COMPARATIVE GENOMICS WORKSHOP - Day 3
A GLIMPSE of the PATRIC DATABASE – PATHOSYSTEMS RESOURCE
INTEGRATION CENTER
Answer Key: Functional prediction for Q9KTK5 in Vibrio cholera (protein
family DUF423, COG2363)
Leads from comparative genome analysis:
- Vibrio gene is induced 10-fold by bile (PMID:18776020 found through PATRIC database) and
the top correlated gene is involved in lipid A biosynthesis
- Small membrane protein?
- Strong physical clustering with a regulator gene of the putative choline sulfate-utilization
transcription factor family (see illustration below). These members of the LysR subfamily are
typically divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a
precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate
- Strong physical clustering with a predicted hydrolase of the alpha/beta-hydrolase fold
(COG3571)
Physical clustering on the chromosome between DUF423 (protein family #1 in red), LysR
type regulator (protein family #3 in orange) and a hydrolase (protein family #4 in blue)
General functional prediction:
- Members of the DUF423 family are involved in resistance to bile in combination
with the hydrolase. Most certainly involved in bile degradation