The motivation behind this analysis was to determine whether the proposed mechanism in B. subtilis 168 strain can possibly serve as a general mechanism for pH sensing by dCACHE_1 containing bacterial chemoreceptors. Our approach here was to assess the conservation of the key pH-sensing and the neighboring residues across bacterial species. Detailed description of the analysis is provided in Materials and Methods of the corresponding manuscript.
Python (v-3.6)
numpy (v-1.16.4)
matplotlib (v-3.1.1)
blastp (v-2.9.0+)
hmmscan (HMMER v-3.2.1)
CLUSTAL OMEGA (v-1.2.4)
MUSCLE (v-3.8.31)
taxonkit (v-0.50)
trimal (v-1.2)
Run "bash find_hits.sh" to obtain all significant hits.
Run "python ph-paper.py" for full processing and analysis of the resulting hits from previous step.