Databases

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.

Taxonomic Range:

Arabidopsis thaliana col

Protein Sequence Source:

AraPort v11: Araport11_genes.201606.pep.repr.fasta

Enzyme Functional Annotation Method:

Primarily E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

6117

BananaCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Musa acuminata

Protein Sequence Source:

Phytozome v12: Macuminata_304_v1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3874

BarleyCyc 5.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Hordeum vulgare

Protein Sequence Source:

EnsemblPlants v34: Hordeum_vulgare.ASM32608v1.pep.all.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4024

Boleracea_capitataCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Brassica oleracea var. capitata

Protein Sequence Source:

Phytozome v12: Boleraceacapitata_446_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3765

Boleracea_oleraceaCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Brassica oleracea var. oleracea

Protein Sequence Source:

EnsemblPlants v34: Brassica_oleracea.v2.1.pep.all.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3815

BrachypodiumCyc 5.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Brachypodium distachyon

Protein Sequence Source:

Phytozome v12: Bdistachyon_314_v3.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3839

Brapa_fpscCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Brassica rapa FPsc

Protein Sequence Source:

Phytozome v12: BrapaFPsc_277_v1.3.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3836

BreadwheatCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Triticum aestivum

Protein Sequence Source:

Phytozome v11 (early): Taestivum_296_v2.2.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4379

BstrictaCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Boechera stricta

Protein Sequence Source:

Phytozome v12: Bstricta_278_v1.2.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3750

Carietinum_icc4958Cyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Cicer arietinum ICC4958

Protein Sequence Source:

CSFL (https://www.coolseasonfoodlegume.org/): Ca_Pep_v2.fasta.txt

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4050

CarrotCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Daucus carota subsp. Sativus

Protein Sequence Source:

Phytozome v12: Dcarota_388_v2.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3882

CassavaCyc 7.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Manihot esculenta esculenta

Protein Sequence Source:

Phytozome v12: Mesculenta_305_v6.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4037

CastorbeanCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Ricinus communis

Protein Sequence Source:

Phytozome v12: Rcommunis_119_v0.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4215

CgrandifloraCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Capsella grandiflora

Protein Sequence Source:

Phytozome v12: Cgrandiflora_266_v1.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3697

ChineseCabbageCyc 5.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Brassica rapa ssp. pekinensis

Protein Sequence Source:

EnsemblPlants v34: Brassica_rapa.IVFCAASv1.pep.all.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3786

ChlamyCyc 7.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Chlamydomonas reinhardtii

Protein Sequence Source:

Phytozome v12: Creinhardtii_281_v5.5.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

SAVI pathway validation lists:

Pathway Evidence:

Primarily computational prediction of pathways followed by SAVI refinement and curator review
Additional pathways imported from MetaCyc and ChlamyCyc 1.0 (created by the GoFORSYS project at the Max Planck Institute of Molecular Plant Physiology) based on experimental evidence or curator inference

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3666

ClementineCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Citrus clementina

Protein Sequence Source:

Phytozome v12: Cclementina_182_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4008

CocoaCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Theobroma cacao

Protein Sequence Source:

Phytozome v12: Tcacao_233_v1.1.protein.fahttp://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=Phytozome

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3982

CommonbeanCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Phaseolus vulgaris

Protein Sequence Source:

Phytozome v11: Pvulgaris_218_v1.0.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3997

CornCyc 8.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Zea mays mays

Protein Sequence Source:

EnsemblPlants v34: Zea_mays.AGPv4.pep.all.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4718

CroseusCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Catharanthus roseus

Protein Sequence Source:

Medicinal Plant Genomics Resource (http://medicinalplantgenomics.msu.edu): cra.trans.estscan.pep.10072011.fasta

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4289

CrubellaCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Capsella rubella

Protein Sequence Source:

Phytozome v12: Crubella_183_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3687

Csativa_pkCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Cannabis sativa Purple Kush

Protein Sequence Source:

Cannabis genome project (http://genome.ccbr.utoronto.ca): canSat3_transcriptome-representative_ORFs.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3905

CsubellipsoideaCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Coccomyxa subellipsoidea C-169

Protein Sequence Source:

Phytozome v12: CsubellipsoideaC_169_227_v2.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

2872

CucumberCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Cucumis sativus

Protein Sequence Source:

Phytozome v12: Csativus_122_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4045

EgrandisCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Eucalyptus grandis

Protein Sequence Source:

Phytozome v12: Egrandis_297_v2.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4031

EsalsugineumCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Eutrema salsugineum

Protein Sequence Source:

Phytozome v12: Esalsugineum_173_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3711

FlaxCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Linum usitatissimum

Protein Sequence Source:

Phytozome v12: Lusitatissimum_200_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4062

Fvesca_vescaCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Fragaria vesca subsp. Vesca

Protein Sequence Source:

Phytozome v12: Fvesca_226_v1.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3878

GraimondiiCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Gossypium raimondii

Protein Sequence Source:

Phytozome v12: Graimondii_221_v2.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3966

GrapeCyc 7.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Vitis vinifera

Protein Sequence Source:

Phytozome v12: Vvinifera_145_Genoscope.12X.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4006

KlaxifloraCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Kalanchoe laxiflora

Protein Sequence Source:

Phytozome v12: Klaxiflora_309_v1.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3743

LjaponicusCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Lotus japonicus

Protein Sequence Source:

Kazusa (http://www.kazusa.or.jp/lotus/): Lj3.0_pep.fna

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4010

LperrieriCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Leersia perrieri

Protein Sequence Source:

EnsemblPlants v34: Leersia_perrieri.Lperr_V1.4.pep.all.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3757

McommodaCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Micromonas commoda RCC299

Protein Sequence Source:

Phytozome v12: MspRCC299_229_v3.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

2763

MdomesticaCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Malus domestica

Protein Sequence Source:

Phytozome v12: Mdomestica_196_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4123

MguttatusCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Mimulus guttatus

Protein Sequence Source:

Phytozome v12: Mguttatus_256_v2.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3820

MossCyc 6.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Physcomitrella patens

Protein Sequence Source:

Phytozome v10: Ppatens_251_v3.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3224

MpusillaCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Micromonas pusilla CCMP1545

Protein Sequence Source:

Phytozome v12: MpusillaCCMP1545_228_v3.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

2822

MtruncatulaCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Medicago truncatula

Protein Sequence Source:

Phytozome v12: Mtruncatula_285_Mt4.0v1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4110

Ntabacum_tn90Cyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Nicotiana tabacum TN90

Protein Sequence Source:

SGN: Ntab-TN90_AYMY-SS_NGS.prot.annot.faa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4385

ObrachyanthaCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Oryza brachyantha

Protein Sequence Source:

EnsemblPlants v34: Oryza_brachyantha.Oryza_brachyantha.v1.4b.pep.all.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3816

OglaberrimaCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Oryza glaberrima

Protein Sequence Source:

EnsemblPlants v34: Oryza_glaberrima.AGI1.1.pep.all.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3787

OilseedrapeCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Brassica napus

Protein Sequence Source:

EnsemblPlants v34: Brassica_napus.AST_PRJEB5043_v1.pep.all.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4151

OlucimarinusCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Ostreococcus lucimarinus

Protein Sequence Source:

Phytozome v12: Olucimarinus_231_v2.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

2689

OpunctataCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Oryza punctata

Protein Sequence Source:

EnsemblPlants v34: Oryza_punctata.AVCL00000000.pep.all.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3804

OrufipogonCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Oryza rufipogon

Protein Sequence Source:

EnsemblPlants v34: Oryza_rufipogon.OR_W1943.pep.all.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3824

OryzaCyc 5.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Oryza sativa japonica group

