Databases Overview

PlantCyc 11.0

Parent

Overview
Released: 

PlantCyc is a metabolic pathway reference database containing more than 800 pathways and their catalytic enzymes and genes, as well as compounds from over 350 plant species (See Database Statistics).

  • The majority of the pathways have been curated from experimental literature by curators at the PMN and collaborators' sites. In addition, PlantCyc includes hypothetical pathways that are published in peer-reviewed journals based on the educated conjectures of experts, and computationally predicted pathways that have been manually validated by PMN curators.
  • Similarly, enzymes in PlantCyc may have experimental support or may be based solely on computational predictions.
  • For both pathways and enzymes, evidence codes are assigned to clearly indicate the type of support associated with these database items.
Protein Sequence Source: 

Varies according to source: All enzymes have been imported from PMN databases or MetaCyc.

Enzyme Functional Annotation Method: 

Varies according to source: All enzymes have been imported from PMN databases or MetaCyc.

Enzyme Evidence: 
  • Substantial manual curation of enzymes
  • In addition, large-scale computational predictions of enzyme function not subject to curator review
Pathway Prediction Program: 
All pathways have been manually imported from PMN databases or MetaCyc
SAVI pathway validation lists: 
Pathway Evidence: 
  • Substantial manual curation of pathways
  • Some computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on curator inference

AraCyc 14.0

Parent

Overview
Released: 

AraCyc is the most highly curated species-specific database present at the PMN. It has a large number of experimentally supported enzymes and metabolic pathways, but it also houses a substantial number of computationally predicted enzymes and pathways.

More information on AraCyc curation is available.

Protein Sequence Source: 

Phytozome v10 (nuclear): Athaliana_167_peptide.fa and TAIR (organellar): various genome releases including TAIR10_pep_20110103_representative_gene_model

Enzyme Functional Annotation Method: 

Primarily E2P2 v3.0

Enzyme Evidence: 
  • Substantial manual curation of enzymes
  • In addition, large-scale computational predictions of enzyme function not subject to curator review
Pathway Prediction Program: 
Pathway Tools v18.5 (primarily)
SAVI pathway validation lists: 
Pathway Evidence: 
  • Substantial manual curation of pathways
  • Some computational prediction of pathways followed by curator review
  • Additional pathways imported from MetaCyc based on curator inference

BarleyCyc 4.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

BrachypodiumCyc 4.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

CassavaCyc 6.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

ChineseCabbageCyc 4.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

ChlamyCyc 6.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Primarily large-scale computational predictions of enzyme function not subject to curator review supplemented with data and references curated by the GoFORSYS project at the Max Planck Institute of Molecular Plant Physiology
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5 (primarily)
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc and ChlamyCyc 1.0 (created by the GoFORSYS project at the Max Planck Institute of Molecular Plant Physiology) based on experimental evidence or curator inference

CornCyc 7.0

Parent

Overview
Released: 
Protein Sequence Source: 

MaizeGDB (downloaded from EnsemblPlants):Zea_mays.AGPv3.22.pep.all.fa

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc and MaizeGDB based on experimental evidence or curator inference

GrapeCyc 6.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

MossCyc 5.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

OryzaCyc 4.0

Parent

Overview
Released: 
Protein Sequence Source: 

Phytozome v10: Osativa_204_protein.fa

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

PapayaCyc 5.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

PoplarCyc 9.0

Parent

Overview
Released: 

More information on PoplarCyc curation is available.

Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

PotatoCyc 3.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SelaginellaCyc 5.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SetariaCyc 4.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SorghumBicolorCyc 4.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SoyCyc 7.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SpirodelaCyc 2.0

Parent

Overview
Released: 
Protein Sequence Source: 

Phytozome v10 (early release): Spolyrhiza_290_v2.protein.fa

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SwitchgrassCyc 4.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

TomatoCyc 2.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

WheatACyc 2.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

WheatDCyc 2.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

PlantCyc 11.0

Parent

Overview
Released: 

PlantCyc is a metabolic pathway reference database containing more than 800 pathways and their catalytic enzymes and genes, as well as compounds from over 350 plant species (See Database Statistics).

  • The majority of the pathways have been curated from experimental literature by curators at the PMN and collaborators' sites. In addition, PlantCyc includes hypothetical pathways that are published in peer-reviewed journals based on the educated conjectures of experts, and computationally predicted pathways that have been manually validated by PMN curators.
  • Similarly, enzymes in PlantCyc may have experimental support or may be based solely on computational predictions.
  • For both pathways and enzymes, evidence codes are assigned to clearly indicate the type of support associated with these database items.
Protein Sequence Source: 

Varies according to source: All enzymes have been imported from PMN databases or MetaCyc.

Enzyme Functional Annotation Method: 

Varies according to source: All enzymes have been imported from PMN databases or MetaCyc.

Enzyme Evidence: 
  • Substantial manual curation of enzymes
  • In addition, large-scale computational predictions of enzyme function not subject to curator review
Pathway Prediction Program: 
All pathways have been manually imported from PMN databases or MetaCyc
SAVI pathway validation lists: 
Pathway Evidence: 
  • Substantial manual curation of pathways
  • Some computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on curator inference

PlantCyc 10.0

Parent

Overview
Released: 

PlantCyc is a metabolic pathway reference database containing more than 800 pathways and their catalytic enzymes and genes, as well as compounds from over 350 plant species (See Database Statistics).

