polymerase sigma factor FliA (fliA) from Escherichia coli (strain K12)

KEGG orthology group: K02405, RNA polymerase sigma factor for flagellar operon FliA (inferred from 82% identity to vap:Vapar_4144)

MetaCyc: 48% 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 (244 amino acids)

>GFF5774 RNA polymerase sigma factor for flagellar operon (Variovorax sp. SCN45)
VYTAQGTIEKSHLLAQHQPLVRRIALQMMAKLPASVELDDLIQAGMLGLLDASSRYQDNR
GAQFETFVSQRIRGAMLDELRANDWGSRGLRQSARGIEKAIHALGHRLGRAPSEGEIAKE
LKMDLEAYQSMLQEIQGCQLLYVEDFAKDDPDNPFLDIHSKDARRDRRGGDDPLEQLLES
GFRHQLVDAISALPERDQLLLNLYYEEELNLREIGAILEVSQSRVCQLHSQAISRLRAKL
KDLL