Protein Sequence Source:

Phytozome v12: Osativa_323_v7.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4525

OthomaeumCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Oropetium thomaeum

Protein Sequence Source:

Phytozome v12: Othomaeum_386_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3644

PapayaCyc 6.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Carica papaya

Protein Sequence Source:

Phytozome v12: Cpapaya_113_ASGPBv0.4.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3750

PineappleCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Ananas comosus

Protein Sequence Source:

Phytozome v12: Acomosus_321_v3.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3759

PlantCyc 12.0

Parent

Overview

Released:

May 2017

PlantCyc is a metabolic pathway reference database containing more than 1000 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.

Taxonomic Range:

primarily Viridiplantae

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

10836

PoplarCyc 10.0

Parent

Overview

Released:

May 2017

More information on PoplarCyc curation is available.

Taxonomic Range:

Populus trichocarpa

other Populus species and hybrids

Protein Sequence Source:

Phytozome v12: Ptrichocarpa_210_v3.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4106

PotatoCyc 4.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Solanum tuberosum

Protein Sequence Source:

Phytozome v12: Stuberosum_448_v4.03.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4381

PpersicaCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Prunus persica

Protein Sequence Source:

Phytozome v12: Ppersica_298_v2.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3970

RedcloverCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Trifolium pratense

Protein Sequence Source:

Phytozome v12: Tpratense_385_v2.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3974

RedsageCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Salvia miltiorrhiza Bunge

Protein Sequence Source:

Herbal Medicine Omics Database (http://www.herbal-genome.cn/): danshen.pep

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3828

SelaginellaCyc 6.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Selaginella moellendorffii

Protein Sequence Source:

Phytozome v12: Smoellendorffii_91_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3345

SetariaCyc 5.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Setaria italica

Protein Sequence Source:

Phytozome v11: Sitalica_312_v2.2.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3818

SoleraceaCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Spinacia oleracea

Protein Sequence Source:

The Beta vulgaris Resource: SpiSet-1.genes.1408.pep

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4250

SorghumBicolorCyc 5.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Sorghum bicolor

Protein Sequence Source:

Phytozome v12: Sbicolor_313_v3.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3812

SoyCyc 8.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Glycine max

Protein Sequence Source:

Phytozome v12: Gmax_275_Wm82.a2.v1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4797

SpirodelaCyc 3.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Spirodela polyrhiza

Protein Sequence Source:

Phytozome v12: Spolyrhiza_290_v2.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3596

SugarbeetCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Beta vulgaris subsp. vulgaris

Protein Sequence Source:

The Beta vulgaris Resource: BeetSet-2.genes.1408.pep

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5 (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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3944

SviridisCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Setaria viridis

Protein Sequence Source:

Phytozome v12: Sviridis_311_v1.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3814

SweetorangeCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Citrus sinensis

Protein Sequence Source:

Phytozome v12: Csinensis_154_v1.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4045

SwitchgrassCyc 5.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Panicum virgatum

Protein Sequence Source:

Phytozome v12: Pvirgatum_273_v1.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3995

TomatoCyc 3.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Solanum lycopersicum

Protein Sequence Source:

SGN: ITAG3.0_proteins.fasta

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4388

TparvulaCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Thellungiella parvula

Protein Sequence Source:

Thellungiella.org: TpV84ORFs.protein

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3727

VcarteriCyc 1.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Volvox carteri

Protein Sequence Source:

Phytozome v12: Vcarteri_317_v2.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

2808

WheatACyc 3.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Triticum urartu

Protein Sequence Source:

EnsemblPlants v34: Triticum_urartu.ASM34745v1.pep.all.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3889

WheatDCyc 3.0

Parent

Overview

Released:

May 2017

Taxonomic Range:

Aegilops tauschii

Protein Sequence Source:

EnsemblPlants v34: Aegilops_tauschii.ASM34733v1.pep.all.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

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 v20.5

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

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3790