  • The majority of the pathways have been curated from experimental literature by curators at the PMN and collaborators' sites. In addition, PlantCyc includes hypothetical pathways that are published in peer-reviewed journals based on the educated conjectures of experts, and computationally predicted pathways that have been manually validated by PMN curators.
  • Similarly, enzymes in PlantCyc may have experimental support or may be based solely on computational predictions.
  • For both pathways and enzymes, evidence codes are assigned to clearly indicate the type of support associated with these database items.
Protein Sequence Source: 

Varies according to source: All enzymes have been imported from PMN databases or MetaCyc.

Enzyme Functional Annotation Method: 

Varies according to source: All enzymes have been imported from PMN databases or MetaCyc.

Enzyme Evidence: 
  • Substantial manual curation of enzymes
  • In addition, large-scale computational predictions of enzyme function not subject to curator review
Pathway Prediction Program: 
All pathways have been manually imported from PMN databases or MetaCyc
SAVI pathway validation lists: 
Pathway Evidence: 
  • Substantial manual curation of pathways
  • Some computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on curator inference

PlantCyc 9.5

Parent

Overview
Released: 

PlantCyc is a metabolic pathway reference database containing more than 800 pathways and their catalytic enzymes and genes, as well as compounds from over 350 plant species (See Database Statistics).

  • The majority of the pathways have been curated from experimental literature by curators at the PMN and collaborators' sites. In addition, PlantCyc includes hypothetical pathways that are published in peer-reviewed journals based on the educated conjectures of experts, and computationally predicted pathways that have been manually validated by PMN curators.
  • Similarly, enzymes in PlantCyc may have experimental support or may be based solely on computational predictions.
  • For both pathways and enzymes, evidence codes are assigned to clearly indicate the type of support associated with these database items.
Protein Sequence Source: 

Varies according to source: All enzymes have been imported from PMN databases or MetaCyc.

Enzyme Functional Annotation Method: 

Varies according to source: All enzymes have been imported from PMN databases or MetaCyc.

Enzyme Evidence: 
  • Substantial manual curation of enzymes
  • In addition, large-scale computational predictions of enzyme function not subject to curator review
Pathway Prediction Program: 
All pathways have been manually imported from PMN databases or MetaCyc
SAVI pathway validation lists: 
Pathway Evidence: 
  • Substantial manual curation of pathways
  • Some computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on curator inference

PlantCyc 9.0

Parent

Overview
Released: 

PlantCyc is a metabolic pathway reference database containing more than 800 pathways and their catalytic enzymes and genes, as well as compounds from over 350 plant species (See Database Statistics).

  • The majority of the pathways have been curated from experimental literature by curators at the PMN and collaborators' sites. In addition, PlantCyc includes hypothetical pathways that are published in peer-reviewed journals based on the educated conjectures of experts, and computationally predicted pathways that have been manually validated by PMN curators.
  • Similarly, enzymes in PlantCyc may have experimental support or may be based solely on computational predictions.
  • For both pathways and enzymes, evidence codes are assigned to clearly indicate the type of support associated with these database items.
Protein Sequence Source: 

Varies according to source: All enzymes have been imported from PMN databases or MetaCyc.

Enzyme Functional Annotation Method: 

Varies according to source: All enzymes have been imported from PMN databases or MetaCyc

Enzyme Evidence: 
  • Substantial manual curation of enzymes
  • In addition, large-scale computational predictions of enzyme function not subject to curator review
Pathway Prediction Program: 
All pathways have been manually imported from PMN databases
SAVI pathway validation lists: 
Pathway Evidence: 
  • Substantial manual curation of pathways
  • Some computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on curator inference

PlantCyc 8.0

Parent

Overview

PlantCyc is a metabolic pathway reference database containing more than 800 pathways and their catalytic enzymes and genes, as well as compounds from over 350 plant species (See Database Statistics).

  • The majority of the pathways have been curated from experimental literature by curators at the PMN and collaborators' sites. In addition, PlantCyc includes hypothetical pathways that are published in peer-reviewed journals based on the educated conjectures of experts, and computationally predicted pathways that have been manually validated by PMN curators.
  • Similarly, enzymes in PlantCyc may have experimental support or may be based solely on computational predictions.
  • For both pathways and enzymes, evidence codes are assigned to clearly indicate the type of support associated with these database items.
Protein Sequence Source: 

Varies according to source: All enzymes have been imported from PMN databases or MetaCyc.

Enzyme Functional Annotation Method: 

Varies according to source: All enzymes have been imported from PMN databases or MetaCyc.

Enzyme Evidence: 
  • Substantial manual curation of enzymes
  • In addition, large-scale computational predictions of enzyme function not subject to curator review
Pathway Prediction Program: 
All pathways have been manually imported from PMN databases or MetaCyc
SAVI pathway validation lists: 
Pathway Evidence: 
  • Substantial manual curation of pathways
  • Some computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on curator inference

PlantCyc 7.0

Parent

Overview

PlantCyc is a metabolic pathway reference database containing more than 800 pathways and their catalytic enzymes and genes, as well as compounds from over 300 plant species (See Database Statistics).

  • The majority of the pathways have been curated from experimental literature by curators at the PMN and collaborators' sites. In addition, PlantCyc includes hypothetical pathways that are published in peer-reviewed journals based on the educated conjectures of experts, and computationally predicted pathways that have been manually validated by PMN curators.
  • Similarly, enzymes in PlantCyc may have experimental support or may be based solely on computational predictions.
  • For both pathways and enzymes, evidence codes are assigned to clearly indicate the type of support associated with these database items.
Protein Sequence Source: 

Varies according to source: All enzymes have been imported from PMN databases, MetaCyc, LycoCyc, RiceCyc, or MedicCyc.

