Databases Overview

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 1.5

Parent

Overview

Released:

Taxonomic Range:

Musa acuminata

Protein Sequence Source:

Phytozome v12: Macuminata_304_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 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 5.5

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

EnsemblPlants v34: Hordeum_vulgare.ASM32608v1.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 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 1.5

Parent

Overview

Released:

Brassica oleracea var. capitata

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Boleraceacapitata_446_v1.0.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 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 1.5

Parent

Overview

Released:

Brassica oleracea var. oleracea

Taxonomic Range:

Protein Sequence Source:

EnsemblPlants v34: Brassica_oleracea.v2.1.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 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 5.5

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Bdistachyon_314_v3.1.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Brassica rapa FPsc

Protein Sequence Source:

Phytozome v12: BrapaFPsc_277_v1.3.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Triticum aestivum

Protein Sequence Source:

Phytozome v11 (early): Taestivum_296_v2.2.protein_primaryTranscriptOnly.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Boechera stricta

Protein Sequence Source:

Phytozome v12: Bstricta_278_v1.2.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Cicer arietinum ICC4958

Protein Sequence Source:

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

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 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 1.5

Parent

Overview

Released:

Daucus carota subsp. Sativus

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Dcarota_388_v2.0.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 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 7.5

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Mesculenta_305_v6.1.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Ricinus communis

Protein Sequence Source:

Phytozome v12: Rcommunis_119_v0.1.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Capsella grandiflora

Protein Sequence Source:

Phytozome v12: Cgrandiflora_266_v1.1.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 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 5.5

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

EnsemblPlants v34: Brassica_rapa.IVFCAASv1.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 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 7.5

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Creinhardtii_281_v5.5.protein.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Citrus clementina

Protein Sequence Source:

Phytozome v12: Cclementina_182_v1.0.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 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 1.5

Parent

Overview

Released:

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:

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 1.5

Parent

Overview

Released:

Taxonomic Range:

Phaseolus vulgaris

Protein Sequence Source:

Phytozome v11: Pvulgaris_218_v1.0.protein_primaryTranscriptOnly.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 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 8.5

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

EnsemblPlants v34: Zea_mays.AGPv4.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 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 1.5

Parent

Overview

Released:

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:

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 1.5

Parent

Overview

Released:

Taxonomic Range:

Capsella rubella

Protein Sequence Source:

Phytozome v12: Crubella_183_v1.0.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 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 1.5

Parent

Overview

Released:

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:

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 1.5

Parent

Overview

Released:

Coccomyxa subellipsoidea C-169

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: CsubellipsoideaC_169_227_v2.0.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Cucumis sativus

Protein Sequence Source:

Phytozome v12: Csativus_122_v1.0.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Eucalyptus grandis

Protein Sequence Source:

Phytozome v12: Egrandis_297_v2.0.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Eutrema salsugineum

Protein Sequence Source:

Phytozome v12: Esalsugineum_173_v1.0.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Linum usitatissimum

Protein Sequence Source:

Phytozome v12: Lusitatissimum_200_v1.0.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 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 1.5

Parent

Overview

Released:

Fragaria vesca subsp. Vesca

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Fvesca_226_v1.1.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Gossypium raimondii

Protein Sequence Source:

Phytozome v12: Graimondii_221_v2.1.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 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 7.5

Parent

Overview

Released:

Taxonomic Range:

Vitis vinifera

Protein Sequence Source:

Phytozome v12: Vvinifera_145_Genoscope.12X.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Kalanchoe laxiflora

Protein Sequence Source:

Phytozome v12: Klaxiflora_309_v1.1.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Lotus japonicus

Protein Sequence Source:

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

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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Leersia perrieri

Protein Sequence Source:

EnsemblPlants v34: Leersia_perrieri.Lperr_V1.4.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 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 1.5

Parent

Overview

Released:

Micromonas commoda RCC299

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: MspRCC299_229_v3.0.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Malus domestica

