Entering edit mode
5.1 years ago
Alec Watanabe
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60
Hi,
I want to compare the metabolic pathways of the pathogen (bacteria) with the host (Homo sapiens) using KEGG to find which pathways are common and which are unique to the pathogen. The input file contains fasta sequences with non-host homologous proteins so, in theory, there are no common proteins. Even though, there may be common pathways between the two organisms and, thus, I will also exclude pathogen proteins involved in common pathways. How can I do this?
Do you have the pathways annotated?
In what ways do you want to compare them?
Hi Vincent,
I don't have the pathways annotated. I would like to know which pathways are unique to the pathogen (not present in the host) and common (present in both pathogen and host). This investigation constitutes a step of a subtractive proteomics and reverse vaccinology study to identify novel vaccine targets of pathogens as you can see in this article published in Nature Reviews (https://www.nature.com/articles/s41598-018-26689-7). Many studies have adopted this step and many have not. In my opinion, it could help to filter out undesirable proteins from the analysis.