Enzyme Functional Annotation Method: 

Varies according to source: All enzymes have been imported from PMN databases, MetaCyc, LycoCyc, RiceCyc, or MedicCyc.

Enzyme Evidence: 
  • Substantial manual curation of enzymes
  • In addition, large-scale computational predictions of enzyme function not subject to curator review
Pathway Prediction Program: 
All pathways have been manually imported from PMN databases or MetaCyc
SAVI pathway validation lists: 
Pathway Evidence: 
  • Substantial manual curation of pathways
  • Some computational prediction of pathways followed by curator review
  • Additional pathways imported from MetaCyc based on curator inference

PlantCyc 6.0

Parent

Overview
Released: 

PlantCyc is a metabolic pathway reference database containing more than 800 pathways and their catalytic enzymes and genes, as well as compounds from over 300 plant species (See Database Statistics).

  • The majority of the pathways have been curated from experimental literature by curators at the PMN and collaborators' sites. In addition, PlantCyc includes hypothetical pathways that are published in peer-reviewed journals based on the educated conjectures of experts, and computationally predicted pathways that have been manually validated by PMN curators.
  • Similarly, enzymes in PlantCyc may have experimental support or may be based solely on computational predictions.
  • For both pathways and enzymes, evidence codes are assigned to clearly indicate the type of support associated with these database items.
Protein Sequence Source: 

Varies according to source: All enzymes have been imported from PMN databases, MetaCyc, LycoCyc, RiceCyc, or MedicCyc.

Enzyme Functional Annotation Method: 

Varies according to source: All enzymes have been imported from PMN databases, MetaCyc, LycoCyc, RiceCyc, or MedicCyc.

Enzyme Evidence: 
  • Substantial manual curation of enzymes
  • In addition, large-scale computational predictions of enzyme function not subject to curator review
Pathway Prediction Program: 
All pathways have been manually imported from PMN databases or MetaCyc
SAVI pathway validation lists: 
Pathway Evidence: 
  • Substantial manual curation of pathways
  • Some computational prediction of pathways followed by curator review
  • Additional pathways imported from MetaCyc based on curator inference

PlantCyc 5.0

Parent

Overview
Released: 

PlantCyc is a metabolic pathway reference database containing more than 800 pathways and their catalytic enzymes and genes, as well as compounds from over 300 plant species (See Database Statistics).

  • The majority of the pathways have been curated from experimental literature by curators at the PMN and collaborators' sites. In addition, PlantCyc includes hypothetical pathways that are published in peer-reviewed journals based on the educated conjectures of experts, and computationally predicted pathways that have been manually validated by PMN curators.
  • Similarly, enzymes in PlantCyc may have experimental support or may be based solely on computational predictions.
  • For both pathways and enzymes, evidence codes are assigned to clearly indicate the type of support associated with these database items.

AraCyc 14.0

Parent

Overview
Released: 

AraCyc is the most highly curated species-specific database present at the PMN. It has a large number of experimentally supported enzymes and metabolic pathways, but it also houses a substantial number of computationally predicted enzymes and pathways.

More information on AraCyc curation is available.

Protein Sequence Source: 

Phytozome v10 (nuclear): Athaliana_167_peptide.fa and TAIR (organellar): various genome releases including TAIR10_pep_20110103_representative_gene_model

Enzyme Functional Annotation Method: 

Primarily E2P2 v3.0

Enzyme Evidence: 
  • Substantial manual curation of enzymes
  • In addition, large-scale computational predictions of enzyme function not subject to curator review
Pathway Prediction Program: 
Pathway Tools v18.5 (primarily)
SAVI pathway validation lists: 
Pathway Evidence: 
  • Substantial manual curation of pathways
  • Some computational prediction of pathways followed by curator review
  • Additional pathways imported from MetaCyc based on curator inference

AraCyc 13.0

Parent

Overview
Released: 

AraCyc is the most highly curated species-specific database present at the PMN. It has a large number of experimentally supported enzymes and metabolic pathways, but it also houses a substantial number of computationally predicted enzymes and pathways.

More information on AraCyc curation is available.

Protein Sequence Source: 

Phytozome v10 (nuclear): Athaliana_167_peptide.fa and TAIR (organellar): various genome releases including TAIR10_pep_20110103_representative_gene_model

Enzyme Functional Annotation Method: 

Primarily E2P2 v3.0

Enzyme Evidence: 
  • Substantial manual curation of enzymes
  • In addition, large-scale computational predictions of enzyme function not subject to curator review
Pathway Prediction Program: 
Pathway Tools v18.5 (primarily)
SAVI pathway validation lists: 
Pathway Evidence: 
  • Substantial manual curation of pathways
  • Some computational prediction of pathways followed by curator review
  • Additional pathways imported from MetaCyc based on curator inference

AraCyc 12.0

Parent

Overview
Released: 

AraCyc is the most highly curated species-specific database present at the PMN. It has a large number of experimentally supported enzymes and metabolic pathways, but it also houses a substantial number of computationally predicted enzymes and pathways.

More information on AraCyc curation is available.

