Some other replaced databases for KEGG paywalled

  • PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System have a set of Pathways. Not many prokaryotic genomes are available at PANTHER. List of species here
  • Biocyc BioCyc is a collection of 1962 Pathway/Genome Databases (PGDBs). Each PGDB in the BioCyc collection describes the genome and metabolic pathways of a single organism.

    BioCyc is a collection of 1962 Pathway/Genome Databases (PGDBs). Each PGDB in the BioCyc collection describes the genome and metabolic pathways of a single organism.

    The BioCyc Web site contains many tools for navigating, visualizing, and analyzing these databases, and for analyzing omics data, including the following:

    • Genome browser
    • Display of individual metabolic pathways, and of full metabolic maps
    • Visual analysis of user-supplied omics datasets by painting onto metabolic maps, regulatory maps, and genome maps
    • Enrichment analysis of omics datasets
    • Store groups of genes and pathways in your account; share, analyze, transform those groups
    • Comparative analysis tools

    The BioCyc Web site contains many tools for navigating, visualizing, and analyzing these databases, and for analyzing omics data, including the following:

    • Genome browser
    • Display of individual metabolic pathways, and of full metabolic maps
    • Visual analysis of user-supplied omics datasets by painting onto metabolic maps, regulatory maps, and genome maps
    • Enrichment analysis of omics datasets
    • Store groups of genes and pathways in your account; share, analyze, transform those groups
    • Comparative analysis tools
  • Reactome have orthology derived pathways for some prokaryotes. Extensive data in the level of molecular events available for human (Read about definition of Reactome molecular events here). See species comparison tool for pathways between human and any of the other species inferred from Reactome by orthology
  • WikiPathways Not many prokaryotes there, but still useful for human/eukaryote-centric analysis

You may also start from PathGuide and see if there is any dedicated pathway resource for your taxa / species of interest

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