Databases

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

Parent

Overview

Released:

July 2018

Taxonomic Range:

Arabidopsis halleri

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

AhalleriCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

3983

Parent

Overview

Released:

July 2018

Taxonomic Range:

Amaranthus hypochondriacus

Protein Sequence Source:

Phytozome v12: Ahypochondriacus_459_v2.1.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

AhypochondriacusCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4157

Parent

Overview

Released:

July 2018

Taxonomic Range:

Arabidopsis lyrata

Protein Sequence Source:

Phytozome v12: Alyrata_384_v2.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

AlyrataCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4108

Parent

Overview

Released:

July 2018

Taxonomic Range:

Amborella trichopoda

Protein Sequence Source:

Phytozome v12: Atrichopoda_291_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

AmborellaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4148

Parent

Overview

Released:

July 2018

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

More information on AraCyc curation is available.

Taxonomic Range:

Arabidopsis thaliana col

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

Primarily E2P2 v3.1

Enzyme Evidence:

Substantial manual curation of enzymes
In addition, large-scale computational predictions of enzyme function not subject to curator review

Pathway Prediction Program:

Pathway Tools 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:

AraCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

6335

AsparagusCyc 1.0

Parent

Overview

Released:

July 2018

Taxonomic Range:

Asparagus officinalis

Protein Sequence Source:

Phytozome v12: Aofficinalis_498_V1.1.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Musa acuminata

Protein Sequence Source:

Phytozome v12: Macuminata_304_v1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

BananaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4128

BarleyCyc 6.0

Parent

Overview

Released:

July 2018

Taxonomic Range:

Hordeum vulgare

Protein Sequence Source:

EnsemblPlants v38: Hordeum_vulgare.Hv_IBSC_PGSB_v2.pep.all.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

BarleyCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4235

Boleracea_capitataCyc 2.0

Parent

Overview

Released:

July 2018

Taxonomic Range:

Brassica oleracea var. capitata

Protein Sequence Source:

Phytozome v12: Boleraceacapitata_446_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

Boleracea_capitataCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4026

Boleracea_oleraceaCyc 2.0

Parent

Overview

Released:

July 2018

Taxonomic Range:

Brassica oleracea var. oleracea

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

Boleracea_oleraceaCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4077

BrachypodiumCyc 6.0

Parent

Overview

Released:

July 2018

Taxonomic Range:

Brachypodium distachyon

Protein Sequence Source:

Phytozome v12: Bdistachyon_314_v3.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

BrachypodiumCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

4141

Brapa_fpscCyc 2.0

Parent

Overview

Released:

July 2018

Taxonomic Range:

Brassica rapa FPsc

Protein Sequence Source:

Phytozome v12: BrapaFPsc_277_v1.3.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Triticum aestivum

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Boechera stricta

Protein Sequence Source:

Phytozome v12: Bstricta_278_v1.2.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Camptotheca acuminata

Protein Sequence Source:

Medicinal Plant Genomics Resource: cac_hc_gene_models.repr.pep

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Capsicum annuum

Protein Sequence Source:

SGN: Pepper.v.1.55.PEP.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Cicer arietinum ICC4958

Protein Sequence Source:

CSFL: Ca_Pep_v2.fasta.txt

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Dianthus caryophyllus

Protein Sequence Source:

Kazusa Genome Database: DCA_r1.0_pep_woTE.faa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Daucus carota subsp. Sativus

Protein Sequence Source:

Phytozome v12: Dcarota_388_v2.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Anacardium occidentale

Protein Sequence Source:

Phytozome v12: Aoccidentale_449_v0.9.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Manihot esculenta esculenta

Protein Sequence Source:

Phytozome v12: Mesculenta_305_v6.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Ricinus communis

Protein Sequence Source:

Phytozome v12: Rcommunis_119_v0.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Corchorus capsularis

Protein Sequence Source:

EnsemblPlants v38: Corchorus_capsularis.CCACVL1_1.0.pep.all.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Calotropis gigantea

Protein Sequence Source:

Medicinal Plant Genomics Resource: cal_hc_gene_models.rmscaff.repr.pep

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Capsella grandiflora

Protein Sequence Source:

