PhytoClust
A Tool to Detect Plant Metabolic Gene Clusters
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Choose a genome to search for metabolic gene clusters:
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Arabidopsis_lyrata.v.1.0.31
Arabidopsis_thaliana.TAIR10.31 (Co-Expression available)
Brachypodium_distachyon.v1.0.31
Brassica_oleracea.v2.1.31
Brassica_rapa.IVFCAASv1.31
Chlamydomonas_reinhardtii.v3.1.31
Cyanidioschyzon_merolae.ASM9120v1.31
Leersia_perrieri.Lperr_V1.4.31
Lotus_japonicus
Medicago_truncatula.MedtrA17_4.0.31
Musa_acuminata.MA1.31
Oryza_barthii.O.barthii_v1.31
Oryza_brachyantha.Oryza_brachyantha.v1.4b.31
Oryza_glaberrima.AGI1.1.31
Oryza_glumaepatula.ALNU02000000.31
Oryza_meridionalis.Oryza_meridionalis_v1.3.31
Oryza_nivara.AWHD00000000.31
Oryza_punctata.AVCL00000000.31
Oryza_rufipogon.OR_W1943.31
Oryza_sativa.IRGSP-1.0.31 (Co-Expression available)
Ostreococcus_lucimarinus.ASM9206v1.31
Physcomitrella_patens.ASM242v1.31
Populus_trichocarpa.JGI2.0.31
Prunus_persica.Prupe1_0.31
Selaginella_moellendorffii.v1.0.31
Setaria_italica.JGIv2.0.31
Solanum_lycopersicum.SL2.50.31 (Co-Expression available)
Solanum_tuberosum.SolTub_3.0.31 (Co-Expression available)
Theobroma_cacao.Theobroma_cacao_20110822.31
Vitis_vinifera.IGGP_12x.31
Zea_mays.AGPv3.31
or upload your own genome sequence (
FASTA
,
EMBL
or
GBK
):
Use last uploaded File
Search for known gene clusters
Create your own gene cluster rule (combine up to 4 secondary metabolism enzymes families)
Enzyme 1:
--select enzyme--
2-Isopropylmalate synthase (2Isopropylmalate S)
2-Oxoglutarate-dependent dioxygenase (2OG-dep Diox)
Acyl-activating enzymes/CoA ligase (AAE/CoA ligase)
Acyl transferase (Acyl TF)
Aldehyde dehydrogenase (Aldehyde DH)
BAHD (BEAT_AHCT_HCBT and DAT)
Carboxy methylesterase (Carboxy methylE)
Carboxylesterase (CarboxylE)
Cytochrome P450 (C p450)
Dehydrogenase/Reductase (DH/Reductase)
Dioxygenase (Diox)
Glucuronosyltransferase (Sugar transferase) (GlucuronosylTF)
Glutathione-S-transferase (GHS S TF)
Glycosyl transferase (Glycosyl TF)
Glycoside hydrolase family I (Glycosyl hydrolase fam 1)
Marneral synthase_Oxidosqualene cyclase_Prenyltransferase (Marneral S OSC Prenyl TF)
Methylene bridge-forming enzymes (MBE)
Methyltransferase (MethyTF)
NADPH-dependent dehydrogenase (NADPH dep DH)
Oxidoreductase (OxidoR)
Pathogenesis related lipase-like proteins (PRLIP)
Polyketide synthase (PKS)
Serine carboxy-peptidase like acyltransferase (SCPL) (SCP like acylTF)
Terpene synthase (TS)
Transaminase
Tryptophane synthase alpha homolog= Indole-3-glycerol phosphate lyase (Trp S alpha homolog)
Enzyme 2:
--select enzyme--
2-Isopropylmalate synthase (2Isopropylmalate S)
2-Oxoglutarate-dependent dioxygenase (2OG-dep Diox)
Acyl-activating enzymes/CoA ligase (AAE/CoA ligase)
Acyl transferase (Acyl TF)
Aldehyde dehydrogenase (Aldehyde DH)
BAHD (BEAT_AHCT_HCBT and DAT)
Carboxy methylesterase (Carboxy methylE)
Carboxylesterase (CarboxylE)
Cytochrome P450 (C p450)
Dehydrogenase/Reductase (DH/Reductase)
Dioxygenase (Diox)
Glucuronosyltransferase (Sugar transferase) (GlucuronosylTF)
Glutathione-S-transferase (GHS S TF)
Glycosyl transferase (Glycosyl TF)
Glycoside hydrolase family I (Glycosyl hydrolase fam 1)
Marneral synthase_Oxidosqualene cyclase_Prenyltransferase (Marneral S OSC Prenyl TF)
