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I am currently working on a project that involves analyzing the pathways in which certain proteins are involved. I have compiled a list of proteins, and I am keen to explore the pathways they participate in within the context of human biology.

In this regard, I am in need of a reliable and comprehensive website or database that catalogs pathways in humans. I am particularly interested in a resource that allows me to input a list of proteins and retrieve information about the pathways in which they are known to be involved.

Could you please suggest a website or database that meets these criteria? Your recommendation would be immensely helpful in advancing my research objectives.

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  • $\begingroup$ we would need to know which sort of pathways you are looking at there are about 1,000 different databases out there with various bioinformatic resources. Try the NAR database summary for the extent. $\endgroup$
    – bob1
    Commented May 21 at 21:11

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The Problem

There may well be a web facility that allows input of a simple list of enzyme names and outputs a list of associated pathways. However there are two main reasons why this may be hard to find. The first is that most databases relating to metabolic pathways are not established from the standpoint of enzymes: their focus tends to be the pathways themselves, metabolites (because of the advent of the field of metabolomics) and gene sequences (because they are abundantly available). The second is the anarchy of enzyme nomenclature: the Enzyme Classification (EC) system allows several different enzymes under a single category, and there are generally several names for a particular enzyme (see, for example, the situation for hexokinase).

KEGG

One of the major databases of metabolic pathways with a web interface is KEGG (https://www.kegg.jp).

This is searchable using their specific enzyme nomenclature, rather than a protein name or EC number.

However, one can also apparently search on the basis of the amino acid sequence of the protein, as described in: Kanehisa, M.; Enzyme annotation and metabolic reconstruction using KEGG. Methods Mol. Biol. 1611, 135-145 (2017). This is available here, but requires a (e.g. institutional) subscription for access.

[KEGG contains information on many organisms, but one can filter by Homo sapiens etc.]

MetaCyc

The other major database of metabolic pathways is MetaCyc, which I merely mention as its use now requires a subscription (after a trial period). It is certainly possible to search MetaCyc interactively for a particular enzyme name like hexokinase, but I do not know whether bulk searches are possible and how flexible it is regarding nomenclature.

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