Databases

CcampestrisCyc 2.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Cuscuta campestris

Protein Sequence Source:

Cuscuta campestris Genome Project: data_cucam_0.32.annot.protein.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

CcampestrisCyc

Content Statistics

Number of Pathways:

515

Number of Reactions:

3426

Number of Compounds:

2789

Number of Enzymes:

9559

Number of Citations:

4523

SugarbeetCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Beta vulgaris vulgaris

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

SugarbeetCyc

Content Statistics

Number of Pathways:

527

Number of Reactions:

3529

Number of Compounds:

2849

Number of Enzymes:

5707

Number of Citations:

4726

CzofingiensisCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Chromochloris zofingiensis

Protein Sequence Source:

Phytozome v12: Czofingiensis_461_v5.2.3.2.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

358

Number of Reactions:

2773

Number of Compounds:

2204

Number of Enzymes:

3198

Number of Citations:

3416

WheatDCyc 6.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Aegilops tauschii

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

546

Number of Reactions:

3808

Number of Compounds:

3083

Number of Enzymes:

81358

Number of Citations:

4851

HopCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Humulus lupulus

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

526

Number of Reactions:

3517

Number of Compounds:

2838

Number of Enzymes:

12061

Number of Citations:

4585

MossCyc 9.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Physcomitrium patens

Protein Sequence Source:

Phytozome v12: Ppatens_318_v3.3.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

430

Number of Reactions:

3127

Number of Compounds:

2483

Number of Enzymes:

18964

Number of Citations:

3903

Aagrestis_oxfordCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Anthoceros agrestis

Protein Sequence Source:

Hornwort genomes: AagrOXF_genome_PROT.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

Aagrestis_oxfordCyc

Content Statistics

Number of Pathways:

289

Number of Reactions:

1673

Number of Compounds:

1459

Number of Enzymes:

1725

Number of Citations:

2425

OnivaraCyc 2.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Oryza nivara

Protein Sequence Source:

Ensembl: Oryza_nivara.Oryza_nivara_v1.0.pep.all.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

OnivaraCyc

Content Statistics

Number of Pathways:

508

Number of Reactions:

3248

Number of Compounds:

2637

Number of Enzymes:

8988

Number of Citations:

4384

Boleracea_capitataCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Brassica oleracea capitata

Protein Sequence Source:

Phytozome v12: Boleraceacapitata_446_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

Boleracea_capitataCyc

Content Statistics

Number of Pathways:

480

Number of Reactions:

3114

Number of Compounds:

2495

Number of Enzymes:

7628

Number of Citations:

4040

RedsageCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Salvia miltiorrhiza

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

RedsageCyc

Content Statistics

Number of Pathways:

516

Number of Reactions:

3371

Number of Compounds:

2731

Number of Enzymes:

7233

Number of Citations:

4462

CcapsularisCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Corchorus capsularis

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

503

Number of Reactions:

3179

Number of Compounds:

2528

Number of Enzymes:

5256

Number of Citations:

4381

SunflowerCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Helianthus annuus

Protein Sequence Source:

Phytozome v12: Hannuus_494_r1.2.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

524

Number of Reactions:

3440

Number of Compounds:

2779

Number of Enzymes:

11463

Number of Citations:

4623

DatepalmCyc 2.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Phoenix dactylifera

Protein Sequence Source:

Date Palm Research Program: PDK30-pep.fsa.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

DatepalmCyc

Content Statistics

Number of Pathways:

528

Number of Reactions:

3380

Number of Compounds:

2710

Number of Enzymes:

5908

Number of Citations:

4526

WildsugarcaneCyc 2.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Saccharum spontaneum

Protein Sequence Source:

The Ming Laboratory, University of Illinois: Sspon.v20190103.protein.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

WildsugarcaneCyc

Content Statistics

Number of Pathways:

571

Number of Reactions:

3855

Number of Compounds:

3121

Number of Enzymes:

19663

Number of Citations:

5017

HuskTomatoCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Physalis pubescens

Protein Sequence Source:

NGDC: GWHANUX00000000.Protein.faa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

HuskTomatoCyc

Content Statistics

Number of Pathways:

334

Number of Reactions:

1916

Number of Compounds:

1670

Number of Enzymes:

1362

Number of Citations:

2892

MpolymorphaCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Marchantia polymorpha

Protein Sequence Source:

Phytozome v12: Mpolymorpha_320_v3.1.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

432

Number of Reactions:

2926

Number of Compounds:

2327

Number of Enzymes:

5159

Number of Citations:

3759

AangustusCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Anthoceros angustus

Protein Sequence Source:

Data Dryad: Anthoceros.angustus.coding.gene.pep

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

AangustusCyc

Content Statistics

Number of Pathways:

284

Number of Reactions:

1587

Number of Compounds:

1385

Number of Enzymes:

640

Number of Citations:

2431

OpunctataCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Oryza punctata

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

OpunctataCyc

Content Statistics

Number of Pathways:

498

Number of Reactions:

3197

Number of Compounds:

2578

Number of Enzymes:

8322

Number of Citations:

4318

Boleracea_oleraceaCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Brassica oleracea

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

Boleracea_oleraceaCyc

Content Statistics

Number of Pathways:

504

Number of Reactions:

3319

Number of Compounds:

2645

Number of Enzymes:

12347

Number of Citations:

4247

RmultifloraCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Rosa multiflora

Protein Sequence Source:

Kazusa Genome Database: RMU_r2.0.pep

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

530

Number of Reactions:

3496

Number of Compounds:

2861

Number of Enzymes:

13808

Number of Citations:

4655

RosemaryCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Salvia rosmarinus

Protein Sequence Source:

Data Dryad: ros_aa.gene_models.hc.pep.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

RosemaryCyc

Content Statistics

Number of Pathways:

392

Number of Reactions:

2295

Number of Compounds:

1936

Number of Enzymes:

2441

Number of Citations:

3337

CgrandifloraCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Capsella grandiflora

Protein Sequence Source:

Phytozome v12: Cgrandiflora_266_v1.1.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

CgrandifloraCyc

Content Statistics

Number of Pathways:

491

Number of Reactions:

3169

Number of Compounds:

2496

Number of Enzymes:

6027

Number of Citations:

4135

SviridisCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Setaria viridis

Protein Sequence Source:

Phytozome v12: Sviridis_500_v2.1.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

SviridisCyc

Content Statistics

Number of Pathways:

518

Number of Reactions:

3318

Number of Compounds:

2705

Number of Enzymes:

10579

Number of Citations:

4471

DrabaCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Draba nivalis

Protein Sequence Source:

Data Dryad: Dniva.Maker.Run5.all.proteins.NumberedGenes.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

DrabaCyc

Content Statistics

Number of Pathways:

333

Number of Reactions:

1901

Number of Compounds:

1691

Number of Enzymes:

1409

Number of Citations:

2833

ValleyoakCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Quercus lobata

Protein Sequence Source:

Valley Oak Genome Project: Qlobata.v3.0.PCG.prot.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

ValleyoakCyc

Content Statistics

Number of Pathways:

531

Number of Reactions:

3449

Number of Compounds:

2813

Number of Enzymes:

9710

Number of Citations:

4600

JackfruitCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Artocarpus heterophyllus

Protein Sequence Source:

AOCC: Arthe_prot_LATEST.tfa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

JackfruitCyc

Content Statistics

Number of Pathways:

371

Number of Reactions:

2182

Number of Compounds:

1906

Number of Enzymes:

1667

Number of Citations:

3173

MpusillaCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Micromonas pusilla

Protein Sequence Source:

Phytozome v12: MpusillaCCMP1545_228_v3.0.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

MpusillaCyc

Content Statistics

Number of Pathways:

323

Number of Reactions:

2283

Number of Compounds:

1869

Number of Enzymes:

2110

Number of Citations:

3133

AcoeruleaCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Aquilegia coerulea

Protein Sequence Source:

Phytozome v12: Acoerulea_322_v3.1.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

525

Number of Reactions:

3351

Number of Compounds:

2687

Number of Enzymes:

9730

Number of Citations:

4489

OrufipogonCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Oryza rufipogon

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

OrufipogonCyc

Content Statistics

Number of Pathways:

504

Number of Reactions:

3279

Number of Compounds:

2653

Number of Enzymes:

8787

Number of Citations:

4447

BrachypodiumCyc 9.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Brachypodium distachyon

Protein Sequence Source:

Phytozome v13:Bdistachyon_314_v3.1.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

500

Number of Reactions:

3246

Number of Compounds:

2638

Number of Enzymes:

12097

Number of Citations:

4341

RubbertreeCyc 2.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Hevea brasiliensis

Protein Sequence Source:

Rubber Genome & Transcriptome Database: hevea_amino.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

RubbertreeCyc

Content Statistics

Number of Pathways:

575

Number of Reactions:

3886

Number of Compounds:

3187

Number of Enzymes:

9880

Number of Citations:

5072

CgiganteaCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Calotropis gigantea

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

490

Number of Reactions:

3205

Number of Compounds:

2601

Number of Enzymes:

4629

Number of Citations:

4236

SweetcherryCyc 2.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Prunus avium

Protein Sequence Source:

PAV_r1.0.proteins.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

SweetcherryCyc

Content Statistics

Number of Pathways:

521

Number of Reactions:

3326

Number of Compounds:

2695

Number of Enzymes:

6897

Number of Citations:

4471

DrotundataCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Dioscorea cayenensis rotundata

Protein Sequence Source:

EnsemblPlants v54: Dioscorea_rotundata.TDr96_F1_v2_PseudoChromosome.pep.all.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

524

Number of Reactions:

3443

Number of Compounds:

2808

Number of Enzymes:

13260

Number of Citations:

4569

VanillaCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Vanilla planifolia

Protein Sequence Source:

NCBI Genome: GCA_016413895.1_Elo_Vpla-A_principal_1.0_protein.faa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

VanillaCyc

Content Statistics

Number of Pathways:

310

Number of Reactions:

1740

Number of Compounds:

1545

Number of Enzymes:

1069

Number of Citations:

2504

KfedtschenkoiCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Kalanchoe fedtschenkoi

Protein Sequence Source:

Phytozome v12: Kfedtschenkoi_382_v1.1.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

504

Number of Reactions:

3312

Number of Compounds:

2689

Number of Enzymes:

10403

Number of Citations:

4413

MsinensisCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Miscanthus sinensis

Protein Sequence Source:

Phytozome v12: Msinensis_497_v7.1.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

520

Number of Reactions:

3507

Number of Compounds:

2813

Number of Enzymes:

17581

Number of Citations:

4614

AfilliculoidesCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Azolla filiculoides

Protein Sequence Source:

FernBase: Azolla_filiculoides.protein.highconfidence_v1.1.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

AfilliculoidesCyc

Content Statistics

Number of Pathways:

303

Number of Reactions:

1731

Number of Compounds:

1484

Number of Enzymes:

941

Number of Citations:

2673

OthomaeumCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Oropetium thomaeum

Protein Sequence Source:

Phytozome v12: Othomaeum_386_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

OthomaeumCyc

Content Statistics

Number of Pathways:

489

Number of Reactions:

3052

Number of Compounds:

2443

Number of Enzymes:

5409

Number of Citations:

4256

Brapa_fpscCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Brassica rapa

Protein Sequence Source:

Phytozome v12: BrapaFPsc_277_v1.3.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

Brapa_fpscCyc

Content Statistics

Number of Pathways:

505

Number of Reactions:

3279

Number of Compounds:

2602

Number of Enzymes:

9667

Number of Citations:

4270

RyeCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Secale cereale

Protein Sequence Source:

NGDC: GWHASIY00000000.Protein.faa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