Protein Sequence Source:

Phytozome v12: Mdomestica_196_v1.0.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Mimulus guttatus

Protein Sequence Source:

Phytozome v12: Mguttatus_256_v2.0.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 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 6.5

Parent

Overview

Released:

Taxonomic Range:

Physcomitrella patens

Protein Sequence Source:

Phytozome v10: Ppatens_251_v3.0.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 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 1.5

Parent

Overview

Released:

Micromonas pusilla CCMP1545

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: MpusillaCCMP1545_228_v3.0.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Medicago truncatula

Protein Sequence Source:

Phytozome v12: Mtruncatula_285_Mt4.0v1.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Nicotiana tabacum TN90

Protein Sequence Source:

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

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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Oryza brachyantha

Protein Sequence Source:

EnsemblPlants v34: Oryza_brachyantha.Oryza_brachyantha.v1.4b.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Oryza glaberrima

Protein Sequence Source:

EnsemblPlants v34: Oryza_glaberrima.AGI1.1.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Brassica napus

Protein Sequence Source:

EnsemblPlants v34: Brassica_napus.AST_PRJEB5043_v1.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Ostreococcus lucimarinus

Protein Sequence Source:

Phytozome v12: Olucimarinus_231_v2.0.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Oryza punctata

Protein Sequence Source:

EnsemblPlants v34: Oryza_punctata.AVCL00000000.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Oryza rufipogon

Protein Sequence Source:

EnsemblPlants v34: Oryza_rufipogon.OR_W1943.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 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 5.5

Parent

Overview

Released:

Oryza sativa japonica group

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Osativa_323_v7.0.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Oropetium thomaeum

Protein Sequence Source:

Phytozome v12: Othomaeum_386_v1.0.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 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 6.5

Parent

Overview

Released:

Taxonomic Range:

Carica papaya

Protein Sequence Source:

Phytozome v12: Cpapaya_113_ASGPBv0.4.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Ananas comosus

Protein Sequence Source:

Phytozome v12: Acomosus_321_v3.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 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 12.5

Parent

Overview

Released:

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:

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 10.5

Parent

Overview

Released:

other Populus species and hybrids

More information on PoplarCyc curation is available.

Taxonomic Range:

Populus trichocarpa

Protein Sequence Source:

Phytozome v12: Ptrichocarpa_210_v3.0.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 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 4.5

Parent

Overview

Released:

Taxonomic Range:

Solanum tuberosum

Protein Sequence Source:

Phytozome v12: Stuberosum_448_v4.03.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Prunus persica

Protein Sequence Source:

Phytozome v12: Ppersica_298_v2.1.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Trifolium pratense

Protein Sequence Source:

Phytozome v12: Tpratense_385_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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Salvia miltiorrhiza Bunge

Protein Sequence Source:

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

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 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 6.5

Parent

Overview

Released:

Selaginella moellendorffii

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Smoellendorffii_91_v1.0.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 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 5.5

Parent

Overview

Released:

Taxonomic Range:

Setaria italica

Protein Sequence Source:

Phytozome v11: Sitalica_312_v2.2.protein_primaryTranscriptOnly.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Spinacia oleracea

Protein Sequence Source:

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

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 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 5.5

Parent

Overview

Released:

Taxonomic Range:

Sorghum bicolor

Protein Sequence Source:

Phytozome v12: Sbicolor_313_v3.1.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 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 8.5

Parent

Overview

Released:

Taxonomic Range:

Glycine max

Protein Sequence Source:

Phytozome v12: 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 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 3.5

Parent

Overview

Released:

Taxonomic Range:

Spirodela polyrhiza

Protein Sequence Source:

Phytozome v12: 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 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 1.5

Parent

Overview

Released:

Beta vulgaris subsp. vulgaris

Taxonomic Range:

Protein Sequence Source:

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

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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Setaria viridis

Protein Sequence Source:

