Where is my flagellum?

asked 2016-08-25 04:29:28 -0500

Anonymous

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

answered 2016-08-29 15:08:05 -0500

ptools-admin
468 ●10 ●14 ●15

Dear Clarissa,

The pathways in BioCyc are in general small molecule pathways (although there are some exceptions). The software does not permit using an image, as in the KEGG Flagellar Assembly "pathway", and we are limited to showing pathways that consist of chemical reactions. Thus there is no flagellar biosynthesis pathway in MetaCyc, and no such pathway can be predicted in any database. This explains why you couldn't find the pathway.

What can be done is to specify the flagellum as a giant protein complex. This has been done in EcoCyc (http://www.biocyc.org/ECOLI/NEW-IMAGE...), but this operation is not performed automatically and is thus missing from all of the tier 3 PGDBs. You could generate it yourself using EcoCyc as a guide.

Regarding the missing genes, this is a different issue, and I do not have an explanation. The Pathway Tools software uses the annotation found in the genome, so if a gene has been annotated with a particular name such as "flagellar motor switching and energizing component", the name should appear in the database. Are you sure the genes are missing? if this is indeed the case, you will probably need to contact ptools-support, and they may ask you to send them your PGDB so they could troubleshoot the issue.

I hope this helps, Ron

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