Gene to pathway analysis
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7.2 years ago
glady ▴ 320

Hello friends, I have some genes which I do know that they code for Rhamnolipid compound but I do not know how these genes are getting arranged in a pathway that produces this Rhamnolipid compound. How can I see the arrangement of these genes inside my genome ?

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Try to be as informative as possible when asking questions. It would be valuable to add here which your organism of interest is. The annotation of genes and pathways is most likely better for human and mice than it is for the sweet potato.

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I have an bacterial genome (Pseudomonas species). I have the genes which are producing that Rhamnolipid compound, but I want to predict the pathway, so that I can get to know how it is getting produced inside the genome.

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Googling Rhamnolipid pathway brings up many hits, but those are not satisfactory? How is what you need different from that?

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I have found a research paper which shows the complete pathway production of Rhamnolipid, and also the genes involved in that pathway which is shown in the paper are exactly the same genes which I have detected for my genome. By looking at this can I say that the production of Rhamnolipid in my bacterial genome is same as it is found in the research paper ? Or should I carry some other analysis for finding the pathway?

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I have no idea how you found those genes and how those were found in that paper, but if you independently come to the same conclusion then that's reassuring that those genes are relevant for the Rhamnolipid pathway. To be entirely sure you would probably need to knock out each gene separately and investigate the production of Rhamnolipid and it's intermediates.

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How can I investigate the production of Rhamnolipid ? Is there any in-silico method available for this task ?

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