Protein Info for PP_0994 in Pseudomonas putida KT2440

Annotation: putative 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 50 100 150 178 signal peptide" amino acids 1 to 16 (16 residues), see Phobius details PF07638: Sigma70_ECF" amino acids 11 to 156 (146 residues), 23.8 bits, see alignment E=7.8e-09 TIGR02937: RNA polymerase sigma factor, sigma-70 family" amino acids 25 to 168 (144 residues), 77 bits, see alignment E=6.5e-26 PF04542: Sigma70_r2" amino acids 27 to 87 (61 residues), 41.8 bits, see alignment E=1.5e-14 PF08281: Sigma70_r4_2" amino acids 114 to 166 (53 residues), 51.8 bits, see alignment E=9.9e-18 PF04545: Sigma70_r4" amino acids 119 to 166 (48 residues), 34.2 bits, see alignment E=3e-12

Best Hits

Swiss-Prot: 60% 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 99% identity to ppu:PP_0994)

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 Q88P59 at UniProt or InterPro

Protein Sequence (178 amino acids)

>PP_0994 putative RNA polymerase sigma factor (Pseudomonas putida KT2440)
MKALLLQGLTGDQLAYQDFLGTLALHVRAFLRSRLSRRPAEIEDMVQDVLLAVHNARHTY
QPQQPLTAWVQAIARYKLADHLRSVSRRDARHDVLDDDAQLFAVSEVESAEASRDLTKLL
KQLPERQRLPIVHVKLEGLSVEETAQLTGLSSSAVKVGIHRGLKALSRLIGGANNHED