Protein Info for GFF6854 in Variovorax sp. SCN45

Annotation: RNA polymerase ECF-type 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 50 100 150 186 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 12 to 161 (150 residues), 63.2 bits, see alignment E=1.1e-21 PF08281: Sigma70_r4_2" amino acids 109 to 161 (53 residues), 53.3 bits, see alignment E=2.5e-18 PF04545: Sigma70_r4" amino acids 114 to 159 (46 residues), 28.6 bits, see alignment E=1.2e-10 PF13384: HTH_23" amino acids 120 to 155 (36 residues), 24.7 bits, see alignment 2.5e-09

Best Hits

KEGG orthology group: K03088, RNA polymerase sigma-70 factor, ECF subfamily (inferred from 77% identity to mms:mma_2384)

Predicted SEED Role

"RNA polymerase sigma-70 factor, ECF subfamily"

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Compare to protein 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 (186 amino acids)

>GFF6854 RNA polymerase ECF-type sigma factor (Variovorax sp. SCN45)
MPDSIKAALRALFLARYAQFRKHLQIRLGSEDLANDALQEAYLRVENTNVRSAVRYPSAY
LFRIALNVAEDQRKSNSRLLSVGEVEELYDMADEMADPARGAEARNELEALERALAELPR
RRRAIVLAARVDEMPHKDIAARYGVSARTVEKELRAGLEHCCERLGRDFIQRFGPGAGKQ
SKRDGS