Methylene bridge-forming enzymes (MBE)
Methyltransferase (MethyTF)
NADPH-dependent dehydrogenase (NADPH dep DH)
Oxidoreductase (OxidoR)
Pathogenesis related lipase-like proteins (PRLIP)
Polyketide synthase (PKS)
Serine carboxy-peptidase like acyltransferase (SCPL) (SCP like acylTF)
Terpene synthase (TS)
Transaminase
Tryptophane synthase alpha homolog= Indole-3-glycerol phosphate lyase (Trp S alpha homolog)
Enzyme 3:
--select enzyme--
2-Isopropylmalate synthase (2Isopropylmalate S)
2-Oxoglutarate-dependent dioxygenase (2OG-dep Diox)
Acyl-activating enzymes/CoA ligase (AAE/CoA ligase)
Acyl transferase (Acyl TF)
Aldehyde dehydrogenase (Aldehyde DH)
BAHD (BEAT_AHCT_HCBT and DAT)
Carboxy methylesterase (Carboxy methylE)
Carboxylesterase (CarboxylE)
Cytochrome P450 (C p450)
Dehydrogenase/Reductase (DH/Reductase)
Dioxygenase (Diox)
Glucuronosyltransferase (Sugar transferase) (GlucuronosylTF)
Glutathione-S-transferase (GHS S TF)
Glycosyl transferase (Glycosyl TF)
Glycoside hydrolase family I (Glycosyl hydrolase fam 1)
Marneral synthase_Oxidosqualene cyclase_Prenyltransferase (Marneral S OSC Prenyl TF)
Methylene bridge-forming enzymes (MBE)
Methyltransferase (MethyTF)
NADPH-dependent dehydrogenase (NADPH dep DH)
Oxidoreductase (OxidoR)
Pathogenesis related lipase-like proteins (PRLIP)
Polyketide synthase (PKS)
Serine carboxy-peptidase like acyltransferase (SCPL) (SCP like acylTF)
Terpene synthase (TS)
Transaminase
Tryptophane synthase alpha homolog= Indole-3-glycerol phosphate lyase (Trp S alpha homolog)
Enzyme 4:
--select enzyme--
2-Isopropylmalate synthase (2Isopropylmalate S)
2-Oxoglutarate-dependent dioxygenase (2OG-dep Diox)
Acyl-activating enzymes/CoA ligase (AAE/CoA ligase)
Acyl transferase (Acyl TF)
Aldehyde dehydrogenase (Aldehyde DH)
BAHD (BEAT_AHCT_HCBT and DAT)
Carboxy methylesterase (Carboxy methylE)
Carboxylesterase (CarboxylE)
Cytochrome P450 (C p450)
Dehydrogenase/Reductase (DH/Reductase)
Dioxygenase (Diox)
Glucuronosyltransferase (Sugar transferase) (GlucuronosylTF)
Glutathione-S-transferase (GHS S TF)
Glycosyl transferase (Glycosyl TF)
Glycoside hydrolase family I (Glycosyl hydrolase fam 1)
Marneral synthase_Oxidosqualene cyclase_Prenyltransferase (Marneral S OSC Prenyl TF)
Methylene bridge-forming enzymes (MBE)
Methyltransferase (MethyTF)
NADPH-dependent dehydrogenase (NADPH dep DH)
Oxidoreductase (OxidoR)
Pathogenesis related lipase-like proteins (PRLIP)
Polyketide synthase (PKS)
Serine carboxy-peptidase like acyltransferase (SCPL) (SCP like acylTF)
Terpene synthase (TS)
Transaminase
Tryptophane synthase alpha homolog= Indole-3-glycerol phosphate lyase (Trp S alpha homolog)
Use default values for cluster range and flanking region
Cluster Range in kbp (range in which the respective enzymes are to be found)
Flanking Region in kbp (searched for additional secondary metabolism enzymes)
Perform Co-expression analysis
Correlation threshold
You will receive an email with a download link once your results are there. You can close the browser window in the meantime.
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Depending on the genome size the calculations might take between minutes to days.
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Task ID:
unfertig