Phytozome v12: Cgrandiflora_266_v1.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Brassica rapa ssp. pekinensis

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Chlamydomonas reinhardtii

Protein Sequence Source:

Phytozome v12: Creinhardtii_281_v5.5.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

Primarily large-scale computational predictions of enzyme function not subject to curator review supplemented with data and references curated by the GoFORSYS project at the Max Planck Institute of Molecular Plant Physiology
Small number of manually curated enzymes

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Citrus clementina

Protein Sequence Source:

Phytozome v12: Cclementina_182_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Theobroma cacao

Protein Sequence Source:

Phytozome v12: Tcacao_233_v1.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Phaseolus vulgaris

Protein Sequence Source:

Phytozome v12: Pvulgaris_442_v2.1.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Zea mays mays

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Catharanthus roseus

Protein Sequence Source:

Medicinal Plant Genomics Resource: cro_ap_asm_v2.proteins.fasta

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Capsella rubella

Protein Sequence Source:

Phytozome v12: Crubella_183_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Cannabis sativa Purple Kush

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Coccomyxa subellipsoidea C-169

Protein Sequence Source:

Phytozome v12: CsubellipsoideaC_169_227_v2.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Cucumis sativus

Protein Sequence Source:

Phytozome v12: Csativus_122_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Chromochloris zofingiensis

Protein Sequence Source:

Phytozome v12: Czofingiensis_461_v5.2.3.2.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Dioscorea rotundata

Protein Sequence Source:

EnsemblPlants v38: Dioscorea_rotundata.TDr96_F1_Pseudo_Chromosome_v1.0.pep.all.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Solanum melongena

Protein Sequence Source:

Kazusas Genome Database: SME_r2.5.1_pep.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Eucalyptus grandis

Protein Sequence Source:

Phytozome v12: Egrandis_297_v2.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Eutrema salsugineum

Protein Sequence Source:

Phytozome v12: Esalsugineum_173_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Linum usitatissimum

Protein Sequence Source:

Phytozome v12: Lusitatissimum_200_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Fragaria vesca subsp. Vesca

Protein Sequence Source:

Phytozome v12: Fvesca_226_v1.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Gossypium raimondii

Protein Sequence Source:

Phytozome v12: Graimondii_221_v2.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Vitis vinifera

Protein Sequence Source:

INRA: vitviv2.pep.fasta

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Humulus lupulus

Protein Sequence Source:

HopBase v1.1: natsume.shinsuwase.v1.1.20160111.pep

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Kalanchoe fedtschenkoi

Protein Sequence Source:

Phytozome v12: Kfedtschenkoi_382_v1.1.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Kalanchoe laxiflora

Protein Sequence Source:

Phytozome v12: Klaxiflora_309_v1.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Lotus japonicus

Protein Sequence Source:

Kazusa Genome Database: Lj3.0_pep.fna

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Leersia perrieri

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Micromonas commoda RCC299

Protein Sequence Source:

Phytozome v12: MspRCC299_229_v3.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Malus domestica

Protein Sequence Source:

Phytozome v12: Mdomestica_196_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Mimulus guttatus

Protein Sequence Source:

Phytozome v12: Mguttatus_256_v2.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Physcomitrella patens

Protein Sequence Source:

Phytozome v12: Ppatens_318_v3.3.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Marchantia polymorpha

Protein Sequence Source:

Phytozome v12: Mpolymorpha_320_v3.1.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Micromonas pusilla CCMP1545

Protein Sequence Source:

Phytozome v12: MpusillaCCMP1545_228_v3.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Miscanthus sinensis

Protein Sequence Source:

Phytozome v12: Msinensis_497_v7.1.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Medicago truncatula

Protein Sequence Source:

Phytozome v12: Mtruncatula_285_Mt4.0v1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Nicotiana tabacum TN90

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Oryza brachyantha

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Olea europaea var. sylvestris

Protein Sequence Source:

Phytozome v12: Oeuropaea_451_v1.0.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Oryza glaberrima

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Brassica napus

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Ostreococcus lucimarinus

Protein Sequence Source:

Phytozome v12: Olucimarinus_231_v2.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Oryza punctata

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Oryza rufipogon

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Oryza sativa japonica group

Protein Sequence Source:

Phytozome v12: Osativa_323_v7.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Oropetium thomaeum

Protein Sequence Source:

Phytozome v12: Othomaeum_386_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Carica papaya

Protein Sequence Source:

Phytozome v12: Cpapaya_113_ASGPBv0.4.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Petunia axillaris

Protein Sequence Source:

SGN: Petunia_axillaris_v1.6.2_proteins.fasta

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Panicum hallii

Protein Sequence Source:

Phytozome v12: Phallii_308_v2.0.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Ananas comosus

Protein Sequence Source:

Phytozome v12: Acomosus_321_v3.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

PlantCyc is a metabolic pathway reference database containing more than 1000 pathways and their catalytic enzymes and genes, as well as compounds from over 350 plant species (See Database Statistics).

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

Taxonomic Range:

primarily Viridiplantae

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

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

Enzyme Evidence:

Substantial manual curation of enzymes
In addition, large-scale computational predictions of enzyme function not subject to curator review

Pathway Prediction Program:

All pathways have been manually imported from PMN databases or MetaCyc

SAVI pathway validation lists:

Pathway Evidence:

Substantial manual curation of pathways
Some computational prediction of pathways followed by SAVI refinement and curator review
Additional pathways imported from MetaCyc based on curator inference

Link to PGDB:

PlantCyc

Content Statistics

Pathways:

Enzymes:

Reactions:

Compounds:

Citations:

10518

PoplarCyc 11.0

Parent

Overview

Released:

July 2018

More information on PoplarCyc curation is available.

Taxonomic Range:

Populus trichocarpa

other Populus species and hybrids

Protein Sequence Source:

Phytozome v12: Ptrichocarpa_444_v3.1.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Solanum tuberosum

Protein Sequence Source:

Phytozome v12: Stuberosum_448_v4.03.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Prunus persica

Protein Sequence Source:

Phytozome v12: Ppersica_298_v2.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Chenopodium quinoa

Protein Sequence Source:

Phytozome v12: Cquinoa_392_v1.0.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Rosa chinensis

Protein Sequence Source:

INRA: OBDH_1.0_sequences_prot.fasta

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Trifolium pratense

Protein Sequence Source:

Phytozome v12: Tpratense_385_v2.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Salvia miltiorrhiza Bunge

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Rosa multiflora

Protein Sequence Source:

Kazusa Genome Database: RMU_r2.0.pep

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Selaginella moellendorffii

Protein Sequence Source:

Phytozome v12: Smoellendorffii_91_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Setaria italica

Protein Sequence Source:

Phytozome v11: Sitalica_312_v2.2.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Sphagnum fallax

Protein Sequence Source:

Phytozome v12: Sfallax_310_v0.5.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Spinacia oleracea

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Sorghum bicolor

Protein Sequence Source:

Phytozome v12: Sbicolor_454_v3.1.1.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Glycine max

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Solanum pennellii

Protein Sequence Source:

SGN: Spenn-v2-aa-annot.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Spirodela polyrhiza

Protein Sequence Source:

Phytozome v12: Spolyrhiza_290_v2.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Beta vulgaris subsp. vulgaris

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Helianthus annuus

Protein Sequence Source:

Phytozome v12: Hannuus_494_r1.2.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Setaria viridis

Protein Sequence Source:

Phytozome v12: Sviridis_500_v2.1.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Citrus sinensis

Protein Sequence Source:

Phytozome v12: Csinensis_154_v1.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Panicum virgatum

Protein Sequence Source:

Phytozome v12: Pvirgatum_450_v4.1.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Solanum lycopersicum

Protein Sequence Source:

SGN: ITAG3.2_proteins.fasta

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Thellungiella parvula

Protein Sequence Source:

Thellungiella.org: TpV84ORFs.protein

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Volvox carteri

Protein Sequence Source:

Phytozome v12: Vcarteri_317_v2.1.protein.fa

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Triticum urartu

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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:

July 2018

Taxonomic Range:

Aegilops tauschii

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2 v3.1

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 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: