Databases Overview

Taxonomic Range:

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 v21.5

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

Link to PGDB:

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3983

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Ahypochondriacus_459_v2.1.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 v21.5

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

Link to PGDB:

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4157

Parent

Overview

Released:

Taxonomic Range:

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 v21.5

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

Link to PGDB:

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4108

Parent

Overview

Released:

Taxonomic Range:

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 v21.5

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

Link to PGDB:

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4148

Parent

Overview

Released:

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

More information on AraCyc curation is available.

Taxonomic Range:

Protein Sequence Source:

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 v21.5

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

Link to PGDB:

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

6335

AsparagusCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Asparagus officinalis

Protein Sequence Source:

Phytozome v12: Aofficinalis_498_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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

AsparagusCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4096

BananaCyc 2.0

Parent

Overview

Released:

Taxonomic Range:

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 v21.5

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

Link to PGDB:

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4128

BarleyCyc 6.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

EnsemblPlants v38: Hordeum_vulgare.Hv_IBSC_PGSB_v2.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 v21.5

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

Link to PGDB:

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4235

Boleracea_capitataCyc 2.0

Parent

Overview

Released:

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 v21.5

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

Link to PGDB:

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4026

Boleracea_oleraceaCyc 2.0

Parent

Overview

Released:

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 v21.5 (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

Link to PGDB:

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4077

BrachypodiumCyc 6.0

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 v21.5

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

Link to PGDB:

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4141

Brapa_fpscCyc 2.0

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 v21.5 (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

Link to PGDB:

Brapa_fpscCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4095

BreadwheatCyc 2.0

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 v21.5 (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

Link to PGDB:

BreadwheatCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4645

BstrictaCyc 2.0

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 v21.5 (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

Link to PGDB:

BstrictaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4023

CacuminataCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Camptotheca acuminata

Protein Sequence Source:

Medicinal Plant Genomics Resource: cac_hc_gene_models.repr.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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

CacuminataCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4283

CannuumCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Capsicum annuum

Protein Sequence Source:

SGN: Pepper.v.1.55.PEP.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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

CannuumCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4278

Carietinum_icc4958Cyc 2.0

Parent

Overview

Released:

Taxonomic Range:

Cicer arietinum ICC4958

Protein Sequence Source:

CSFL: 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 v21.5 (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

Link to PGDB:

Carietinum_icc4958Cyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4314

CarnationCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Dianthus caryophyllus

Protein Sequence Source:

Kazusa Genome Database: DCA_r1.0_pep_woTE.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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

CarnationCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4253

CarrotCyc 2.0

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 v21.5 (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

Link to PGDB:

CarrotCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4121

CashewCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Anacardium occidentale

Protein Sequence Source:

Phytozome v12: Aoccidentale_449_v0.9.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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

CashewCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4167

CassavaCyc 8.0

Parent

Overview

Released:

Manihot esculenta esculenta

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 v21.5

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

Link to PGDB:

CassavaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4257

CastorbeanCyc 2.0

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 v21.5 (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

Link to PGDB:

CastorbeanCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4509

CcapsularisCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Corchorus capsularis

Protein Sequence Source:

EnsemblPlants v38: Corchorus_capsularis.CCACVL1_1.0.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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

CcapsularisCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4111

CgiganteaCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Calotropis gigantea

Protein Sequence Source:

Medicinal Plant Genomics Resource: cal_hc_gene_models.rmscaff.repr.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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

CgiganteaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4100

CgrandifloraCyc 2.0

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 v21.5 (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

Link to PGDB:

CgrandifloraCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3966

ChineseCabbageCyc 6.0

Parent

Overview

Released:

Brassica rapa ssp. pekinensis

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 v21.5

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

Link to PGDB:

ChineseCabbageCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4062

ChlamyCyc 8.0

Parent

Overview

Released:

Chlamydomonas reinhardtii

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 v21.5

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

Link to PGDB:

ChlamyCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3932

ClementineCyc 2.0

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 v21.5 (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

Link to PGDB:

ClementineCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4292

CocoaCyc 2.0

Parent

Overview

Released:

Taxonomic Range:

Theobroma cacao

Protein Sequence Source:

Phytozome v12: Tcacao_233_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 v21.5 (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

Link to PGDB:

CocoaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4250

CommonbeanCyc 2.0

Parent

Overview

Released:

