Databases

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