Protein Info for GFF3942 in Pseudomonas sp. DMC3

Annotation: putative HTH-type transcriptional regulator YddM

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 25 50 75 95 TIGR02607: addiction module antidote protein, HigA family" amino acids 3 to 83 (81 residues), 100 bits, see alignment E=2.5e-33 PF01381: HTH_3" amino acids 20 to 60 (41 residues), 24 bits, see alignment E=1.6e-09

Best Hits

Swiss-Prot: 36% identical to VAPA_DICNO: Virulence-associated protein A (vapA) from Dichelobacter nodosus

KEGG orthology group: None (inferred from 89% identity to pba:PSEBR_a4902)

Predicted SEED Role

"HigA protein (antitoxin to HigB)"

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 (95 amino acids)

>GFF3942 putative HTH-type transcriptional regulator YddM (Pseudomonas sp. DMC3)
MPMHNPPHPGETLLLDVLPELGISVSELARHLGFARPHLSRVLHGHAPISPDLAVRLERA
GIGKARVWLGVQTDYDLWQAEHREQPMIEPLAAHG