Where is my flagellum?
So I was running the genome of the scaly snail endosymbiont (which is a gammaproteobacterium) through pathwaytools. This genome has already been published (https://www.researchgate.net/profile/Hiroko (https://www.researchgate.net/profile/...)Makita/publication/255706185AllyingwitharmoredsnailsThecompletegenomeofgammaproteobacterial_endosymbiont/links/00b7d52f18ef8677dc000000.pdf) and it has all genes except one that are required for a flagellum. The group who published this used "The Kyoto Encyclopedia of Genes and Genomes database" and also found the flagellum in there. Now in Pathwaytools 19.5 (Ubuntu 16.04) I can not find the flagellum or any of the flagellum genes though they are in the .gbk file. The same goes for three other organisms I work with. I also cannot find the pathway in general. If I look for other pathways like Sox (which they have), I find them in the databases and in the general description. Does anyone have an advice? Best, Clarissa