Protein Info for HMPREF1078_RS12860 in Parabacteroides merdae CL09T00C40

Annotation: RNA polymerase sigma-70 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 50 100 150 191 PF07638: Sigma70_ECF" amino acids 10 to 181 (172 residues), 28.8 bits, see alignment E=2.7e-10 TIGR02985: RNA polymerase sigma-70 factor, Bacteroides expansion family 1" amino acids 20 to 180 (161 residues), 139.7 bits, see alignment E=9.9e-45 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 20 to 180 (161 residues), 95 bits, see alignment E=3.7e-31 PF04542: Sigma70_r2" amino acids 25 to 90 (66 residues), 48.9 bits, see alignment E=1.1e-16 PF04545: Sigma70_r4" amino acids 131 to 178 (48 residues), 34.6 bits, see alignment E=2.6e-12 PF08281: Sigma70_r4_2" amino acids 131 to 175 (45 residues), 52.1 bits, see alignment 1e-17 PF00196: GerE" amino acids 133 to 174 (42 residues), 28.1 bits, see alignment 3.1e-10

Best Hits

Predicted SEED Role

"RNA polymerase ECF-type 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 (191 amino acids)

>HMPREF1078_RS12860 RNA polymerase sigma-70 factor (Parabacteroides merdae CL09T00C40)
MHETEIHRNTIEKLKRGSYEAFDTLYDMYADSLYGFALLHTKSSVQAEDIVQETFLKLWN
MRASLSVEGSFKSMLFTIAKNHVIDVFRQQINRPDFEDYIRFCEDEHLLDNTSVEKIYYD
DFIDKLAIAKQKLTPAQRNIFEMSREEGMSNAEIAVLSDISEQTVKNHLSAALKILREEL
RKYNYLFTLFI