Protein Info for GFF320 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 50 100 150 196 PF07638: Sigma70_ECF" amino acids 28 to 174 (147 residues), 21.8 bits, see alignment E=3.1e-08 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 33 to 185 (153 residues), 69.3 bits, see alignment E=1.5e-23 PF04542: Sigma70_r2" amino acids 40 to 104 (65 residues), 40.8 bits, see alignment E=3.1e-14 PF08281: Sigma70_r4_2" amino acids 133 to 184 (52 residues), 50.5 bits, see alignment E=2.6e-17 PF04545: Sigma70_r4" amino acids 137 to 184 (48 residues), 32 bits, see alignment E=1.5e-11

Best Hits

Swiss-Prot: 62% identical to SIGF_AZOOP: ECF RNA polymerase sigma factor SigF (sigF) from Azospira oryzae (strain ATCC BAA-33 / DSM 13638 / PS)

KEGG orthology group: K03088, RNA polymerase sigma-70 factor, ECF subfamily (inferred from 95% identity to vpe:Varpa_3242)

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 (196 amino acids)

>GFF320 RNA polymerase ECF-type sigma factor (Variovorax sp. SCN45)
MARNTVGSRTNPGDAEAALRSLFLRGLDGDARAYRDFLQQLSAHLRAFLGKRLFGWPDEV
EDLVQECLLAMHNQRHTYQSDQPLTAWVHAIARYKMIDLLRAKSVREDLHDPLDDDLAVF
AESAEEASDARRDLGGLLQTLPERQRLPIVHVKIEGLSVAEAASLTGMSESAVKVGIHRG
LKALAARFGNRWGGAA