PlantSME Plant secondary metabolism enzyme database

Rubus idaeus (rubus_idaeus)

Imported from atlas release summary for Rubus idaeus.

2016
Candidate Protein Records
1792
Pathway-Level Records
4497
Family-Level Calls
Phylogenetic Position
The current species is positioned within the lineage framework used by this site. Its taxon group is highlighted below.
Algae
Site group 29
Bryophytes
Site group 125
Lycophytes/Ferns
Site group 4
Gymnosperms
Site group 6
Basal angiosperms
Site group 13
Monocots
Site group 117
Eudicots
Current group 495
Species Metadata
Taxon group
Eudicots
Genome status
Genome-level resource available
Site Placement
  • This page summarizes pathway coverage, family distributions, and protein/isoform records for the species within the current public dataset.
  • If you want to start from the public overview first, open the homepage and then return here for species-level drill-down.
  • Family statistics correspond to enzyme families, while pathway statistics correspond to the real category-level pathways.
  • Download candidate protein FASTA for this species
Pathway Coverage
Terpenoid pathway 28.68% Alkaloid pathway 22.88% Phenylpropanoid pathway 18.3% Flavonoid pathway 14.4% Rosmarinic acid pathway 9.99% Steroid pathway 5.75%
Family Distribution
C4H 6.36% C3'H/CYP98A 6.14% BAHD 5.09% UGT 4.76% 7DLGT 4.56% UFGT 4.4% IFS 4.16% CYP76 3.58%
Other Families 60.95%
More Families (97)
T3O 159 3.54% 4CL 150 3.34% F3H 130 2.89% POD 129 2.87% CAD 102 2.27% DWF4/CYP90B1 93 2.07% BR6OX2/CYP85A2 89 1.98% NMT 83 1.85% CODM/T6ODM 78 1.73% H6H 73 1.62% STR 72 1.6% F3'H/CYP75B 72 1.6% CYP90D1 65 1.45% CAS 62 1.38% TPS 62 1.38% GS 60 1.33% GES 60 1.33% LAC 58 1.29% HCT 57 1.27% CYP71 54 1.2% SMT1/SMT2/SMT3 47 1.05% 7DLH 45 1.0% TRI/TRII 45 1.0% RAS 41 0.91% CSE 40 0.89% PMT 38 0.85% F3'5'H/CYP75A 38 0.85% SGD 36 0.8% TAT 36 0.8% IO 30 0.67% IFR 30 0.67% CCR 30 0.67% T16H 27 0.6% COMT 27 0.6% PYKS 25 0.56% G8O/G8H 25 0.56% BBE 25 0.56% SLS 24 0.53% F5H/CYP84A 22 0.49% DFR 21 0.47% NCS 20 0.44% LAMT 19 0.42% ANR 19 0.42% CNMT 16 0.36% ANS/LDOX 16 0.36% BR6OX1/CYP85A1 15 0.33% CYP51G1 15 0.33% COR 14 0.31% FNS 14 0.31% CPD/CYP90A1 14 0.31% 16OMT 13 0.29% ROT3/CYP90C1 13 0.29% 8HGO 11 0.24% CCoAOMT 11 0.24% SQE 9 0.2% HMGR 9 0.2% ISY 8 0.18% MPO 8 0.18% HPPR 8 0.18% ODC 7 0.16% CHS 7 0.16% SMO1/SMO2 7 0.16% CYP80B1 6 0.13% TYDC_DDC 6 0.13% CYP719 6 0.13% PAL 6 0.13% CPR 6 0.13% FPPS 6 0.13% CMK/IspE 6 0.13% SQS/FDFT1 5 0.11% DET2 5 0.11% AACT 5 0.11% GGPPS 5 0.11% DXS 5 0.11% FLS 4 0.09% MVK 4 0.09% MVD 3 0.07% HMGS 3 0.07% HDR/IspH 3 0.07% XMT_MXMT_DXMT 2 0.04% CHI 2 0.04% DWF1 2 0.04% DWF7 2 0.04% GPPS 2 0.04% MCT/IspD 2 0.04% CYP80F1 1 0.02% ADC 1 0.02% TDC 1 0.02% HYD1 1 0.02% FK 1 0.02% DWF5 1 0.02% CPI1 1 0.02% HDS/IspG 1 0.02% IDI 1 0.02% DXR 1 0.02% MDS/IspF 1 0.02% PMK 1 0.02%
Species Pathway Results
The links below show identification results for this species within each pathway, instead of opening the global pathway overview.
Pathway Pathway-Level Records Detected Families Top family Results
Terpenoid pathway 514 20 UGT (191) View species results
Alkaloid pathway 410 20 7DLGT (109) View species results
Phenylpropanoid pathway 328 12 POD (111) View species results
Flavonoid pathway 258 11 UFGT (185) View species results
Rosmarinic acid pathway 179 7 C4H (72) View species results
Steroid pathway 103 13 CAS (45) View species results
Broad Catalytic Groups
P450/oxygenase and BAHD/acyltransferase are counted separately as broad catalytic groups and are not mixed into the canonical enzyme-family count.
Catalytic group Detected families Assignment calls Included families
P450/oxygenase 24 1723 7DLH, BR6OX1/CYP85A1, BR6OX2/CYP85A2, C3'H/CYP98A, C4H, CPD/CYP90A1, CYP51G1, CYP71, CYP719, CYP76, CYP80B1, CYP80F1, CYP90D1, DWF4/CYP90B1, F3'5'H/CYP75A, F3'H/CYP75B, F5H/CYP84A, G8O/G8H, IFS, IO, ROT3/CYP90C1, SLS, T16H, T3O
BAHD/acyltransferase 3 327 BAHD, HCT, RAS
Identification Result List
Search the public protein/isoform identification results for this species; click pathway or family legends above to narrow within this species.
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Protein/Isoform Record Pathway Family Confidence Status
rubus_idaeus_g6381.t1 Alkaloid 7DLGT low borderline
rubus_idaeus_g6450.t1 Alkaloid 7DLGT medium pass
rubus_idaeus_g676.t1 Alkaloid 7DLGT low borderline
rubus_idaeus_g7405.t1 Alkaloid 7DLGT low borderline
rubus_idaeus_g8199.t1 Alkaloid 7DLGT low borderline