Phytozome v12: Sviridis_311_v1.1.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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Citrus sinensis

Protein Sequence Source:

Phytozome v12: Csinensis_154_v1.1.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 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 5.5

Parent

Overview

Released:

Taxonomic Range:

Panicum virgatum

Protein Sequence Source:

Phytozome v12: Pvirgatum_273_v1.1.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 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 3.5

Parent

Overview

Released:

Taxonomic Range:

Solanum lycopersicum

Protein Sequence Source:

SGN: ITAG3.0_proteins.fasta

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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Thellungiella parvula

Protein Sequence Source:

Thellungiella.org: TpV84ORFs.protein

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 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 1.5

Parent

Overview

Released:

Taxonomic Range:

Volvox carteri

Protein Sequence Source:

Phytozome v12: Vcarteri_317_v2.1.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 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 3.5

Parent

Overview

Released:

Taxonomic Range:

Triticum urartu

Protein Sequence Source:

EnsemblPlants v34: Triticum_urartu.ASM34745v1.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 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 3.5

Parent

Overview

Released:

Taxonomic Range:

Aegilops tauschii

Protein Sequence Source:

EnsemblPlants v34: Aegilops_tauschii.ASM34733v1.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 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

ZmarinaCyc 1.5

Parent

Overview

Released:

Taxonomic Range:

Zostera marina

Protein Sequence Source:

Phytozome v12: Zmarina_324_v2.2.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 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:

3435

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.

Taxonomic Range:

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:

1213

Enzymes:

140581

Reactions:

6051

Compounds:

5128

Citations:

11114

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.

Taxonomic Range:

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:

1214

Enzymes:

152416

Reactions:

6200

Compounds:

5138

Citations:

10960

PlantCyc 9.5

Parent

Overview

Released:

November 2014

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.

Taxonomic Range:

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:

1119

Enzymes:

189957

Reactions:

5475

Compounds:

4539

Citations:

9476

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.

Taxonomic Range:

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

Content Statistics

Pathways:

1119

Enzymes:

189957

Reactions:

5475

Compounds:

4539

Citations:

9476

PlantCyc 8.0

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.

Taxonomic Range:

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:

1050

Enzymes:

188798

Reactions:

5332

Compounds:

4410

Citations:

7634

PlantCyc 7.0

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.

Taxonomic Range:

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:

UPP 3.0

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:

978

Enzymes:

34663

Reactions:

3617

Compounds:

3455

Citations:

7634

PlantCyc 6.0

Parent

Overview

Released:

March 2012

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.

Taxonomic Range:

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:

NPP 2.0

UPP 2.0

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:

898

Enzymes:

27652

Reactions:

3421

Compounds:

3334

Citations:

6939

PlantCyc 5.0

Parent

Overview

Released:

April 2011

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.

Taxonomic Range:

Content Statistics

Pathways:

810

Enzymes:

11217

Reactions:

3167

Compounds:

3146

Citations:

5734

PlantCyc 4.0

Parent

Overview

Released:

June 2010

Taxonomic Range:

Content Statistics

Pathways:

762

Enzymes:

11058

Reactions:

2929

Compounds:

2966

Citations:

5204

PlantCyc 3.0

Parent

Overview

Released:

October 2009

Taxonomic Range:

Content Statistics

Pathways:

714

Enzymes:

10964

Reactions:

2709

Compounds:

2679

Citations:

4803

PlantCyc 2.0

Parent

Overview

Released:

March 2009

Taxonomic Range:

Content Statistics

Pathways:

581

Enzymes:

8558

Reactions:

2501

Compounds:

2464

Citations:

4971

PlantCyc 1.0

Parent

Overview

Released:

June 2008

Taxonomic Range:

Content Statistics

Pathways:

508

Enzymes:

3389

Reactions:

2277

Compounds:

2314

Citations:

4208

AhalleriCyc 1.5

Parent

Overview

Released:

