Protein Info for HER17_RS15360 in Pectobacterium carotovorum WPP14

Annotation: sigma-70 family RNA polymerase sigma factor

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 50 100 173 PF04542: Sigma70_r2" amino acids 16 to 80 (65 residues), 28.7 bits, see alignment E=1.9e-10 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 26 to 162 (137 residues), 59.2 bits, see alignment E=1.9e-20 PF07638: Sigma70_ECF" amino acids 40 to 157 (118 residues), 23.8 bits, see alignment E=7.5e-09 PF08281: Sigma70_r4_2" amino acids 112 to 163 (52 residues), 53.9 bits, see alignment E=2.2e-18 PF04545: Sigma70_r4" amino acids 116 to 162 (47 residues), 26.7 bits, see alignment E=6.3e-10

Best Hits

Swiss-Prot: 46% identical to FECI_ECOLI: Probable RNA polymerase sigma factor FecI (fecI) from Escherichia coli (strain K12)

KEGG orthology group: K03088, RNA polymerase sigma-70 factor, ECF subfamily (inferred from 99% identity to eca:ECA1274)

MetaCyc: 46% identical to RNA polymerase sigma factor FecI (Escherichia coli K-12 substr. MG1655)

Predicted SEED Role

"RNA polymerase sigma-70 factor" in subsystem 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 (173 amino acids)

>HER17_RS15360 sigma-70 family RNA polymerase sigma factor (Pectobacterium carotovorum WPP14)
MYTEAVKKPDLLSLIFRSDYRWLTEKLRRRIAYGCEAEDVASEAFLRLASLPNLANVQEP
RAMLTTLAKRVLYENWRRRDLEKAYLTALASKPEFHHPSPEEQQLLMEALLTIDQALDGL
SIKARQAFLFSQLDGMTYADIAVQLDVSASMVRKYIAKALTNCYLATQDSSDL