Protein Info for PP_3006 in Pseudomonas putida KT2440

Annotation: RNA polymerase sigma-70 factor, ECF subfamily

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 50 100 150 182 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 24 to 181 (158 residues), 80.6 bits, see alignment E=5.2e-27 PF04542: Sigma70_r2" amino acids 28 to 96 (69 residues), 64.2 bits, see alignment E=1.1e-21 PF08281: Sigma70_r4_2" amino acids 126 to 177 (52 residues), 55.3 bits, see alignment E=6.3e-19 PF04545: Sigma70_r4" amino acids 130 to 179 (50 residues), 30.5 bits, see alignment E=3.2e-11

Best Hits

KEGG orthology group: K03088, RNA polymerase sigma-70 factor, ECF subfamily (inferred from 100% identity to ppu:PP_3006)

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

See Q88IJ3 at UniProt or InterPro

Protein Sequence (182 amino acids)

>PP_3006 RNA polymerase sigma-70 factor, ECF subfamily (Pseudomonas putida KT2440)
MNSPAAPFDFHRCLLACAQGDRRALQALYDHEGARLLGVARRIARDDATAEDIVHDAIIR
IWTRAASYDPARGSARGWIYSITRHLALNSIRDTRRETVLTDADTETASTLHGRVDDLDL
WSGSAKIYRCLEQLQPAPQRCILHAYVDGCSHAEIAGLLGAPLGTVKAWIKRSLKALREC
LE