Protein Info for GFF3817 in Variovorax sp. SCN45

Annotation: 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 50 100 150 197 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 30 to 193 (164 residues), 98 bits, see alignment E=2.2e-32 PF04542: Sigma70_r2" amino acids 34 to 101 (68 residues), 52.5 bits, see alignment E=5.2e-18 PF08281: Sigma70_r4_2" amino acids 138 to 189 (52 residues), 52.5 bits, see alignment E=4.6e-18 PF04545: Sigma70_r4" amino acids 142 to 190 (49 residues), 48.2 bits, see alignment E=9e-17

Best Hits

KEGG orthology group: K03088, RNA polymerase sigma-70 factor, ECF subfamily (inferred from 96% identity to vpe:Varpa_1486)

Predicted SEED Role

"RNA polymerase sigma factor"

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 (197 amino acids)

>GFF3817 RNA polymerase sigma factor (Variovorax sp. SCN45)
MPDNPWMTAPSPDAELMALIDRIGHRDEAALRLLYDRTSPKLMGLAMRVVRQREWAEDVL
QEAFLTVWRVAGDYRSSLSPPLAWLGLIVRSRALDLLRRRTADRAQLTQEFDELMADTLE
SDAPNPADTADASEQAWALHQCLSQLEGRQREVVSLAYLREMSHGELADQLKLPLGTVKT
WIRRGLEKLRVCMGRFA