Taxonomic Range:

Arabidopsis halleri

Protein Sequence Source:

Phytozome v11 (early): Ahalleri_264_v1.1.protein_primaryTranscriptOnly.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 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:

3716

AhalleriCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Arabidopsis halleri

Protein Sequence Source:

Phytozome v11 (early): Ahalleri_264_v1.1.protein_primaryTranscriptOnly.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 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:

490

Enzymes:

4743

Reactions:

3232

Compounds:

2371

Citations:

3716

AhypochondriacusCyc 1.5

Parent

Overview

Released:

Amaranthus hypochondriacus

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Ahypochondriacus_315_v1.0.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 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:

3869

AhypochondriacusCyc 1.0

Parent

Overview

Released:

Amaranthus hypochondriacus

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Ahypochondriacus_315_v1.0.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 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:

483

Enzymes:

4609

Reactions:

2945

Compounds:

2244

Citations:

3869

AlyrataCyc 1.5

Parent

Overview

Released:

Taxonomic Range:

Arabidopsis lyrata

Protein Sequence Source:

Phytozome v12: Alyrata_384_v2.1.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 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:

3834

AlyrataCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Arabidopsis lyrata

Protein Sequence Source:

Phytozome v12: Alyrata_384_v2.1.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 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:

502

Enzymes:

5504

Reactions:

3211

Compounds:

2384

Citations:

3834

AmborellaCyc 1.5

Parent

Overview

Released:

Taxonomic Range:

Amborella trichopoda

Protein Sequence Source:

Phytozome v12: Atrichopoda_291_v1.0.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 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:

3890

AmborellaCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Amborella trichopoda

Protein Sequence Source:

Phytozome v12: Atrichopoda_291_v1.0.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 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:

490

Enzymes:

4586

Reactions:

3128

Compounds:

2397

Citations:

3890

AraCyc 15.5

Parent

Overview

Released:

More information on AraCyc curation is available.

Taxonomic Range:

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

AraCyc 15.0

Parent

Overview

Released:

More information on AraCyc curation is available.

Taxonomic Range:

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:

610

Enzymes:

5716

Reactions:

3557

Compounds:

2971

Citations:

6117

AraCyc 14.0

Parent

Overview

Released:

More information on AraCyc curation is available.

Taxonomic Range:

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

Content Statistics

Pathways:

619

Enzymes:

5472

Reactions:

3482

Compounds:

2802

Citations:

5485

AraCyc 13.0

Parent

Overview

Released:

More information on AraCyc curation is available.

Taxonomic Range:

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

Content Statistics

Pathways:

620

Enzymes:

5995

Reactions:

3635

Compounds:

2802

Citations:

5242

AraCyc 12.0

Parent

Overview

Released:

More information on AraCyc curation is available.

Taxonomic Range:

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

Content Statistics

Pathways:

634

Enzymes:

10064

Reactions:

3646

Compounds:

2661

Citations:

5054

AraCyc 11.5

Parent

Overview

Released:

** 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.

Taxonomic Range:

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

Content Statistics

Pathways:

597

Enzymes:

9041

Reactions:

3490

Compounds:

2613

Citations:

4798

AraCyc 11.0

Parent

Overview

Released:

More information on AraCyc curation is available.

Taxonomic Range:

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

Content Statistics

Pathways:

597

Enzymes:

9993

Reactions:

3490

Compounds:

2613

Citations:

4798

AraCyc 10.0

Parent

Overview

Released:

More information on AraCyc curation is available.

Taxonomic Range:

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:

UPP 3.0

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:

540

Enzymes:

7127

Reactions:

3418

Compounds:

3323

Citations:

4225

AraCyc 9.0

Parent

Overview

Released:

March 2012

More information on AraCyc curation is available.

Taxonomic Range:

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:

NPP 2.0

UPP 2.0

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:

502

Enzymes:

7100

Reactions:

3320

Compounds:

3320

Citations:

3210

AraCyc 8.0

Parent

Overview

Released:

April 2011

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.

