Hi, I would like to obtain IDs (preferably NCBI) of proteins involved in particular biological pathways (such as Krebs cycle, etc.) across prokaryotic genomes. Is the NCBI BioSystems Database the right choice? KEGG seems to be a paid service but 2-years old files can be get for free from BioCyc. Thanks for the hints!
Kegg is one of the best databases for biological pathways, I have used it several times and is not a paid service... The problem is that to obtain NCBI ID from kegg you need to convert it, as kegg uses its own IDs and that is a little bit of work.
Perhaps, you could also find information in the COGs db (ncbi.nlm.nih.gov/research/cog), but it's the same problem with kegg it has its own IDs. Why do you need the NCBI ID? To download sequences?
Jazmín Sánchez-Pérez , The KEGG IDs for genes are the same as the NCBI Gene IDs. For instance KEGG "hsa4967" is NCBI gene 4967 (OGDH). The mouse orthologue is mmu18293 what corresponds to the NCBI gene 18293 (Ogdh).
@jochen Thanks!
When you search it like that do you lose information on the organism?
Hi Jazmín Sánchez-Pérez
You are right, KEGG is free: https://www.pathway.jp/en/academic.html. Regarding the NCBI ids, I need them only to get protein sequences. This can be done directly from KEGG data, I guess?
Although this may only partly answer the original question, the most comprehensive, open-source method of performing pathway enrichment is enrichR (https://maayanlab.cloud/Enrichr/). Though I prefer the R interface, it also has a GUI version that allows users to paste a gene list into the web interface. This enrichment program parses through all of the major pathway databases to yield a better understanding of the biological enrichment by the biases intrinsic to each individual database. The enrichment statistics can then be downloaded into tabular form to examine the genes populating each pathway.
Article Enrichr: Interactive and collaborative HTML5 gene list enric...
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