The data was generated on August 11, 2022 by the MaizeGDB project.

For B73 RefGen_v5 and each of the 25 NAM founder genomes, we ran the E2P2 pipeline on the official protein annotations to predict enzymatic function. Pathway assignments were made by using pathway/reaction assignments found in CornCyc, AraCyc, and OryzaCyc.  Evidence codes were assigned based on SAVI validation lists.


Summary files:

Pathway_final_gene_count (.tsv / .xlxs)
Columns
Pathway - Biocyc pathway ID
Description -  Biocyc pathway description
Reaction - Reaction name
EC number - Enzyme Commission Number
Evidence - Savi evidence code (Corncyc is listed if it was unique to CornCyc only)
CORNCYC9 - A count of the number of gene models (RefGen_v4) assigned to this pathway in CornCyc 9.0
B73, B97, …, TZI8 - 26 columnss each with a count of the number of gene models assigned to this pathway in the given genome protein annotation.

Pathway_final_genemodel_list (.tsv / .xlsx)
Columns
Pathway - Biocyc pathway ID
Description -  Biocyc pathway description
Reaction - Reaction name
EC number - Enzyme Commission Number
Evidence - Savi evidence code (Corncyc is listed if it was unique to CornCyc only)
CORNCYC9 - A list of gene models (RefGen_v4) assigned to this pathway in CornCyc 9.0
B73, B97, …, TZI8 - 26 columns each with a list of gene models assigned to this pathway in the given genome protein annotation.


26 pathway annotation files: B73_pathways.txt .. Tzi8_pathways.txt
Columns
Pathway ID  - Biocyc pathway ID
Description -  Biocyc pathway description
Reaction ID - Reaction name
EC number - Enzyme Commission Number
Gene Model ID - Gene Model ID for given genome
Protein ID - Protein ID
Evidence - Savi evidence code, NA if it is not found

Evidence codes (from PlantCyc):

conditional - The Conditionally Accepted PMN Pathway (CAPP) list contains pathways that are only accepted if they are predicted by the Pathologic program and meet additional criteria assigned to each pathway by PMN curators. Each CAPP can have criteria based on reactions and/or expected taxonomic range that are used to determine whether it should be accepted for a given species.
corncyc - The Pathway/reaction pair is found in the curated CornCyc 9.0 database.
excluded - The Non-PMN Pathway (NPP) list contains pathways that are excluded from PMN databases
expected = The Accept-if-Predicted Pathway (AIPP) list contains pathways that are automatically accepted if they are predicted for any plant species database, similar to the UPP or CVP.
manual - The Manually Check Pathway (MCP) list contains a very small number of pathways that are likely to be relevant to the users of the databases and are likely to be reported in published literature for many plant species.
NA - The pathway was not found in any of the SAVI pathway sets.
ubiquitous - The Ubiquitous land Plant Pathway (UPP) list contains pathways that are expected to be present in all "land"plants, also referred to as "higher" plants or Embryophyta.
viridiplantae - The Common Viridiplantae Pathway (CVP) list contains pathways that are expected to be present in all or most Viridiplantae species including algae. The CVP is a subset of the UPP.

Commands and code:

PMN E2P2 description: https://plantcyc.org/about/documentation/e2p2-description
PMN files: https://ftp.dpb.carnegiescience.edu/rpsd/release_2019-03-07/
E2P2 code: https://github.com/carnegie/E2P2
PRIAM java archive: http://priam.prabi.fr/utilities/PRIAM_search.jar
SAVI evidence information: https://plantcyc.org/about/savi-pipeline
SAVI validation lists: ftp://ftp.plantcyc.org/Pathways/SAVI_validation_lists/

Example command:

python3 .run_pipeline.py --input Zm-B73-REFERENCE-NAM-5.0_Zm00001eb.1.protein.fa --blastp blastp --java java --priam_search PRIAM_search.jar --rpsd rpsd-4.2.fasta --priam_profile profiles/ --num_threads 10 --output B73_annotations_out.txt