Taxonomic Range:

Content Statistics

Pathways:

446

Enzymes:

5520

Reactions:

2689

Compounds:

2825

Citations:

3346

AraCyc 7.0

Parent

Overview

Released:

June 2010

Taxonomic Range:

Content Statistics

Pathways:

423

Enzymes:

5506

Reactions:

2418

Compounds:

2719

Citations:

2907

AraCyc 6.0

Parent

Overview

Released:

October 2009

Taxonomic Range:

Content Statistics

Pathways:

408

Enzymes:

5501

Reactions:

2323

Compounds:

2630

Citations:

2691

AraCyc 5.0

Parent

Overview

Released:

March 2009

Taxonomic Range:

Content Statistics

Pathways:

332

Enzymes:

5869

Reactions:

1928

Compounds:

2312

Citations:

2543

AraCyc 4.5

Parent

Overview

Released:

June 2008

Taxonomic Range:

Content Statistics

Pathways:

288

Enzymes:

6214

Reactions:

1723

Compounds:

1956

Citations:

2279

AraCyc 4.1

Parent

Overview

Taxonomic Range:

Content Statistics

Pathways:

283

Enzymes:

6021

Reactions:

1701

Compounds:

1908

Citations:

2192

AraCyc 4.0

Parent

Overview

Taxonomic Range:

Content Statistics

Pathways:

285

Enzymes:

6011

Reactions:

1701

Compounds:

1902

BananaCyc 1.5

Parent

Overview

Released:

Taxonomic Range:

Musa acuminata

Protein Sequence Source:

Phytozome v12: Macuminata_304_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 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

BananaCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Musa acuminata

Protein Sequence Source:

Phytozome v12: Macuminata_304_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 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:

480

Enzymes:

6589

Reactions:

2988

Compounds:

2298

Citations:

3874

BarleyCyc 5.5

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

EnsemblPlants v34: Hordeum_vulgare.ASM32608v1.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 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

BarleyCyc 5.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

EnsemblPlants v34: Hordeum_vulgare.ASM32608v1.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 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:

487

Enzymes:

4660

Reactions:

2942

Compounds:

2339

Citations:

4024

BarleyCyc 4.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Ensembl Release 25: Hordeum_vulgare.082214v1.25.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 based on experimental evidence or curator inference

Content Statistics

Pathways:

540

Enzymes:

4662

Reactions:

3033

Compounds:

2942

Citations:

3637

BarleyCyc 3.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Ensembl Release 25: Hordeum_vulgare.082214v1.25.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 based on experimental evidence or curator inference

Content Statistics

Pathways:

541

Enzymes:

5126

Reactions:

3033

Compounds:

2255

Citations:

3392

BarleyCyc 2.0

Parent

Overview

Released:

Taxonomic Range:

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

Content Statistics

Pathways:

472

Enzymes:

7573

Reactions:

2955

Compounds:

2109

Citations:

3012

BarleyCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

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

Content Statistics

Pathways:

465

Enzymes:

7572

Reactions:

2901

Compounds:

2135

Citations:

2880

Boleracea_capitataCyc 1.5

Parent

Overview

Released:

Brassica oleracea var. capitata

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Boleraceacapitata_446_v1.0.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 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_capitataCyc 1.0

Parent

Overview

Released:

Brassica oleracea var. capitata

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Boleraceacapitata_446_v1.0.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 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:

483

Enzymes:

6478

Reactions:

3100

Compounds:

2322

Citations:

3765

Boleracea_oleraceaCyc 1.5

Parent

Overview

Released:

Brassica oleracea var. oleracea

Taxonomic Range:

Protein Sequence Source:

EnsemblPlants v34: Brassica_oleracea.v2.1.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 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

Boleracea_oleraceaCyc 1.0

Parent

Overview

Released:

Brassica oleracea var. oleracea

Taxonomic Range:

Protein Sequence Source:

EnsemblPlants v34: Brassica_oleracea.v2.1.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 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:

500

Enzymes:

10526

Reactions:

3320

Compounds:

2462

Citations:

3815

BrachypodiumCyc 5.5

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Bdistachyon_314_v3.1.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 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

BrachypodiumCyc 5.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Bdistachyon_314_v3.1.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 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:

495

Enzymes:

5339

Reactions:

3033

Compounds:

2324

Citations:

3839

BrachypodiumCyc 4.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome v10: Bdistachyon_283_v2.1.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

Content Statistics

Pathways:

531

Enzymes:

5319

Reactions:

3004

Compounds:

2285

Citations:

3567

BrachypodiumCyc 3.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome v10: Bdistachyon_283_v2.1.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

Content Statistics

Pathways:

532

Enzymes:

5845

Reactions:

3092

Compounds:

2289

Citations:

3321

BrachypodiumCyc 2.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome 9.0: Bdistachyon_192_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

Content Statistics

Pathways:

475

Enzymes:

8804

Reactions:

2950

Compounds:

2108

Citations:

2108

BrachypodiumCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome 9.0: Bdistachyon_192_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

Content Statistics

Pathways:

473

Enzymes:

8802

Reactions:

2915

Compounds:

2128

Citations:

2884

Brapa_fpscCyc 1.5

Parent

Overview

Released:

Taxonomic Range:

Brassica rapa FPsc

Protein Sequence Source:

Phytozome v12: BrapaFPsc_277_v1.3.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 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

Brapa_fpscCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Brassica rapa FPsc

Protein Sequence Source:

Phytozome v12: BrapaFPsc_277_v1.3.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 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:

500

Enzymes:

7647

Reactions:

3211

Compounds:

2411

Citations:

3836

BreadwheatCyc 1.5

Parent

Overview

Released:

Taxonomic Range:

Triticum aestivum

Protein Sequence Source:

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

BreadwheatCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Triticum aestivum

Protein Sequence Source:

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

540

Enzymes:

22446

Reactions:

3470

Compounds:

2778

Citations:

4379

BstrictaCyc 1.5

Parent

Overview

Released:

Taxonomic Range:

Boechera stricta

Protein Sequence Source:

Phytozome v12: Bstricta_278_v1.2.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 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

BstrictaCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Boechera stricta

Protein Sequence Source:

Phytozome v12: Bstricta_278_v1.2.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 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:

493

Enzymes:

5081

Reactions:

3171

Compounds:

2350

Citations:

3750

Carietinum_icc4958Cyc 1.5

Parent

Overview

Released:

Taxonomic Range:

Cicer arietinum ICC4958

Protein Sequence Source:

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

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 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

Carietinum_icc4958Cyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Cicer arietinum ICC4958

Protein Sequence Source:

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

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 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:

520

Enzymes:

5664

Reactions:

3349

Compounds:

2489

Citations:

4050

CarrotCyc 1.5

Parent

Overview

Released:

Daucus carota subsp. Sativus

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Dcarota_388_v2.0.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 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

CarrotCyc 1.0

Parent

Overview

Released:

Daucus carota subsp. Sativus

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Dcarota_388_v2.0.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 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:

496

Enzymes:

6284

Reactions:

3062

Compounds:

2345

Citations:

3882

CassavaCyc 7.5

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Mesculenta_305_v6.1.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 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

CassavaCyc 7.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Mesculenta_305_v6.1.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 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:

513

Enzymes:

6297

Reactions:

3178

Compounds:

2424

Citations:

4037

CassavaCyc 6.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome v10: Mesculenta_147_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 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

Content Statistics

Pathways:

567

Enzymes:

6371

Reactions:

3183

Compounds:

2386

Citations:

3808

CassavaCyc 5.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome v10: Mesculenta_147_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 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

Content Statistics

Pathways:

568

Enzymes:

6957

Reactions:

3276

Compounds:

2391

Citations:

3560

CassavaCyc 4.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome 9.0: Mesculenta_147_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

Content Statistics

Pathways:

494

Enzymes:

10010

Reactions:

3074

Compounds:

2205

Citations:

3167

CassavaCyc 3.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome 9.0: Mesculenta_147_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

Content Statistics

Pathways:

491

Enzymes:

10007

Reactions:

3058

Compounds:

2232

Citations:

2986

CassavaCyc 2.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome 7.0: Mesculenta_147_peptide.fa

Enzyme Functional Annotation Method:

E2P2 1.0

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:

UPP 3.0

Pathway Evidence:

Primarily computational prediction followed by curator review
Additional pathways imported from MetaCyc based on experimental evidence or curator inference

Content Statistics

Pathways:

351

Enzymes:

7178

Reactions:

2137

Compounds:

1538

Citations:

1905

CassavaCyc 1.0

Parent

Overview

Released:

March 2012

Taxonomic Range:

Protein Sequence Source:

Phytozome 7.0: Mesculenta_147_peptide.fa

Enzyme Functional Annotation Method:

E2P2 1.0

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:

NPP 2.0

UPP 2.0

Pathway Evidence:

Primarily computational prediction followed by curator review
Additional pathways imported from MetaCyc based on experimental evidence or curator inference

Content Statistics

Pathways:

323

Enzymes:

7178

Reactions:

2103

Compounds:

1815

Citations:

1815

CastorbeanCyc 1.5

Parent

Overview

Released:

Taxonomic Range:

Ricinus communis

Protein Sequence Source:

Phytozome v12: Rcommunis_119_v0.1.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 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

CastorbeanCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Ricinus communis

Protein Sequence Source:

Phytozome v12: Rcommunis_119_v0.1.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 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:

534

Enzymes:

6142

Reactions:

3761

Compounds:

2922

Citations:

4215

CgrandifloraCyc 1.5

Parent

Overview

Released:

Taxonomic Range:

Capsella grandiflora

Protein Sequence Source:

Phytozome v12: Cgrandiflora_266_v1.1.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 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

CgrandifloraCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Capsella grandiflora

Protein Sequence Source:

Phytozome v12: Cgrandiflora_266_v1.1.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 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:

489

Enzymes:

4750

Reactions:

3121

Compounds:

2309

Citations:

3697

ChineseCabbageCyc 5.5

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

EnsemblPlants v34: Brassica_rapa.IVFCAASv1.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 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

ChineseCabbageCyc 5.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

EnsemblPlants v34: Brassica_rapa.IVFCAASv1.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 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:

497

Enzymes:

7869

Reactions:

3206

Compounds:

2375

Citations:

3786

ChineseCabbageCyc 4.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Ensembl Release 25: Brassica_rapa.IVFCAASv1.25.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 based on experimental evidence or curator inference

Content Statistics

Pathways:

533

Enzymes:

7825

Reactions:

3146

Compounds:

2331

Citations:

3522

ChineseCabbageCyc 3.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Ensembl Release 25: Brassica_rapa.IVFCAASv1.25.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 based on experimental evidence or curator inference

Content Statistics

Pathways:

534

Enzymes:

8564

Reactions:

3238

Compounds:

2337

Citations:

3275

ChineseCabbageCyc 2.0

Parent

Overview

Released:

Taxonomic Range:

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

Content Statistics

Pathways:

497

Enzymes:

10980

Reactions:

3103

Compounds:

2218

Citations:

3149

ChineseCabbageCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

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 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

Content Statistics

Pathways:

499

Enzymes:

10976

Reactions:

3104

Compounds:

2270

Citations:

2968

ChlamyCyc 7.5

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Creinhardtii_281_v5.5.protein.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 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

ChlamyCyc 7.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Creinhardtii_281_v5.5.protein.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 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:

379

Enzymes:

2888

Reactions:

2471

Compounds:

1803

Citations:

3666

ChlamyCyc 6.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome v10: Creinhardtii_281_v5.5.protein.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 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

Content Statistics

Pathways:

373

Enzymes:

2768

Reactions:

2435

Compounds:

1750

Citations:

3221

ChlamyCyc 5.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome v10: Creinhardtii_281_v5.5.protein.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 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

Content Statistics

Pathways:

374

Enzymes:

3235

Reactions:

2597

Compounds:

1755

Citations:

2963

ChlamyCyc 4.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome 9.0: Creinhardtii_236_protein.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.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

Content Statistics

Pathways:

380

Enzymes:

3368

Reactions:

2442

Compounds:

1614

Citations:

2898

ChlamyCyc 3.5

Parent

Overview

Released:

** 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).

Taxonomic Range:

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

Content Statistics

Pathways:

349

Enzymes:

3330

Reactions:

2263

Compounds:

1514

Citations:

2708

ChlamyCyc 3.0

Parent

Overview

Released:

Taxonomic Range:

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

Content Statistics

Pathways:

349

Enzymes:

5163

Reactions:

2263

Compounds:

1514

Citations:

2708

ChlamyCyc 2.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2 1.0

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:

CVP 1.0

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

Content Statistics

Pathways:

283

Enzymes:

2157

Reactions:

1688

Compounds:

1130

Citations:

2036

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.

Taxonomic Range:

Content Statistics

Pathways:

299

Enzymes:

14732

Reactions:

1648

Compounds:

1255

Citations:

1263

ClementineCyc 1.5

Parent

Overview

Released:

Taxonomic Range:

Citrus clementina

Protein Sequence Source:

Phytozome v12: Cclementina_182_v1.0.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 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

ClementineCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Citrus clementina

Protein Sequence Source:

Phytozome v12: Cclementina_182_v1.0.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 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:

509

Enzymes:

5192

Reactions:

3140

Compounds:

2379

Citations:

4008

CocoaCyc 1.5

Parent

Overview

Released:

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:

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

CocoaCyc 1.0

Parent

Overview

Released:

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:

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:

509

Enzymes:

5182

Reactions:

3192

Compounds:

2446

Citations:

3982

CommonbeanCyc 1.5

Parent

Overview

Released:

Taxonomic Range:

Phaseolus vulgaris

Protein Sequence Source:

Phytozome v11: Pvulgaris_218_v1.0.protein_primaryTranscriptOnly.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 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

CommonbeanCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Phaseolus vulgaris

Protein Sequence Source:

Phytozome v11: Pvulgaris_218_v1.0.protein_primaryTranscriptOnly.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 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:

515

Enzymes:

5583

Reactions:

3144

Compounds:

2416

Citations:

3997

CornCyc 8.5

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

EnsemblPlants v34: Zea_mays.AGPv4.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 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

CornCyc 8.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

EnsemblPlants v34: Zea_mays.AGPv4.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 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:

556

Enzymes:

7507

Reactions:

3259

Compounds:

2616

Citations:

4718

CornCyc 7.0

Parent

Overview

Released:

Taxonomic Range:

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

Content Statistics

Pathways:

545

Enzymes:

6778

Reactions:

3151

Compounds:

2525

Citations:

4256

CornCyc 6.0

Parent

Overview

Released:

Taxonomic Range:

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

Content Statistics

Pathways:

546

Enzymes:

7391

Reactions:

3296

Compounds:

2526

Citations:

4000

CornCyc 5.0

Parent

Overview

Released:

Taxonomic Range:

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

Content Statistics

Pathways:

536

Enzymes:

14737

Reactions:

3088

Compounds:

2304

Citations:

3710

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.

Taxonomic Range:

Protein Sequence Source:

Phytozome 9.0 Zmays_181_peptide.fa

Enzyme Functional Annotation Method: