I need to check if the enzymes for certain metabolic pathways exist in different strains of my bacteria of interest. I have the complete genome sequence in fasta format, and also labelled by prokka.
I found my gene of interest in a related bacteria in the Uniprot database, then I tried using BLAST for 2 sequences to align my gene of interest against a whole genome, but the results are strange, possibly because the whole genome sequence is too long as compared with the target gene?
The Max Score is 37.4, Total Score is 1811, Query Cover is 45%, E value is 0.013, Identity is 92%, but basically what occurred was many short alignments along the genome, that do not seem to indicate the presence of the gene. How do people generally search for a gene in a genome, and how do you evaluate BLAST results? Isn't there a better method?
I found KEGG pathways for 2 reference strains (fully sequenced), but they were incomplete. Does this definitively mean that the enzymes do not exist in that strain?
Also, I'm slightly confused about the KEGG colour coding. This is green, yes? Meaning that the information is organism-specific? https://www.genome.jp/kegg-bin/show_pathway?category=Campylobacter%20concisus&category_type=species&mapno=00010 So is this turquoise colour what they refer to as blue? But there are hyperlinks to gene/protein sequences which seem like they are strain-specific? https://www.genome.jp/kegg-bin/show_pathway?org_name=cco&mapno=00030&mapscale=&show_description=hide