RyeCyc

Content Statistics

Number of Pathways:

377

Number of Reactions:

2175

Number of Compounds:

1923

Number of Enzymes:

2070

Number of Citations:

3231

ChinesecabbageCyc 9.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Brassica rapa pekinensis

Protein Sequence Source:

BrassicaDB: Brara_Chiifu_V3.5_pep.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

508

Number of Reactions:

3354

Number of Compounds:

2666

Number of Enzymes:

20905

Number of Citations:

4335

SweetorangeCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Citrus sinensis

Protein Sequence Source:

Phytozome v12: Csinensis_154_v1.1.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

SweetorangeCyc

Content Statistics

Number of Pathways:

514

Number of Reactions:

3378

Number of Compounds:

2734

Number of Enzymes:

11835

Number of Citations:

4491

EggplantCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Solanum melongena

Protein Sequence Source:

Kazusas Genome Database: SME_r2.5.1_pep.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

518

Number of Reactions:

3358

Number of Compounds:

2685

Number of Enzymes:

6997

Number of Citations:

4581

ZmarinaCyc 5.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Zostera marina

Protein Sequence Source:

Phytozome v13: Zmarina_668_v3.1.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

ZmarinaCyc

Content Statistics

Number of Pathways:

449

Number of Reactions:

2859

Number of Compounds:

2284

Number of Enzymes:

4494

Number of Citations:

3774

KlaxifloraCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Kalanchoe laxiflora

Protein Sequence Source:

Phytozome v12: Klaxiflora_309_v1.1.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

KlaxifloraCyc

Content Statistics

Number of Pathways:

508

Number of Reactions:

3294

Number of Compounds:

2670

Number of Enzymes:

16221

Number of Citations:

4470

MtruncatulaCyc 5.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Medicago truncatula

Protein Sequence Source:

INRA: MtrunA17r5.0-ANR.faa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

MtruncatulaCyc

Content Statistics

Number of Pathways:

534

Number of Reactions:

3412

Number of Compounds:

2773

Number of Enzymes:

9212

Number of Citations:

4643

AhalleriCyc 5.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Arabidopsis halleri

Protein Sequence Source:

Phytozome v13: Ahalleri_765_v2.1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

AhalleriCyc

Content Statistics

Number of Pathways:

503

Number of Reactions:

3265

Number of Compounds:

2603

Number of Enzymes:

9302

Number of Citations:

4274

PapayaCyc 9.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Carica papaya

Protein Sequence Source:

Phytozome v12: Cpapaya_113_ASGPBv0.4.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

493

Number of Reactions:

3248

Number of Compounds:

2605

Number of Enzymes:

5052

Number of Citations:

4197

BreadfruitCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Artocarpus altilis

Protein Sequence Source:

AOCC: Artal_prot_LATEST.tfa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

BreadfruitCyc

Content Statistics

Number of Pathways:

353

Number of Reactions:

2059

Number of Compounds:

1782

Number of Enzymes:

1540

Number of Citations:

3095

SacredlotusCyc 2.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Nelumbo nucifera

Protein Sequence Source:

NCBI: GCF_000365185.1_Chinese_Lotus_1.1_protein.faa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

SacredlotusCyc

Content Statistics

Number of Pathways:

498

Number of Reactions:

3210

Number of Compounds:

2588

Number of Enzymes:

8674

Number of Citations:

4296

ClementineCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Citrus x clementina

Protein Sequence Source:

Phytozome v12: Cclementina_182_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

ClementineCyc

Content Statistics

Number of Pathways:

510

Number of Reactions:

3308

Number of Compounds:

2672

Number of Enzymes:

8480

Number of Citations:

4426

SweetWormwoodCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Artemisia annua

Protein Sequence Source:

NCBI Genome: GCA_003112345.1_ASM311234v1_protein.faa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

SweetWormwoodCyc

Content Statistics

Number of Pathways:

420

Number of Reactions:

2566

Number of Compounds:

2176

Number of Enzymes:

2967

Number of Citations:

3541

EgrandisCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Eucalyptus grandis

Protein Sequence Source:

Phytozome v12: Egrandis_297_v2.0.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

EgrandisCyc

Content Statistics

Number of Pathways:

520

Number of Reactions:

3406

Number of Compounds:

2782

Number of Enzymes:

12168

Number of Citations:

4477

LerCyc 2.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Arabidopsis thaliana ler

Protein Sequence Source:

NCBI: a_thaliana_thale_cress_protein.faa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

LerCyc

Content Statistics

Number of Pathways:

309

Number of Reactions:

2875

Number of Compounds:

2383

Number of Enzymes:

7033

Number of Citations:

3135

MuskmelonCyc 2.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Cucumis melo

Protein Sequence Source:

Melonomics: CM4.0_protein.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

MuskmelonCyc

Content Statistics

Number of Pathways:

493

Number of Reactions:

3139

Number of Compounds:

2530

Number of Enzymes:

5509

Number of Citations:

4329

AhypochondriacusCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Amaranthus hypochondriacus

Protein Sequence Source:

Phytozome v12: Ahypochondriacus_459_v2.1.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

AhypochondriacusCyc

Content Statistics

Number of Pathways:

502

Number of Reactions:

3144

Number of Compounds:

2560

Number of Enzymes:

5422

Number of Citations:

4463

PaxillarisCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Petunia axillaris

Protein Sequence Source:

SGN: Petunia_axillaris_v1.6.2_proteins.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

570

Number of Reactions:

3788

Number of Compounds:

3024

Number of Enzymes:

8015

Number of Citations:

4898

BreadwheatCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Triticum aestivum

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

BreadwheatCyc

Content Statistics

Number of Pathways:

576

Number of Reactions:

3888

Number of Compounds:

3158

Number of Enzymes:

30897

Number of Citations:

5116

SelaginellaCyc 9.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Selaginella moellendorffii

Protein Sequence Source:

Phytozome v12: Smoellendorffii_91_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

445

Number of Reactions:

3103

Number of Compounds:

2495

Number of Enzymes:

5466

Number of Citations:

3941

CoastRedwoodCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Sequoia sempervirens

Protein Sequence Source:

TreeGenes: SESE.2_1.peptides.fa.gz

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

CoastRedwoodCyc

Content Statistics

Number of Pathways:

432

Number of Reactions:

2795

Number of Compounds:

2366

Number of Enzymes:

6617

Number of Citations:

3789

SwitchgrassCyc 8.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Panicum virgatum

Protein Sequence Source:

Phytozome v12: Pvirgatum_450_v4.1.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

530

Number of Reactions:

3492

Number of Compounds:

2866

Number of Enzymes:

25856

Number of Citations:

4660

EsalsugineumCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Eutrema salsugineum

Protein Sequence Source:

Phytozome v12: Esalsugineum_173_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

EsalsugineumCyc

Content Statistics

Number of Pathways:

485

Number of Reactions:

3193

Number of Compounds:

2527

Number of Enzymes:

6730

Number of Citations:

4047

LettuceCyc 2.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Lactuca sativa

Protein Sequence Source:

Phytozome 12: Lsativa_467_v5.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

LettuceCyc

Content Statistics

Number of Pathways:

519

Number of Reactions:

3429

Number of Compounds:

2790

Number of Enzymes:

14776

Number of Citations:

4541

Ntabacum_tn90Cyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Nicotiana tabacum

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

Ntabacum_tn90Cyc

Content Statistics

Number of Pathways:

605

Number of Reactions:

4008

Number of Compounds:

3247

Number of Enzymes:

14074

Number of Citations:

5384

AlyrataCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Arabidopsis lyrata

Protein Sequence Source:

Phytozome v12: Alyrata_384_v2.1.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

AlyrataCyc

Content Statistics

Number of Pathways:

506

Number of Reactions:

3306

Number of Compounds:

2636

Number of Enzymes:

6990

Number of Citations:

4311

PhalliiCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Panicum hallii

Protein Sequence Source:

Phytozome v13Phallii_590_v3.2.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

512

Number of Reactions:

3272

Number of Compounds:

2643

Number of Enzymes:

8553

Number of Citations:

4373

BstrictaCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Boechera stricta

Protein Sequence Source:

Phytozome v12: Bstricta_278_v1.2.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

BstrictaCyc

Content Statistics

Number of Pathways:

492

Number of Reactions:

3190

Number of Compounds:

2531

Number of Enzymes:

6734

Number of Citations:

4120

SetariaCyc 8.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Setaria italica

Protein Sequence Source:

Phytozome v11: Sitalica_312_v2.2.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

514

Number of Reactions:

3293

Number of Compounds:

2676

Number of Enzymes:

9162

Number of Citations:

4404

CocoaCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Theobroma cacao

Protein Sequence Source:

Phytozome v12: Tcacao_233_v1.1.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

CocoaCyc

Content Statistics

Number of Pathways:

515

Number of Reactions:

3320

Number of Compounds:

2686

Number of Enzymes:

8863

Number of Citations:

4470

TeaCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Camellia sinensis sinensis

Protein Sequence Source:

Tea Plant Information Archive:

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

TeaCyc

Content Statistics

Number of Pathways:

513

Number of Reactions:

3285

Number of Compounds:

2669

Number of Enzymes:

10655

Number of Citations:

4437

EuropeanpearCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Pyrus communis

Protein Sequence Source:

Genome Database for Rosaceae: PyrusCommunis_BartlettDHv2.0.pep.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

EuropeanpearCyc

Content Statistics

Number of Pathways:

503

Number of Reactions:

3257

Number of Compounds:

2625

Number of Enzymes:

8468

Number of Citations:

4372

LjaponicusCyc 5.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Lotus japonicus

Protein Sequence Source:

Phytozome v13: Ljaponicus_571_Lj1.0v1.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

LjaponicusCyc

Content Statistics

Number of Pathways:

513

Number of Reactions:

3195

Number of Compounds:

2593

Number of Enzymes:

6690

Number of Citations:

4345

ObarthiiCyc 2.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Oryza barthii

Protein Sequence Source:

Ensembl: Oryza_barthii.O.barthii_v1.pep.all.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

ObarthiiCyc

Content Statistics

Number of Pathways:

506

Number of Reactions:

3306

Number of Compounds:

2686

Number of Enzymes:

7943

Number of Citations:

4456

AlyssumCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Lobularia maritima

Protein Sequence Source:

NGDC: GWHANWC00000000.Protein.faa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

AlyssumCyc

Content Statistics

Number of Pathways:

333

Number of Reactions:

1938

Number of Compounds:

1687

Number of Enzymes:

1211

Number of Citations:

2738

PigeonpeaCyc 2.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Cajanus cajan

Protein Sequence Source:

Legume Information System: cajca.ICPL87119.gnm1.ann1.Y27M.protein_main.faa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

PigeonpeaCyc

Content Statistics

Number of Pathways:

518

Number of Reactions:

3393

Number of Compounds:

2694

Number of Enzymes:

7445

Number of Citations:

4476

CacuminataCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Camptotheca acuminata

Protein Sequence Source:

Medicinal Plant Genomics Resource: Lachesis_assembly.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

506

Number of Reactions:

3244

Number of Compounds:

2621

Number of Enzymes:

6602

Number of Citations:

4362

SfallaxCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Sphagnum fallax

Protein Sequence Source:

Phytozome v13: Sfallax_522_v1.1.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

422

Number of Reactions:

2979

Number of Compounds:

2398

Number of Enzymes:

10646

Number of Citations:

3815

CommonbeanCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Phaseolus vulgaris

Protein Sequence Source:

Phytozome v12: Pvulgaris_442_v2.1.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

CommonbeanCyc

Content Statistics

Number of Pathways:

515

Number of Reactions:

3280

Number of Compounds:

2610

Number of Enzymes:

8794

Number of Citations:

4432

TeffCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Eragrostis tef

Protein Sequence Source:

CoGe: 50954-CDS-prot.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

TeffCyc

Content Statistics

Number of Pathways:

421

Number of Reactions:

2613

Number of Compounds:

2239

Number of Enzymes:

2903

Number of Citations:

3759

FlaxCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Linum usitatissimum

Protein Sequence Source:

Phytozome v12: Lusitatissimum_200_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

FlaxCyc

Content Statistics

Number of Pathways:

536

Number of Reactions:

3435

Number of Compounds:

2778

Number of Enzymes:

10564

Number of Citations:

4654

LperrieriCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Leersia perrieri

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

LperrieriCyc

Content Statistics

Number of Pathways:

507

Number of Reactions:

3248

Number of Compounds:

2660

Number of Enzymes:

8095

Number of Citations:

4324

ObrachyanthaCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Oryza brachyantha

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

ObrachyanthaCyc

Content Statistics

Number of Pathways:

506

Number of Reactions:

3217

Number of Compounds:

2607

Number of Enzymes:

6138

Number of Citations:

4427

AmborellaCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Amborella trichopoda

Protein Sequence Source:

Phytozome v12: Atrichopoda_291_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

AmborellaCyc

Content Statistics

Number of Pathways:

500

Number of Reactions:

3265

Number of Compounds:

2662

Number of Enzymes:

5242

Number of Citations:

4393

PineappleCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Ananas comosus

Protein Sequence Source:

Phytozome v12: Acomosus_321_v3.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

PineappleCyc

Content Statistics

Number of Pathways:

481

Number of Reactions:

3082

Number of Compounds:

2484

Number of Enzymes:

5511

Number of Citations:

4218

CamelinaCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Camelina sativa

Protein Sequence Source:

Ensembl: Camelina_sativa.Cs.pep.all.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

CamelinaCyc

Content Statistics

Number of Pathways:

415

Number of Reactions:

2715

Number of Compounds:

2263

Number of Enzymes:

4221

Number of Citations:

3697

SoleraceaCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Spinacia oleracea

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

SoleraceaCyc

Content Statistics

Number of Pathways:

528

Number of Reactions:

3451

Number of Compounds:

2782

Number of Enzymes:

5188

Number of Citations:

4733

CorkoakCyc 2.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Quercus suber

Protein Sequence Source:

NCBI: GCF_002906115.1_CorkOak1.0_protein.faa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

CorkoakCyc

Content Statistics

Number of Pathways:

542

Number of Reactions:

4191

Number of Compounds:

3438

Number of Enzymes:

15232

Number of Citations:

5112

TidestromiaCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Tidestromia suffruticosa oblongifolia

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

TidestromiaCyc

Content Statistics

Number of Pathways:

486

Number of Reactions:

3106

Number of Compounds:

2503

Number of Enzymes:

8497

Number of Citations:

4235

Fvesca_vescaCyc 5.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Fragaria vesca

Protein Sequence Source:

Phytozome v13: Fvesca_677_v4.0.a2.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

Fvesca_vescaCyc

Content Statistics

Number of Pathways:

517

Number of Reactions:

3368

Number of Compounds:

2726

Number of Enzymes:

14504

Number of Citations:

4525

MbalbisianaCyc 2.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Musa balbisiana

Protein Sequence Source:

Banana Genome Hub: PKW_pep.faa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

MbalbisianaCyc

Content Statistics

Number of Pathways:

492

Number of Reactions:

3074

Number of Compounds:

2470

Number of Enzymes:

6932

Number of Citations:

4268

Oeuropaea_sylvestrisCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Olea europaea

Protein Sequence Source:

Phytozome v12: Oeuropaea_451_v1.0.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

507

Number of Reactions:

3320

Number of Compounds:

2687

Number of Enzymes:

8601

Number of Citations:

4472

AppleRingAcaciaCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Faidherbia albida

Protein Sequence Source:

GigaDB: Faidherbia_albida.pep

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

AppleRingAcaciaCyc

Content Statistics

Number of Pathways:

367

Number of Reactions:

2071

Number of Compounds:

1771

Number of Enzymes:

1410

Number of Citations:

3125

PocketWaterLilyCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Nymphaea colorata

Protein Sequence Source:

Phytozome 13: ?Ncolorata_566_v1.2.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

PocketWaterLilyCyc

Content Statistics

Number of Pathways:

320

Number of Reactions:

1858

Number of Compounds:

1581

Number of Enzymes:

2195

Number of Citations:

2778

CannuumCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Capsicum annuum

Protein Sequence Source:

SGN: Pepper.v.1.55.PEP.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

568

Number of Reactions:

3730

Number of Compounds:

3100

Number of Enzymes:

8134

Number of Citations:

5081

SorghumbicolorCyc 8.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Sorghum bicolor

Protein Sequence Source:

Phytozome v12: Sbicolor_454_v3.1.1.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

511

Number of Reactions:

3319

Number of Compounds:

2695

Number of Enzymes:

9869

Number of Citations:

4516

CroseusCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Catharanthus roseus

Protein Sequence Source:

Medicinal Plant Genomics Resource: cro_ap_asm_v2.proteins.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

CroseusCyc

Content Statistics

Number of Pathways:

515

Number of Reactions:

3318

Number of Compounds:

2702

Number of Enzymes:

5411

Number of Citations:

4499

TomatoCyc 7.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Solanum lycopersicum

Protein Sequence Source:

SGN: ITAG4.1_proteins.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

562

Number of Reactions:

3546

Number of Compounds:

2870

Number of Enzymes:

7671

Number of Citations:

4880

GamNuiCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Gnetum montanum

Protein Sequence Source:

Data Dryad: Gmm.final.pep

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

GamNuiCyc

Content Statistics

Number of Pathways:

331

Number of Reactions:

1900

Number of Compounds:

1693

Number of Enzymes:

1582

Number of Citations:

2784

McommodaCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Micromonas commoda

Protein Sequence Source:

Phytozome v12: MspRCC299_229_v3.0.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

McommodaCyc

Content Statistics

Number of Pathways:

325

Number of Reactions:

2300

Number of Compounds:

1865

Number of Enzymes:

2176

Number of Citations:

3118

AraCyc 18.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Arabidopsis thaliana col

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

AraCyc

Content Statistics

Number of Pathways:

618

Number of Reactions:

3837

Number of Compounds:

3080

Number of Enzymes:

10038

Number of Citations:

7656

OglaberrimaCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Oryza glaberrima

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

OglaberrimaCyc

Content Statistics

Number of Pathways:

494

Number of Reactions:

3162

Number of Compounds:

2537

Number of Enzymes:

6448

Number of Citations:

4263

ApunctatusCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Anthoceros punctatus

Protein Sequence Source:

Hornwort genomes: Apunct_genome_PROT.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

ApunctatusCyc

Content Statistics

Number of Pathways:

305

Number of Reactions:

1755

Number of Compounds:

1502

Number of Enzymes:

1451

Number of Citations:

2528

PoplarCyc 14.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Populus trichocarpa

Protein Sequence Source:

Phytozome v13:Ptrichocarpa_533_v4.1.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

524

Number of Reactions:

3367

Number of Compounds:

2703

Number of Enzymes:

12053

Number of Citations:

4697

Carietinum_icc4958Cyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Cicer arietinum

Protein Sequence Source:

CSFL: Ca_Pep_v2.fasta.txt

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

Carietinum_icc4958Cyc

Content Statistics

Number of Pathways:

513

Number of Reactions:

3469

Number of Compounds:

2752

Number of Enzymes:

6518

Number of Citations:

4527

SpennelliiCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Solanum pennellii

Protein Sequence Source:

SGN: Spenn-v2-aa-annot.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

559

Number of Reactions:

3714

Number of Compounds:

2986

Number of Enzymes:

7953

Number of Citations:

4830

CrubellaCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Capsella rubella

Protein Sequence Source:

Phytozome v12: Crubella_183_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

CrubellaCyc

Content Statistics

Number of Pathways:

498

Number of Reactions:

3227

Number of Compounds:

2552

Number of Enzymes:

6486

Number of Citations:

4193

TparvulaCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Schrenkiella parvula

Protein Sequence Source:

Thellungiella.org: TpV84ORFs.protein

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

TparvulaCyc

Content Statistics

Number of Pathways:

522

Number of Reactions:

3546

Number of Compounds:

2841

Number of Enzymes:

5839

Number of Citations:

4459

GarlicCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Allium sativum

Protein Sequence Source:

Figshare: Garlic.pep

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

GarlicCyc

Content Statistics

Number of Pathways:

388

Number of Reactions:

2341

Number of Compounds:

2028

Number of Enzymes:

2833

Number of Citations:

3338

MdomesticaCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Malus domestica

Protein Sequence Source:

Phytozome v12: Mdomestica_196_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

MdomesticaCyc

Content Statistics

Number of Pathways:

524

Number of Reactions:

3485

Number of Compounds:

2814

Number of Enzymes:

10667

Number of Citations:

4591

ChlamyCyc 11.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Chlamydomonas reinhardtii

Protein Sequence Source:

Phytozome v13: CreinhardtiiCC_4532_707_v6.1.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

Enzyme Evidence:

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

Pathway Prediction Program:

Pathway Tools 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

375

Number of Reactions:

2854

Number of Compounds:

2081

Number of Enzymes:

6633

Number of Citations:

4270

OilpalmCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Elaeis guineensis

Protein Sequence Source:

Plaza Monocots 5.0: proteome.all_transcripts.egu.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

OilpalmCyc

Content Statistics

Number of Pathways:

467

Number of Reactions:

3041

Number of Compounds:

2440

Number of Enzymes:

6222

Number of Citations:

4127

AsparagusCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Asparagus officinalis

Protein Sequence Source:

Phytozome v12: Aofficinalis_498_V1.1.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

494

Number of Reactions:

3230

Number of Compounds:

2651

Number of Enzymes:

5732

Number of Citations:

4324

PotatoCyc 8.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Solanum tuberosum

Protein Sequence Source:

Phytozome v13:Stuberosum_686_v6.1.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

561

Number of Reactions:

3591

Number of Compounds:

2906

Number of Enzymes:

11678

Number of Citations:

5060

CarnationCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Dianthus caryophyllus

Protein Sequence Source:

Kazusa Genome Database: DCA_r1.0_pep_woTE.faa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

510

Number of Reactions:

3286

Number of Compounds:

2702

Number of Enzymes:

7737

Number of Citations:

4428

SpiderflowerCyc 2.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Tarenaya hassleriana

Protein Sequence Source:

NCBI: GCF_000463585.1_ASM46358v1_protein.faa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

SpiderflowerCyc

Content Statistics

Number of Pathways:

499

Number of Reactions:

3251

Number of Compounds:

2604

Number of Enzymes:

9087

Number of Citations:

4216

Csativa_pkCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Cannabis sativa

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

Csativa_pkCyc

Content Statistics

Number of Pathways:

511

Number of Reactions:

3347

Number of Compounds:

2682

Number of Enzymes:

5790

Number of Citations:

4406

VcarteriCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Volvox carteri

Protein Sequence Source:

Phytozome v12: Vcarteri_317_v2.1.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

VcarteriCyc

Content Statistics

Number of Pathways:

358

Number of Reactions:

2732

Number of Compounds:

2115

Number of Enzymes:

3117

Number of Citations:

3442

GinkgoCyc 2.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Ginkgo biloba

Protein Sequence Source:

GIGA DB: Ginkgo_biloba.HiC.protein.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

GinkgoCyc

Content Statistics

Number of Pathways:

468

Number of Reactions:

3160

Number of Compounds:

2554

Number of Enzymes:

7282

Number of Citations:

4108

MexicanAvocadoCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Persea americana drymifolia

Protein Sequence Source:

CoGe: 29305-CDS-prot.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

MexicanAvocadoCyc

Content Statistics

Number of Pathways:

328

Number of Reactions:

1898

Number of Compounds:

1662

Number of Enzymes:

1115

Number of Citations:

2745

CornCyc 12.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Zea mays mays

Protein Sequence Source:

EnsemblPlants v55: Zea_mays.Zm-B73-REFERENCE-NAM-5.0.pep.all.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

512

Number of Reactions:

3475

Number of Compounds:

2769

Number of Enzymes:

16347

Number of Citations:

5238

OilseedrapeCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Brassica napus

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

OilseedrapeCyc

Content Statistics

Number of Pathways:

522

Number of Reactions:

3487

Number of Compounds:

2801

Number of Enzymes:

20946

Number of Citations:

4517

BambaraBeanCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Vigna subterranea

Protein Sequence Source:

GigaDB: vigna_subterranea.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

BambaraBeanCyc

Content Statistics

Number of Pathways:

361

Number of Reactions:

2074

Number of Compounds:

1771

Number of Enzymes:

1400

Number of Citations:

3083

PpersicaCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Prunus persica

Protein Sequence Source:

Phytozome v12: Ppersica_298_v2.1.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

PpersicaCyc

Content Statistics

Number of Pathways:

514

Number of Reactions:

3299

Number of Compounds:

2657

Number of Enzymes:

11142

Number of Citations:

4424

CarrotCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Daucus carota

Protein Sequence Source:

Phytozome v12: Dcarota_388_v2.0.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

CarrotCyc

Content Statistics

Number of Pathways:

497

Number of Reactions:

3233

Number of Compounds:

2617

Number of Enzymes:

7166

Number of Citations:

4412

SpirodelaCyc 6.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Spirodela polyrhiza

Protein Sequence Source:

Phytozome v12: Spolyrhiza_290_v2.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

469

Number of Reactions:

2883

Number of Compounds:

2304

Number of Enzymes:

4179

Number of Citations:

3976

CsubellipsoideaCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Coccomyxa subellipsoidea C-169

Protein Sequence Source:

Phytozome v12: CsubellipsoideaC_169_227_v2.0.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

CsubellipsoideaCyc

Content Statistics

Number of Pathways:

339

Number of Reactions:

2489

Number of Compounds:

1971

Number of Enzymes:

2373

Number of Citations:

3357

WatermelonCyc 2.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Citrullus lanatus

Protein Sequence Source:

CuGenDB: WCG_protein_v2.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

WatermelonCyc

Content Statistics

Number of Pathways:

486

Number of Reactions:

3108

Number of Compounds:

2546

Number of Enzymes:

4786

Number of Citations:

4283

GraimondiiCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Gossypium raimondii

Protein Sequence Source:

Phytozome v12: Graimondii_221_v2.1.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

GraimondiiCyc

Content Statistics

Number of Pathways:

506

Number of Reactions:

3398

Number of Compounds:

2765

Number of Enzymes:

18360

Number of Citations:

4482

MguttatusCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Erythranthe guttata

Protein Sequence Source:

Phytozome v12: Mguttatus_256_v2.0.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

MguttatusCyc

Content Statistics

Number of Pathways:

496

Number of Reactions:

3247

Number of Compounds:

2665

Number of Enzymes:

7676

Number of Citations:

4363

SoyCyc 11.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Glycine max

Protein Sequence Source:

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

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

546

Number of Reactions:

3543

Number of Compounds:

2803

Number of Enzymes:

19410

Number of Citations:

5381

OlongistaminataCyc 2.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Oryza longistaminata

Protein Sequence Source:

Ensembl: Oryza_longistaminata.O_longistaminata_v1.0.pep.all.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

OlongistaminataCyc

Content Statistics

Number of Pathways:

511

Number of Reactions:

3274

Number of Compounds:

2697

Number of Enzymes:

6950

Number of Citations:

4441

BananaCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Musa acuminata

Protein Sequence Source:

Phytozome v12: Macuminata_304_v1.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

BananaCyc

Content Statistics

Number of Pathways:

500

Number of Reactions:

3159

Number of Compounds:

2539

Number of Enzymes:

9872

Number of Citations:

4325

QuinoaCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Chenopodium quinoa

Protein Sequence Source:

Phytozome v12: Cquinoa_392_v1.0.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

524

Number of Reactions:

3335

Number of Compounds:

2683

Number of Enzymes:

10520

Number of Citations:

4496

CashewCyc 3.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Anacardium occidentale

Protein Sequence Source:

Phytozome v12: Aoccidentale_449_v0.9.protein_primaryTranscriptOnly.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

518

Number of Reactions:

3414

Number of Compounds:

2757

Number of Enzymes:

19150

Number of Citations:

4571

StoraCyc 2.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Senna tora

Protein Sequence Source:

NABIC: SETOT.complete.protein.20191226.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

StoraCyc

Content Statistics

Number of Pathways:

345

Number of Reactions:

1961

Number of Compounds:

1696

Number of Enzymes:

1356

Number of Citations:

2982

CucumberCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Cucumis sativus

Protein Sequence Source:

Phytozome v12: Csativus_122_v1.0.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

CucumberCyc

Content Statistics

Number of Pathways:

495

Number of Reactions:

3142

Number of Compounds:

2534

Number of Enzymes:

7228

Number of Citations:

4344

WatermossCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Salvinia cucullata

Protein Sequence Source:

FernBase: Salvinia_cucullata.protein.highconfidence_v1.2.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

WatermossCyc

Content Statistics

Number of Pathways:

301

Number of Reactions:

1642

Number of Compounds:

1396

Number of Enzymes:

760

Number of Citations:

2447

GrapeCyc 11.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Vitis vinifera

Protein Sequence Source:

Ensembl Plants v54:Vitis_vinifera.PN40024.v4.pep.all.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

535

Number of Reactions:

3471

Number of Compounds:

2834

Number of Enzymes:

9360

Number of Citations:

4753

MoringaCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Moringa oleifera

Protein Sequence Source:

GigaDB: moringa_oleifera.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

MoringaCyc

Content Statistics

Number of Pathways:

312

Number of Reactions:

1805

Number of Compounds:

1600

Number of Enzymes:

887

Number of Citations:

2576

OryzaCyc 8.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Oryza sativa Japonica Group

Protein Sequence Source:

Phytozome v12: Osativa_323_v7.0.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

524

Number of Reactions:

3439

Number of Compounds:

2736

Number of Enzymes:

8338

Number of Citations:

5305

OlucimarinusCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Ostreococcus sp. lucimarinus

Protein Sequence Source:

Phytozome v12: Olucimarinus_231_v2.0.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

OlucimarinusCyc

Content Statistics

Number of Pathways:

312

Number of Reactions:

2119

Number of Compounds:

1743

Number of Enzymes:

1797

Number of Citations:

3017

BarleyCyc 9.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Hordeum vulgare

Protein Sequence Source:

EnsemblPlants v55: Hordeum_vulgare.MorexV3_pseudomolecules_assembly.pep.all.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

493

Number of Reactions:

3092

Number of Compounds:

2519

Number of Enzymes:

7893

Number of Citations:

4373

RchinensisCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Rosa chinensis

Protein Sequence Source:

Genome Database for Rosaceae: Rosa_chinensis_Old_Blush_homozygous_genome-v2.0.a1.prot.faa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

523

Number of Reactions:

3442

Number of Compounds:

2811

Number of Enzymes:

9617

Number of Citations:

4533

CassavaCyc 11.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Manihot esculenta

Protein Sequence Source:

Phytozome v13:Mesculenta_671_v8.1.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

519

Number of Reactions:

3364

Number of Compounds:

2718

Number of Enzymes:

13522

Number of Citations:

4528

CastorbeanCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Ricinus communis

Protein Sequence Source:

Phytozome v12: Rcommunis_119_v0.1.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

CastorbeanCyc

Content Statistics

Number of Pathways:

532

Number of Reactions:

4034

Number of Compounds:

3254

Number of Enzymes:

6978

Number of Citations:

4998

StrawberryCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Fragaria x ananassa

Protein Sequence Source:

GDR: Fragaria_ananassa_v1.0.a2.proteins.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

StrawberryCyc

Content Statistics

Number of Pathways:

357

Number of Reactions:

2166

Number of Compounds:

1909

Number of Enzymes:

5344

Number of Citations:

3218

CvariabilisCyc 2.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Chlorella variabilis

Protein Sequence Source:

JGI: Chlorella_NC64A.fix_proteins.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

CvariabilisCyc

Content Statistics

Number of Pathways:

356

Number of Reactions:

2662

Number of Compounds:

2090

Number of Enzymes:

17711

Number of Citations:

3496

WheataCyc 7.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Triticum urartu

Protein Sequence Source:

EnsemblPlants v54: Triticum_urartu.IGDB.pep.all.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

495

Number of Reactions:

3312

Number of Compounds:

2695

Number of Enzymes:

11450

Number of Citations:

4440

HaasAvocadoCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Persea americana americana

Protein Sequence Source:

CoGe: 29302-CDS-prot.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

HaasAvocadoCyc

Content Statistics

Number of Pathways:

318

Number of Reactions:

1839

Number of Compounds:

1581

Number of Enzymes:

1155

Number of Citations:

2680

MosobambooCyc 2.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Phyllostachys edulis

Protein Sequence Source:

GIGA DB: Bamboo.Hic.pep.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

MosobambooCyc

Content Statistics

Number of Pathways:

520

Number of Reactions:

3338

Number of Compounds:

2724

Number of Enzymes:

12479

Number of Citations:

4521

Aagrestis_BonnCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Anthoceros agrestis

Protein Sequence Source:

Hornwort genomes: AagrBONN_genome_PROT.fasta

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

Aagrestis_BonnCyc

Content Statistics

Number of Pathways:

309

Number of Reactions:

1802

Number of Compounds:

1579

Number of Enzymes:

1809

Number of Citations:

2652

OmeridionalisCyc 2.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Oryza meridionalis

Protein Sequence Source:

Ensembl: Oryza_meridionalis.Oryza_meridionalis_v1.3.pep.all.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

OmeridionalisCyc

Content Statistics

Number of Pathways:

482

Number of Reactions:

3119

Number of Compounds:

2595

Number of Enzymes:

8563

Number of Citations:

4305

BlackPepperCyc 1.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Piper nigrum

Protein Sequence Source:

Group of Cotton Genetic Improvement: Piper_nigrum.pep

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

BlackPepperCyc

Content Statistics

Number of Pathways:

370

Number of Reactions:

2089

Number of Compounds:

1829

Number of Enzymes:

2380

Number of Citations:

3108

RedcloverCyc 4.0.0

Parent

Overview

Released:

PMN 16 (July 2024)

Taxonomic Range:

Trifolium pratense

Protein Sequence Source:

Phytozome v12: Tpratense_385_v2.protein.fa

Enzyme Functional Annotation Method:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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:

RedcloverCyc

Content Statistics

Number of Pathways:

575

Number of Reactions:

3796

Number of Compounds:

3040

Number of Enzymes:

9072

Number of Citations:

4923

PlantCyc 16.0.0

Parent

Overview

Released:

PMN 16.0 (July 2024)

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:

E2P2v5.0

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 28.0

SAVI pathway validation lists:

MCP 2.0
AIPP 7.0
CAPP 7.0
CVP 7.0
NPP 10.0
UPP 10.0

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

Number of Pathways:

1162

Number of Reactions:

5477

Number of Compounds:

4906

Number of Enzymes:

4549

Number of Citations:

11885