Protein Sequence Source: 

Phytozome 9.0 (nuclear): Athaliana_167_peptide.fa and TAIR (organellar): various genome releases includingTAIR10_pep_20110103_representative_gene_model

Enzyme Functional Annotation Method: 

Primarily E2P2 v2.1

Enzyme Evidence: 
  • Substantial manual curation of enzymes
  • In addition, large-scale computational predictions of enzyme function not subject to curator review
Pathway Prediction Program: 
Pathway Tools v.17.5 (primarily)
SAVI pathway validation lists: 
Pathway Evidence: 
  • Substantial manual curation of pathways
  • Some computational prediction of pathways followed by curator review
  • Additional pathways imported from MetaCyc based on curator inference

AraCyc 11.5

Parent

Overview

AraCyc is the most highly curated species-specific database present at the PMN. It has a large number of experimentally supported enzymes and metabolic pathways, but it also houses a substantial number of computationally predicted enzymes and pathways.

** Please note: The initial PMN 8.0 release in June 2013 included AraCyc 11.0. Proteins not associated to reactions were removed from AraCyc 11.0 to produce this updated version (AraCyc 11.5).

More information on AraCyc curation is available.

Protein Sequence Source: 

 Phytozome 9.0 (nuclear): Athaliana_167_peptide.fa and TAIR (organellar): various genome releases includingTAIR10_pep_20110103_representative_gene_model

Enzyme Functional Annotation Method: 

Primarily E2P2 2.0

Enzyme Evidence: 
  • Substantial manual curation of enzymes
  • In addition, large-scale computational predictions of enzyme function not subject to curator review
Pathway Prediction Program: 
Pathway Tools v.16.5 (primarily)
SAVI pathway validation lists: 
Pathway Evidence: 
  • Substantial manual curation of pathways
  • Some computational prediction of pathways followed by curator review
  • Additional pathways imported from MetaCyc based on curator inference

AraCyc 11.0

Parent

Overview
Released: 

AraCyc is the most highly curated species-specific database present at the PMN. It has a large number of experimentally supported enzymes and metabolic pathways, but it also houses a substantial number of computationally predicted enzymes and pathways.

More information on AraCyc curation is available.

Protein Sequence Source: 

Phytozome 9.0 (nuclear): Athaliana_167_peptide.fa and TAIR (organellar): various genome releases including TAIR10_pep_20110103_representative_gene_model

Enzyme Functional Annotation Method: 

Primarily E2P2 2.0

Enzyme Evidence: 
  • Substantial manual curation of enzymes
  • In addition, large-scale computational predictions of enzyme function not subject to curator review
Pathway Prediction Program: 
Pathway Tools v.16.5 (primarily)
SAVI pathway validation lists: 
Pathway Evidence: 
  • Substantial manual curation of pathways
  • Some computational prediction of pathways followed by curator review
  • Additional pathways imported from MetaCyc based on curator inference

AraCyc 10.0

Parent

Overview
Released: 

AraCyc is the most highly curated species-specific database present at the PMN. It has a large number of experimentally supported enzymes and metabolic pathways, but it also houses a substantial number of computationally predicted enzymes and pathways.

More information on AraCyc curation is available.

Protein Sequence Source: 

TAIR: various genome releases including TAIR10_pep_20110103_representative_gene_model

Enzyme Functional Annotation Method: 

Various methods over time including E2P2 1.0 and process described in Zhang 2010

Enzyme Evidence: 
  • Substantial manual curation of enzymes
  • In addition, large-scale computational predictions of enzyme function not subject to curator review
Pathway Prediction Program: 
several versions of Pathway Tools
SAVI pathway validation lists: 
Pathway Evidence: 
  • Substantial manual curation of pathways
  • Some computational prediction of pathways followed by curator review
  • Additional pathways imported from MetaCyc based on curator inference

AraCyc 9.0

Parent

Overview
Released: 

AraCyc is the most highly curated species-specific database present at the PMN. It has a large number of experimentally supported enzymes and metabolic pathways, but it also houses a substantial number of computationally predicted enzymes and pathways.

More information on AraCyc curation is available.

Protein Sequence Source: 

TAIR: various genome releases includingTAIR10_pep_20110103_representative_gene_model

Enzyme Functional Annotation Method: 

Various methods over time including E2P2 1.0 and process described in Zhang 2010

Enzyme Evidence: 
  • Substantial manual curation of enzymes
  • In addition, large-scale computational predictions of enzyme function not subject to curator review
Pathway Prediction Program: 
several versions of Pathway Tools
SAVI pathway validation lists: 
Pathway Evidence: 
  • Substantial manual curation of pathways
  • Some computational prediction of pathways followed by curator review
  • Additional pathways imported from MetaCyc based on curator inference

AraCyc 8.0

Parent

Overview
Released: 

AraCyc, a single species database maintained in collaboration with TAIR (The Arabidopsis Information Resource), houses a large set of curated metabolic pathways.

  • The majority of the pathways found in AraCyc have some measure of experimental support, but additional computationally-predicted pathways are included to maximize the hypothesis-generating power of the database. These pathways are known to exist in other species or in non-plant organisms, but have not been reported in Arabidopsis. However, some hints indicate that Arabidopsis may utilize the same pathway or similar routes. All predicted pathways are manually reviewed by curators who add comments concerning their potential validity.
  • As in PlantCyc, enzymes present in AraCyc may have experimental support or may be based solely on computational predictions. And, an identical set of evidence codes is used to clearly identify the source of the information.
  • The structures for the genes included in AraCyc are based on TAIR genome annotations. Additional Gene Ontology and Plant Ontology functional annotations derived from experimental data and computational predictions may be listed at the TAIR gene pages. These are categorized using a different set of evidence codes.

BarleyCyc 4.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

BarleyCyc 3.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

BarleyCyc 2.0

Parent

Overview
Released: 
Protein Sequence Source: 

Helmholtz Zentrum Munchen - Munich Information Center for Protein Sequences (MIPS): barley_HighConf_genes_MIPS_23Mar12_ProteinSeq.fa

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 17.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

BarleyCyc 1.0

Parent

Overview
Protein Sequence Source: 

Helmholtz Zentrum Munchen - Munich Information Center for Protein Sequences (MIPS): barley_HighConf_genes_MIPS_23Mar12_ProteinSeq.fa

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 16.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

BrachypodiumCyc 4.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

BrachypodiumCyc 3.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

BrachypodiumCyc 2.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 17.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

BrachypodiumCyc 1.0

Parent

Overview
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 16.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

CassavaCyc 6.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

CassavaCyc 5.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

CassavaCyc 4.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 17.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

CassavaCyc 3.0

Parent

Overview
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 16.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

CassavaCyc 2.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 15.0
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction followed by curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

CassavaCyc 1.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 15.0
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction followed by curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

ChineseCabbageCyc 4.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

ChineseCabbageCyc 3.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

ChineseCabbageCyc 2.0

Parent

Overview
Released: 
Protein Sequence Source: 

Phytozome 9.0: Brapa_197_peptide.fa

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 17.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

ChineseCabbageCyc 1.0

Parent

Overview
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 16.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

ChlamyCyc 6.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Primarily large-scale computational predictions of enzyme function not subject to curator review supplemented with data and references curated by the GoFORSYS project at the Max Planck Institute of Molecular Plant Physiology
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5 (primarily)
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc and ChlamyCyc 1.0 (created by the GoFORSYS project at the Max Planck Institute of Molecular Plant Physiology) based on experimental evidence or curator inference

ChlamyCyc 5.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Primarily large-scale computational predictions of enzyme function not subject to curator review supplemented with data and references curated by the GoFORSYS project at the Max Planck Institute of Molecular Plant Physiology
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5 (primarily)
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc and ChlamyCyc 1.0 (created by the GoFORSYS project at the Max Planck Institute of Molecular Plant Physiology) based on experimental evidence or curator inference

ChlamyCyc 4.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Primarily large-scale computational predictions of enzyme function not subject to curator review supplemented with data and references curated by the GoFORSYS project at the Max Planck Institute of Molecular Plant Physiology
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v.17.5 (primarily)
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc and ChlamyCyc 1.0 (created by the GoFORSYS project at the Max Planck Institute of Molecular Plant Physiology) based on experimental evidence or curator inference

ChlamyCyc 3.5

Parent

Overview

** Please note: The initial PMN 8.0 release in June 2013 included ChlamyCyc 3.0. Proteins not associated to reactions were removed from ChlamyCyc 3.0 to produce this updated version (ChlamyCyc 3.5).

Protein Sequence Source: 

NCBI (organellar) and primarily Phytozome 8.0 (early release)(nuclear) JGI: Creinhardtii_v5.3_223_peptide.fa

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Primarily large-scale computational predictions of enzyme function not subject to curator review supplemented with data and references curated by the GoFORSYS project at the Max Planck Institute of Molecular Plant Physiology
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v.16.5 (primarily
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc and ChlamyCyc 1.0 (created by the GoFORSYS project at the Max Planck Institute of Molecular Plant Physiology) based on experimental evidence or curator inference

ChlamyCyc 3.0

Parent

Overview
Released: 
Protein Sequence Source: 

NCBI (organellar) and Phytozome 7.0 (nuclear) JGI:Creinhardtii_169_peptide.fa

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Primarily large-scale computational predictions of enzyme function not subject to curator review supplemented with data and references curated by the GoFORSYS project at the Max Planck Institute of Molecular Plant Physiology
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v.16.5 (primarily)
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc and ChlamyCyc 1.0 (created by the GoFORSYS project at the Max Planck Institute of Molecular Plant Physiology) based on experimental evidence or curator inference

ChlamyCyc 2.0

Parent

Overview
Released: 
Protein Sequence Source: 

NCBI (organellar) and Phytozome 7.0 (nuclear) JGI:Creinhardtii_169_peptide.fa

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Primarily large-scale computational predictions of enzyme function not subject to curator review supplemented with data and references curated by the GoFORSYS project at the Max Planck Institute of Molecular Plant Physiology
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 15.0
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction followed by curator review
  • Additional pathways imported from MetaCyc and ChlamyCyc 1.0 (created by the GoFORSYS project at the Max Planck Institute of Molecular Plant Physiology) based on experimental evidence or curator inference

ChlamyCyc 1.0

Parent

Overview

ChlamyCyc 1.0 was not officially released at the PMN site because it was generated at the Max Planck Institute and publized at the GoFORSYS website.

CornCyc 7.0

Parent

Overview
Released: 
Protein Sequence Source: 

MaizeGDB (downloaded from EnsemblPlants):Zea_mays.AGPv3.22.pep.all.fa

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc and MaizeGDB based on experimental evidence or curator inference

CornCyc 6.0

Parent

Overview
Released: 
Protein Sequence Source: 

MaizeGDB (downloaded from EnsemblPlants):Zea_mays.AGPv3.22.pep.all.fa

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc and MaizeGDB based on experimental evidence or curator inference

CornCyc 5.0

Parent

Overview
Released: 
Protein Sequence Source: 

MaizeGDB (downloaded from EnsemblPlants):Zea_mays.AGPv3.22.pep.all.fa

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 17.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc and MaizeGDB based on experimental evidence or curator inference

CornCyc 4.0

Parent

Overview
Released: 

** Please note: The intial PMN 8.0 release in June 2013 included CornCyc 3.0. The complete release in July 2013 included CornCyc 3.5. In CornCyc 3.5, we removed proteins that are no longer associated to any reactions, to complete the process of annotation updates of CornCyc 3.0. In CornCyc 4.0 (released in November 2013), we fixed a technical data-processing error and added missing components to CornCyc.

Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 16.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc and MaizeGDB based on experimental evidence or curator inference

CornCyc 3.5

Parent

Overview
Released: 

** Please note: The initial PMN 8.0 release in June 2013 included CornCyc 3.0. Proteins not associated to reactions were removed from CornCyc 3.0 to produce this updated version (CornCyc 3.5).

Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 16.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc and MaizeGDB based on experimental evidence or curator inference

CornCyc 3.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 16.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc and MaizeGDB based on experimental evidence or curator inference

CornCyc 2.0

Parent

Overview
Released: 
Protein Sequence Source: 

Maizesequence.org (filtered set):http://ftp.maizesequence.org/current/filtered-set/

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 15.0
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction followed by curator review
  • Additional pathways imported from MetaCyc and MaizeGDB based on experimental evidence or curator inference

CornCyc 1.0

Parent

Overview
Released: 
Protein Sequence Source: 

Maizesequence.org (filtered set):http://ftp.maizesequence.org/current/filtered-set/

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 15.0
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction followed by curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

GrapeCyc 6.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

GrapeCyc 5.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

GrapeCyc 4.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 17.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

GrapeCyc 3.0

Parent

Overview
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 16.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

GrapeCyc 2.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 15.0
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction followed by curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

GrapeCyc 1.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 15.0
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction followed by curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

MossCyc 5.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

MossCyc 4.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

MossCyc 3.0

Parent

Overview
Released: 
Protein Sequence Source: 

Cosmoss (downloaded from Phytozome 9.0): Ppatens_152_peptide.fa

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 17.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

MossCyc 2.0

Parent

Overview
Protein Sequence Source: 

Cosmoss (downloaded from Phytozome 9.0): Ppatens_152_peptide.fa

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 16.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

MossCyc 1.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 15.0
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction followed by curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

OryzaCyc 4.0

Parent

Overview
Released: 
Protein Sequence Source: 

Phytozome v10: Osativa_204_protein.fa

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

OryzaCyc 3.0

Parent

Overview
Released: 
Protein Sequence Source: 

Phytozome v10: Osativa_204_protein.fa

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

OryzaCyc 2.0

Parent

Overview
Released: 
Protein Sequence Source: 

Phytozome 9.0 Osativa_204_protein.fa

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 17.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

OryzaCyc 1.0

Parent

Overview
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 16.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

PapayaCyc 5.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

PapayaCyc 4.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

PapayaCyc 3.5

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 17.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

PapayaCyc 3.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 17.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

PapayaCyc 2.0

Parent

Overview
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 16.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

PapayaCyc 1.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 15.0
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction followed by curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

PoplarCyc 9.0

Parent

Overview
Released: 

More information on PoplarCyc curation is available.

Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

PoplarCyc 8.0

Parent

Overview
Released: 

More information on PoplarCyc curation is available.

Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

PoplarCyc 7.0

Parent

Overview
Released: 

More information on PoplarCyc curation is available.

Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 17.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

PoplarCyc 6.0

Parent

Overview

More information on PoplarCyc curation is available

Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 16.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

PoplarCyc 5.0

Parent

Overview
Released: 

More information on PoplarCyc curation is available.

Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 15.0
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction followed by curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

PoplarCyc 4.0

Parent

Overview
Released: 

More information on PoplarCyc curation is available.

Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 15.0
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction followed by curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

PoplarCyc 3.0

Parent

Overview
Released: 

PoplarCyc, a genus-level database was developed largely computationally using:

  1. A newly developed enzyme annotation pipeline from the PMN
  2. The Populus trichocarpa 1.1 genome release provided by JGI
  3. The Pathologic pathway prediction software from SRI International

 

  • The majority of the pathways found in PoplarCyc are based on computational predictions, however, these pathways have been reviewed by curators. Comments and references have often been added to try to explain the specific criteria used to establish their potential validity.
  • A few manually curated pathways have been added if there is experimental support for their existence in Populus species or hybrids. The associated enzymes have been included in the database even if they were not isolated from or studied in Populus trichocarpa. In these cases, comments were added on the enzyme page to indicate the species or hybrid of origin (see isoprene synthase). When no species is indicated in the enzyme comments, the enzyme sequence has been taken from Populus trichocarpa.
  • As in the case for all PMN databases, evidence codes on both the pathway and enzyme pages can be used to determine the experimental or computational support for the information in PoplarCyc.

PotatoCyc 3.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

PotatoCyc 2.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SelaginellaCyc 5.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SelaginellaCyc 4.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SelaginellaCyc 3.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 17.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SelaginellaCyc 2.0

Parent

Overview
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 16.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SelaginellaCyc 1.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 15.0
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction followed by curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SetariaCyc 4.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SetariaCyc 3.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SetariaCyc 2.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 17.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SetariaCyc 1.0

Parent

Overview
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 16.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SorghumBicolorCyc 4.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SorghumBicolorCyc 3.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SorghumBicolorCyc 2.0

Parent

Overview
Released: 
Protein Sequence Source: 

Phytozome 9.0 (early release): Sbicolor_v2.1_255_protein.fa

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 17.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SorghumBicolorCyc 1.0

Parent

Overview
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 16.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SoyCyc 7.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SoyCyc 6.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SoyCyc 5.0

Parent

Overview
Released: 
Protein Sequence Source: 

Phytozome 9.0 (early release): Gmax_275_Wm82.a2.v1.protein.fa

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 17.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SoyCyc 4.0

Parent

Overview
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 16.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SoyCyc 3.0

Parent

Overview
Released: 
Protein Sequence Source: 

Phytozome 7.0: Gmax_109_peptide.fa and JGI:Glyma1 (10-20-08)

Enzyme Functional Annotation Method: 

E2P2 1.0 and process described in Zhang 2010

Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 12.5 and 15.0
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction followed by curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SoyCyc 2.0

Parent

Overview
Released: 
Protein Sequence Source: 

Phytozome 7.0: Gmax_109_peptide.fa and JGI:Glyma1 (10-20-08)

Enzyme Functional Annotation Method: 

E2P2 1.0 and process described in Zhang 2010

Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 12.5 and 15.0
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction followed by curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SoyCyc 1.0

Parent

Overview

SpirodelaCyc 2.0

Parent

Overview
Released: 
Protein Sequence Source: 

Phytozome v10 (early release): Spolyrhiza_290_v2.protein.fa

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SpirodelaCyc 1.0

Parent

Overview
Released: 
Protein Sequence Source: 

Phytozome v10 (early release): Spolyrhiza_290_v2.protein.fa

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SwitchgrassCyc 4.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SwitchgrassCyc 3.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SwitchgrassCyc 2.0

Parent

Overview
Released: 
Protein Sequence Source: 

Phytozome 9.0 (early release): Pvirgatum_v1.1_273_protein.fa

Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 17.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

SwitchgrassCyc 1.0

Parent

Overview
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools 16.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

TomatoCyc 2.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

TomatoCyc 1.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

WheatACyc 2.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

WheatACyc 1.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

WheatDCyc 2.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

WheatDCyc 1.0

Parent

Overview
Released: 
Protein Sequence Source: 
Enzyme Functional Annotation Method: 
Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v18.5
SAVI pathway validation lists: 
Pathway Evidence: 
  • Primarily computational prediction of pathways followed by SAVI refinement and curator review
  • Additional pathways imported from MetaCyc based on experimental evidence or curator inference

PlantCyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
PlantCyc 11.0 1213 140581 6051 5128 11114
PlantCyc 10.0 1214 152416 6200 5138 10960
PlantCyc 9.5 1119 189957 5475 4539 9476
PlantCyc 9.0 1119 189957 5475 4539 9476
PlantCyc 8.0 1050 188798 5332 4410 7634
PlantCyc 7.0 978 34663 3617 3455 7634
PlantCyc 6.0 898 27652 3421 3334 6939
PlantCyc 5.0 810 11217 3167 3146 5734
PlantCyc 4.0 762 11058 2929 2966 5204
PlantCyc 3.0 714 10964 2709 2679 4803
PlantCyc 2.0 581 8558 2501 2464 4971
PlantCyc 1.0 508 3389 2277 2314 4208

AraCyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
AraCyc 14.0 619 5472 3482 2802 5485
AraCyc 13.0 620 5995 3635 2802 5242
AraCyc 12.0 634 10064 3646 2661 5054
AraCyc 11.5 597 9041 3490 2613 4798
AraCyc 11.0 597 9993 3490 2613 4798
AraCyc 10.0 540 7127 3418 3323 4225
AraCyc 9.0 502 7100 3320 3320 3210
AraCyc 8.0 446 5520 2689 2825 3346
AraCyc 7.0 423 5506 2418 2719 2907
AraCyc 6.0 408 5501 2323 2630 2691
AraCyc 5.0 332 5869 1928 2312 2543
AraCyc 4.5 288 6214 1723 1956 2279
AraCyc 4.1 283 6021 1701 1908 2192
AraCyc 4.0 285 6011 1701 1902

BarleyCyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
BarleyCyc 4.0 540 4662 3033 2942 3637
BarleyCyc 3.0 541 5126 3033 2255 3392
BarleyCyc 2.0 472 7573 2955 2109 3012
BarleyCyc 1.0 465 7572 2901 2135 2880

BrachypodiumCyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
BrachypodiumCyc 4.0 531 5319 3004 2285 3567
BrachypodiumCyc 3.0 532 5845 3092 2289 3321
BrachypodiumCyc 2.0 475 8804 2950 2108 2108
BrachypodiumCyc 1.0 473 8802 2915 2128 2884

CassavaCyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
CassavaCyc 6.0 567 6371 3183 2386 3808
CassavaCyc 5.0 568 6957 3276 2391 3560
CassavaCyc 4.0 494 10010 3074 2205 3167
CassavaCyc 3.0 491 10007 3058 2232 2986
CassavaCyc 2.0 351 7178 2137 1538 1905
CassavaCyc 1.0 323 7178 2103 1815 1815

ChineseCabbageCyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
ChineseCabbageCyc 4.0 533 7825 3146 2331 3522
ChineseCabbageCyc 3.0 534 8564 3238 2337 3275
ChineseCabbageCyc 2.0 497 10980 3103 2218 3149
ChineseCabbageCyc 1.0 499 10976 3104 2270 2968

ChlamyCyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
ChlamyCyc 6.0 373 2768 2435 1750 3221
ChlamyCyc 5.0 374 3235 2597 1755 2963
ChlamyCyc 4.0 380 3368 2442 1614 2898
ChlamyCyc 3.5 349 3330 2263 1514 2708
ChlamyCyc 3.0 349 5163 2263 1514 2708
ChlamyCyc 2.0 283 2157 1688 1130 2036
ChlamyCyc 1.0 299 14732 1648 1255 1263

CornCyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
CornCyc 7.0 545 6778 3151 2525 4256
CornCyc 6.0 546 7391 3296 2526 4000
CornCyc 5.0 536 14737 3088 2304 3710
CornCyc 4.0 508 14818 2958 2271 3436
CornCyc 3.5 484 13979 2821 2160 3364
CornCyc 3.0 484 15410 2821 2160 3364
CornCyc 2.0 373 10527 2198 1752 2344
CornCyc 1.0 341 10519 2156 1731 2240

GrapeCyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
GrapeCyc 6.0 557 5799 3182 2421 3784
GrapeCyc 5.0 558 6321 3270 2426 3527
GrapeCyc 4.0 485 7576 3043 2189 3170
GrapeCyc 3.0 479 7572 3015 2229 2909
GrapeCyc 2.0 359 5341 2143 1571 2037
GrapeCyc 1.0 330 5338 2101 1540 1933

MossCyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
MossCyc 5.0 473 4952 2801 2035 3135
MossCyc 4.0 474 5533 2896 2038 2883
MossCyc 3.0 428 7806 2791 1929 2764
MossCyc 2.0 416 7805 2713 1901 2507
MossCyc 1.0 335 5664 2018 1409 1869

OryzaCyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
OryzaCyc 4.0 543 6198 3223 2487 3906
OryzaCyc 3.0 544 6721 3373 2488 3647
OryzaCyc 2.0 521 11208 3103 2222 3258
OryzaCyc 1.0 482 15677 3000 2226 2987

PapayaCyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
PapayaCyc 5.0 538 4345 3111 2329 3552
PapayaCyc 4.0 539 4817 3200 2335 3304
PapayaCyc 3.5 483 5717 2999 2143 3124
PapayaCyc 3.0 483 5717 2999 2143 3124
PapayaCyc 2.0 481 5714 2999 2220 2873
PapayaCyc 1.0 370 3898 2165 1557 2036

PoplarCyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
PoplarCyc 9.0 599 7996 3305 2509 3936
PoplarCyc 8.0 600 8735 3395 2514 3691
PoplarCyc 7.0 505 20824 3124 2247 3238
PoplarCyc 6.0 505 20822 3124 2295 3115
PoplarCyc 5.0 381 8691 2256 1613 2099
PoplarCyc 4.0 354 8691 2220 1596 2013
PoplarCyc 3.0 343 3422 1906 1406 1371
PoplarCyc 2.0 323 3420 1707 1397 1092
PoplarCyc 1.0 321 3434 1668 1363 903

PotatoCyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
PotatoCyc 3.0 558 5790 3122 2413 3706
PotatoCyc 2.0 559 6281 3211 2416 3456

SelaginellaCyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
SelaginellaCyc 5.0 481 4840 2811 2105 3261
SelaginellaCyc 4.0 482 5355 2899 2109 3007
SelaginellaCyc 3.0 435 6464 2802 1991 2852
SelaginellaCyc 2.0 421 6462 2737 1987 2630
SelaginellaCyc 1.0 329 3958 1986 1403 1838

SetariaCyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
SetariaCyc 4.0 549 6045 3028 2284 3635
SetariaCyc 3.0 550 6578 3114 2287 3389
SetariaCyc 2.0 481 10216 2977 2129 3061
SetariaCyc 1.0 477 10214 2942 2145 2888

SorghumBicolorCyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
SorghumBicolorCyc 4.0 540 5939 3017 2276 3676
SorghumBicolorCyc 3.0 541 6463 3105 2279 3420
SorghumBicolorCyc 2.0 482 9993 2986 2122 3077
SorghumBicolorCyc 1.0 480 8630 2939 2141 2928

SoyCyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
SoyCyc 7.0 596 10607 3387 2636 4295
SoyCyc 6.0 597 11619 3536 2636 4045
SoyCyc 5.0 556 24119 3199 2263 3623
SoyCyc 4.0 520 20317 3105 2273 3316
SoyCyc 3.0 441 13055 2566 2007 2762
SoyCyc 2.0 412 13094 2528 1987 2673
SoyCyc 1.0 369 4225 1762 1268

SpirodelaCyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
SpirodelaCyc 2.0 496 3638 2722 2045 3402
SpirodelaCyc 1.0 497 4052 2810 2048 3119

SwitchgrassCyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
SwitchgrassCyc 4.0 587 14006 3379 2581 3885
SwitchgrassCyc 3.0 588 15295 3471 2586 3641
SwitchgrassCyc 2.0 494 24705 3093 2204 3158
SwitchgrassCyc 1.0 479 17319 2985 2184 2767

TomatoCyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
TomatoCyc 2.0 588 6503 3288 2550 3880
TomatoCyc 1.0 589 7106 3379 2557 3634

WheatACyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
WheatACyc 2.0 551 6315 3093 2395 3642
WheatACyc 1.0 552 6868 3183 2400 3389

WheatDCyc Content Statistics

Pathways Enzymes Reactions Compounds Citations Released
WheatDCyc 2.0 540 6552 3059 2335 3621
WheatDCyc 1.0 541 7152 3151 2349 3375