Databases

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Michigan State University  

The PMN is funded by the National Science Foundation (Grant #: 2312181, 1546838, 1026003 and 0640769) and the Department of Energy (BER Grant #:  ER65472), governed by an Editorial Board composed of internationally renowned scientists, and executed at Michigan State University's Department of Biochemistry & Molecular Biology and the Plant Resilience Institute