Taxonomic Range:

Phaseolus vulgaris

Protein Sequence Source:

Phytozome v12: Pvulgaris_442_v2.1.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 v21.5 (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

Link to PGDB:

CommonbeanCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4248

CornCyc 9.0

Parent

Overview

Released:

Taxonomic Range:

Zea mays mays

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 v21.5

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

Link to PGDB:

CornCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4966

CroseusCyc 2.0

Parent

Overview

Released:

Taxonomic Range:

Catharanthus roseus

Protein Sequence Source:

Medicinal Plant Genomics Resource: cro_ap_asm_v2.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 v21.5 (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

Link to PGDB:

CroseusCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4377

CrubellaCyc 2.0

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 v21.5 (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

Link to PGDB:

CrubellaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3958

Csativa_pkCyc 2.0

Parent

Overview

Released:

Cannabis sativa Purple Kush

Taxonomic Range:

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 v21.5 (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

Link to PGDB:

Csativa_pkCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4175

CsubellipsoideaCyc 2.0

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 v21.5 (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

Link to PGDB:

CsubellipsoideaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3170

CucumberCyc 2.0

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 v21.5 (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

Link to PGDB:

CucumberCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4290

CzofingiensisCyc 1.0

Parent

Overview

Released:

Chromochloris zofingiensis

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Czofingiensis_461_v5.2.3.2.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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

CzofingiensisCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3117

DrotundataCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Dioscorea rotundata

Protein Sequence Source:

EnsemblPlants v38: Dioscorea_rotundata.TDr96_F1_Pseudo_Chromosome_v1.0.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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

DrotundataCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3907

EggplantCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Solanum melongena

Protein Sequence Source:

Kazusas Genome Database: SME_r2.5.1_pep.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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

EggplantCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4240

EgrandisCyc 2.0

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 v21.5 (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

Link to PGDB:

EgrandisCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4271

EsalsugineumCyc 2.0

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 v21.5 (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

Link to PGDB:

EsalsugineumCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3990

FlaxCyc 2.0

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 v21.5 (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

Link to PGDB:

FlaxCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4320

Fvesca_vescaCyc 2.0

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 v21.5 (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

Link to PGDB:

Fvesca_vescaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4163

GraimondiiCyc 2.0

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 v21.5 (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

Link to PGDB:

GraimondiiCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4244

GrapeCyc 8.0

Parent

Overview

Released:

Taxonomic Range:

Vitis vinifera

Protein Sequence Source:

INRA: vitviv2.pep.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 v21.5

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

Link to PGDB:

GrapeCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4384

HopCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Humulus lupulus

Protein Sequence Source:

HopBase v1.1: natsume.shinsuwase.v1.1.20160111.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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

HopCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4120

KfedtschenkoiCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Kalanchoe fedtschenkoi

Protein Sequence Source:

Phytozome v12: Kfedtschenkoi_382_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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

KfedtschenkoiCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4070

KlaxifloraCyc 2.0

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 v21.5 (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

Link to PGDB:

KlaxifloraCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3998

LjaponicusCyc 2.0

Parent

Overview

Released:

Taxonomic Range:

Lotus japonicus

Protein Sequence Source:

Kazusa Genome Database: 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 v21.5 (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

Link to PGDB:

LjaponicusCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4275

LperrieriCyc 2.0

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 v21.5 (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

Link to PGDB:

LperrieriCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4034

McommodaCyc 2.0

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 v21.5 (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

Link to PGDB:

McommodaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3027

MdomesticaCyc 2.0

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 v21.5 (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

Link to PGDB:

MdomesticaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4378

MguttatusCyc 2.0

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 v21.5 (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

Link to PGDB:

MguttatusCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4072

MossCyc 7.0

Parent

Overview

Released:

Taxonomic Range:

Physcomitrella patens

Protein Sequence Source:

Phytozome v12: Ppatens_318_v3.3.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 v21.5

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

Link to PGDB:

MossCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3478

MpolymorphaCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Marchantia polymorpha

Protein Sequence Source:

Phytozome v12: Mpolymorpha_320_v3.1.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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

MpolymorphaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3490

MpusillaCyc 2.0

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 v21.5 (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

Link to PGDB:

MpusillaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3088

MsinensisCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Miscanthus sinensis

Protein Sequence Source:

Phytozome v12: Msinensis_497_v7.1.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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

MsinensisCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4199

MtruncatulaCyc 2.0

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 v21.5 (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

Link to PGDB:

MtruncatulaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4360

Ntabacum_tn90Cyc 2.0

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 v21.5 (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

Link to PGDB:

Ntabacum_tn90Cyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4658

ObrachyanthaCyc 2.0

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 v21.5 (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

Link to PGDB:

ObrachyanthaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4101

Oeuropaea_sylvestrisCyc 1.0

Parent

Overview

Released:

Olea europaea var. sylvestris

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Oeuropaea_451_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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

Oeuropaea_sylvestrisCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4149

OglaberrimaCyc 2.0

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 v21.5 (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

Link to PGDB:

OglaberrimaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4087

OilseedrapeCyc 2.0

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 v21.5 (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

Link to PGDB:

OilseedrapeCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4364

OlucimarinusCyc 2.0

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 v21.5 (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

Link to PGDB:

OlucimarinusCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

2952

OpunctataCyc 2.0

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 v21.5 (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

Link to PGDB:

OpunctataCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4091

OrufipogonCyc 2.0

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 v21.5 (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

Link to PGDB:

OrufipogonCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4113

OryzaCyc 6.0

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 v21.5

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

Link to PGDB:

OryzaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4818

OthomaeumCyc 2.0

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 v21.5 (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

Link to PGDB:

OthomaeumCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3901

PapayaCyc 7.0

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 v21.5

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

Link to PGDB:

PapayaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4035

PaxillarisCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Petunia axillaris

Protein Sequence Source:

SGN: Petunia_axillaris_v1.6.2_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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

PaxillarisCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4228

PhalliiCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Panicum hallii

Protein Sequence Source:

Phytozome v12: Phallii_308_v2.0.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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

PhalliiCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4082

PineappleCyc 2.0

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 v21.5 (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

Link to PGDB:

PineappleCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4094

PlantCyc 13.0

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

Link to PGDB:

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

10518

PoplarCyc 11.0

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_444_v3.1.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 v21.5

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

Link to PGDB:

PoplarCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4376

PotatoCyc 5.0

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 v21.5

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

Link to PGDB:

PotatoCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4372

PpersicaCyc 2.0

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 v21.5 (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

Link to PGDB:

PpersicaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4214

QuinoaCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Chenopodium quinoa

Protein Sequence Source:

Phytozome v12: Cquinoa_392_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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

QuinoaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4212

RchinensisCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Rosa chinensis

Protein Sequence Source:

INRA: OBDH_1.0_sequences_prot.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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

RchinensisCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4238

RedcloverCyc 2.0

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 v21.5 (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

Link to PGDB:

RedcloverCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4226

RedsageCyc 2.0

Parent

Overview

Released:

Salvia miltiorrhiza Bunge

Taxonomic Range:

Protein Sequence Source:

Herbal Medicine Omics Database: danshen.pep (file no longer available for download online)

Enzyme Functional Annotation Method:

Enzyme Evidence:

Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
Small number of manually curated enzymes

Pathway Prediction Program:

Pathway Tools v21.5 (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

Link to PGDB:

RedsageCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4082

RmultifloraCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Rosa multiflora

Protein Sequence Source:

Kazusa Genome Database: RMU_r2.0.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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

RmultifloraCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4288

SelaginellaCyc 7.0

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 v21.5

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

Link to PGDB:

SelaginellaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3617

SetariaCyc 6.0

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 v21.5

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

Link to PGDB:

SetariaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4092

SfallaxCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Sphagnum fallax

Protein Sequence Source:

Phytozome v12: Sfallax_310_v0.5.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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

SfallaxCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3408

SoleraceaCyc 2.0

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 v21.5 (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

Link to PGDB:

SoleraceaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4507

SorghumBicolorCyc 6.0

Parent

Overview

Released:

Taxonomic Range:

Sorghum bicolor

Protein Sequence Source:

Phytozome v12: Sbicolor_454_v3.1.1.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 v21.5

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

Link to PGDB:

SorghumBicolorCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4076

SoyCyc 9.0

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 v21.5

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

Link to PGDB:

SoyCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

5103

SpennelliiCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Solanum pennellii

Protein Sequence Source:

SGN: Spenn-v2-aa-annot.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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

SpennelliiCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4201

SpirodelaCyc 4.0

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 v21.5

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

Link to PGDB:

SpirodelaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3857

SugarbeetCyc 2.0

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 v21.5 (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

Link to PGDB:

SugarbeetCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4226

SunflowerCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Helianthus annuus

Protein Sequence Source:

Phytozome v12: Hannuus_494_r1.2.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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

SunflowerCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4105

SviridisCyc 2.0

Parent

Overview

Released:

Taxonomic Range:

Setaria viridis

Protein Sequence Source:

Phytozome v12: Sviridis_500_v2.1.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 v21.5

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

Link to PGDB:

SviridisCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4091

SweetorangeCyc 2.0

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 v21.5

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

Link to PGDB:

SweetorangeCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4328

SwitchgrassCyc 6.0

Parent

Overview

Released:

Taxonomic Range:

Panicum virgatum

Protein Sequence Source:

Phytozome v12: Pvirgatum_450_v4.1.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 v21.5

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

Link to PGDB:

SwitchgrassCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4267

TomatoCyc 4.0

Parent

Overview

Released:

Taxonomic Range:

Solanum lycopersicum

Protein Sequence Source:

SGN: ITAG3.2_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 v21.5

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

Link to PGDB:

TomatoCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4431

TparvulaCyc 2.0

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 v21.5

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

Link to PGDB:

TparvulaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4002

VcarteriCyc 2.0

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 v21.5

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

Link to PGDB:

VcarteriCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3067

WheatACyc 4.0

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 v21.5

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

Link to PGDB:

WheatACyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4162

WheatDCyc 4.0

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 v21.5

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

Link to PGDB:

WheatDCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4089

ZmarinaCyc 2.0

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 v21.5

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

Link to PGDB:

ZmarinaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3706

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

Link to PGDB:

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

Link to PGDB:

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

Link to PGDB:

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

Link to PGDB:

Content Statistics

Pathways:

1119

Enzymes:

189957

Reactions:

5475

Compounds:

4539

Citations:

9476

PlantCyc 8.0

Parent

Overview

Released:

November 2013

July 2013

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

Link to PGDB:

Content Statistics

Pathways:

1050

Enzymes:

188798

Reactions:

5332

Compounds:

4410

Citations:

7634

PlantCyc 7.0

Parent

Overview

Released:

June 2013

August 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 3.0

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

Link to PGDB:

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

Link to PGDB:

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:

Link to PGDB:

Content Statistics

Pathways:

810

Enzymes:

11217

Reactions:

3167

Compounds:

3146

Citations:

5734

PlantCyc 4.0

Parent

Overview

Released:

June 2010

Taxonomic Range:

Link to PGDB:

Content Statistics

Pathways:

762

Enzymes:

11058

Reactions:

2929

Compounds:

2966

Citations:

5204

PlantCyc 3.0

Parent

Overview

Released:

October 2009

Taxonomic Range:

Link to PGDB:

Content Statistics

Pathways:

714

Enzymes:

10964

Reactions:

2709

Compounds:

2679

Citations:

4803

PlantCyc 2.0

Parent

Overview

Released:

March 2009

Taxonomic Range:

Link to PGDB:

Content Statistics

Pathways:

581

Enzymes:

8558

Reactions:

2501

Compounds:

2464

Citations:

4971

PlantCyc 1.0

Parent

Overview

Released:

June 2008

Taxonomic Range:

Link to PGDB:

Content Statistics

Pathways:

508

Enzymes:

3389

Reactions:

2277

Compounds:

2314

Citations:

4208

AcoeruleaCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Aquilegia coerulea

Protein Sequence Source:

Phytozome v12: Acoerulea_322_v3.1.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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

AcoeruleaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4119

AhalleriCyc 2.0

Parent

Overview

Released:

Taxonomic Range:

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 v21.5

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

Link to PGDB:

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3983

AhalleriCyc 1.5

Parent

Overview

Released:

Taxonomic Range:

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

Link to PGDB:

Content Statistics

Pathways:

490

Enzymes:

4741

Reactions:

3232

Compounds:

2371

Citations:

3716

AhalleriCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

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

Link to PGDB:

Content Statistics

Pathways:

490

Enzymes:

4743

Reactions:

3232

Compounds:

2371

Citations:

3716

AhypochondriacusCyc 2.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

Phytozome v12: Ahypochondriacus_459_v2.1.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 v21.5

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

Link to PGDB:

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4157

AhypochondriacusCyc 1.5

Parent

Overview

Released:

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

Link to PGDB:

Content Statistics

Pathways:

483

Enzymes:

4608

Reactions:

2945

Compounds:

2242

Citations:

3869

AhypochondriacusCyc 1.0

Parent

Overview

Released:

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

Link to PGDB:

Content Statistics

Pathways:

483

Enzymes:

4609

Reactions:

2945

Compounds:

2244

Citations:

3869

AlyrataCyc 2.0

Parent

Overview

Released:

Taxonomic Range:

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 v21.5

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

Link to PGDB:

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4108

AlyrataCyc 1.5

Parent

Overview

Released:

Taxonomic Range:

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

Link to PGDB:

Content Statistics

Pathways:

502

Enzymes:

5503

Reactions:

3211

Compounds:

2382

Citations:

3834

AlyrataCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

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

Link to PGDB:

Content Statistics

Pathways:

502

Enzymes:

5504

Reactions:

3211

Compounds:

2384

Citations:

3834

AmborellaCyc 2.0

Parent

Overview

Released:

Taxonomic Range:

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 v21.5

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

Link to PGDB:

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4148

AmborellaCyc 1.5

Parent

Overview

Released:

Taxonomic Range:

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

Link to PGDB:

Content Statistics

Pathways:

490

Enzymes:

4585

Reactions:

3128

Compounds:

2396

Citations:

3890

AmborellaCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

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

Link to PGDB:

Content Statistics

Pathways:

490

Enzymes:

4586

Reactions:

3128

Compounds:

2397

Citations:

3890

AraCyc 16.0

Parent

Overview

Released:

More information on AraCyc curation is available.

Taxonomic Range:

Protein Sequence Source:

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 v21.5

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

Link to PGDB:

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

6335

AraCyc 15.5

Parent

Overview

Released:

More information on AraCyc curation is available.

Taxonomic Range:

Protein Sequence Source:

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

Link to PGDB:

Content Statistics

Pathways:

610

Enzymes:

5447

Reactions:

3556

Compounds:

2967

Citations:

6117

AraCyc 15.0

Parent

Overview

Released:

More information on AraCyc curation is available.

Taxonomic Range:

Protein Sequence Source:

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

Link to PGDB:

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

Link to PGDB:

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

Link to PGDB:

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

Link to PGDB:

Content Statistics

Pathways:

634

Enzymes:

10064

Reactions:

3646

Compounds:

2661

Citations:

5054

AraCyc 11.5

Parent

Overview

Released:

November 2013

July 2013

** 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

Link to PGDB:

Content Statistics

Pathways:

597

Enzymes:

9041

Reactions:

3490

Compounds:

2613

Citations:

4798

AraCyc 11.0

Parent

Overview

Released:

June 2013

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

Link to PGDB:

Content Statistics

Pathways:

597

Enzymes:

9993

Reactions:

3490

Compounds:

2613

Citations:

4798

AraCyc 10.0

Parent

Overview

Released:

August 2012

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:

NPP 3.0

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

Link to PGDB:

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

Link to PGDB:

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:

Link to PGDB:

Content Statistics

Pathways:

446

Enzymes:

5520

Reactions:

2689

Compounds:

2825

Citations:

3346

AraCyc 7.0

Parent

Overview

Released:

June 2010

Taxonomic Range:

Link to PGDB:

Content Statistics

Pathways:

423

Enzymes:

5506

Reactions:

2418

Compounds:

2719

Citations:

2907

AraCyc 6.0

Parent

Overview

Released:

October 2009

Taxonomic Range:

Link to PGDB:

Content Statistics

Pathways:

408

Enzymes:

5501

Reactions:

2323

Compounds:

2630

Citations:

2691

AraCyc 5.0

Parent

Overview

Released:

March 2009

Taxonomic Range:

Link to PGDB:

Content Statistics

Pathways:

332

Enzymes:

5869

Reactions:

1928

Compounds:

2312

Citations:

2543

AraCyc 4.5

Parent

Overview

Released:

June 2008

Taxonomic Range:

Link to PGDB:

Content Statistics

Pathways:

288

Enzymes:

6214

Reactions:

1723

Compounds:

1956

Citations:

2279

AraCyc 4.1

Parent

Overview

Taxonomic Range:

Link to PGDB:

Content Statistics

Pathways:

283

Enzymes:

6021

Reactions:

1701

Compounds:

1908

Citations:

2192

AraCyc 4.0

Parent

Overview

Taxonomic Range:

Link to PGDB:

Content Statistics

Pathways:

285

Enzymes:

6011

Reactions:

1701

Compounds:

1902

AsparagusCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

Asparagus officinalis

Protein Sequence Source:

Phytozome v12: Aofficinalis_498_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 v21.5 (primarily)

SAVI pathway validation lists:

Pathway Evidence:

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

Link to PGDB:

AsparagusCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4096

BananaCyc 2.0

Parent

Overview

Released:

Taxonomic Range:

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 v21.5

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

Link to PGDB:

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4128

BananaCyc 1.5

Parent

Overview

Released:

Taxonomic Range:

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

Link to PGDB:

Content Statistics

Pathways:

480

Enzymes:

6588

Reactions:

2988

Compounds:

2293

Citations:

3874

BananaCyc 1.0

Parent

Overview

Released:

Taxonomic Range:

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

Link to PGDB:

Content Statistics

Pathways:

480

Enzymes:

6589

Reactions:

2988

Compounds:

2298

Citations:

3874

BarleyCyc 6.0

Parent

Overview

Released:

Taxonomic Range:

Protein Sequence Source:

EnsemblPlants v38: Hordeum_vulgare.Hv_IBSC_PGSB_v2.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 v21.5

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

Link to PGDB:

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4235

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

Link to PGDB:

Content Statistics

Pathways:

487

Enzymes:

4659

Reactions:

2942

Compounds:

2337

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

Link to PGDB:

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

Link to PGDB:

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

Link to PGDB:

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:

E2P2 v2.1

Enzyme Evidence:

Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
Small number of manually curated enzymes

Pathway Prediction Program:

Pathway Tools 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

Link to PGDB:

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:

E2P2 2.0

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 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

Link to PGDB:

Content Statistics

Pathways:

465

Enzymes:

7572

Reactions:

2901

Compounds:

2135

Citations:

2880

Boleracea_capitataCyc 2.0

Parent

Overview

Released:

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 v21.5

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

Link to PGDB:

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4026

Boleracea_capitataCyc 1.5

Parent

Overview

Released:

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

Link to PGDB:

Content Statistics

Pathways:

483

Enzymes:

6477

Reactions:

3100

Compounds:

2321

Citations:

3765

Boleracea_capitataCyc 1.0

Parent

Overview

Released:

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

Link to PGDB:

Content Statistics

Pathways:

483

Enzymes:

6478

Reactions:

3100

Compounds:

2322

Citations:

3765

Boleracea_oleraceaCyc 2.0

Parent

Overview

Released:

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 v21.5 (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

Link to PGDB:

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4077

Boleracea_oleraceaCyc 1.5

Parent

Overview

Released:

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

Link to PGDB:

Content Statistics

Pathways:

500

Enzymes:

10525

Reactions:

3320

Compounds:

2461

Citations:

3815

Boleracea_oleraceaCyc 1.0

Parent

Overview

Released:

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

Link to PGDB:

Content Statistics

Pathways:

500

Enzymes:

10526

Reactions:

3320

Compounds:

2462

Citations:

3815

BrachypodiumCyc 6.0

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 v21.5

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

Link to PGDB:

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4141

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

Link to PGDB:

Content Statistics

Pathways:

495

Enzymes:

5338

Reactions:

3033

Compounds:

2320

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

Link to PGDB:

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

Link to PGDB:

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

Link to PGDB:

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:

E2P2 v2.1

Enzyme Evidence:

Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
Small number of manually curated enzymes

Pathway Prediction Program:

Pathway Tools 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

Link to PGDB:

Content Statistics

Pathways:

475

Enzymes:

8804

Reactions:

2950

Compounds:

2108

Citations:

2108

BrachypodiumCyc 1.0

Parent

Overview

Released:

November 2013

July 2013

June 2013

Taxonomic Range:

Protein Sequence Source:

Phytozome 9.0: Bdistachyon_192_peptide.fa

Enzyme Functional Annotation Method:

E2P2 2.0

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 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

Link to PGDB: