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executable file
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executable file
·17 lines (17 loc) · 6.59 KB
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,Pathway,Pathway_name,Step,Product,Metacyc,Author,EC,Enzyme_name,interpro_curated_id,pfam_curated_id,Gene_name,Uniprot_ids,interpro_curated,pfam_curated,Note_integration,Interpro_metacyc_link (automatic?),Pfam_metacyc_link,Interpro_pre,Pfam_pre,interpro_name_pre,Status_pre,Unnamed: 21,notes
15,7.0,L-glutamate degradation V (via hydroxyglutarate),1.0,Acetate,P162-PWY,"Pellegrini-Toole A, Caspi R",1.4.1.2,glutamate dehydrogenase (NAD-dependent),"IPR006095, IPR014362, PTHR11606",,gdhA,P28997,"IPR006095, IPR014362, PTHR11606 (hit more specific enzymes)",,,,,IPR014362,,Glutamate dehydrogenase,,,
16,7.0,L-glutamate degradation V (via hydroxyglutarate),2.0,Acetate,P162-PWY,"Pellegrini-Toole A, Caspi R",1.1.1.399,2-oxoglutarate reductase,,,,,,,,,,IPR006236,,D-3-phosphoglycerate dehydrogenase ,,,
17,7.0,L-glutamate degradation V (via hydroxyglutarate),3.0,Acetate,P162-PWY,"Pellegrini-Toole A, Caspi R",2.8.3.12,glutaconate CoA-transferase,"IPR004165, PTHR43293",PF01144,"Af-gctA, Af-gctB (subunit)","Q59111, Q59112","IPR004165, PTHR43293 (may contains some useful info)",PF01144,,IPR037171,PF01144,IPR004165,PF01144 ,Coenzyme A transferase family I ,checked,,
18,7.0,L-glutamate degradation V (via hydroxyglutarate),4.0,Acetate,P162-PWY,"Pellegrini-Toole A, Caspi R",4.2.1.167,active (R)-2-hydroxyglutaryl-CoA dehydratase,IPR010327,PF06050,"HgdA, HgdB (subunit)","P11569, P11570",IPR010327,PF06050,,IPR010327,PF06050,IPR010327,PF06050,FldB/FldC dehydratase alpha/beta subunit,,,
19,7.0,L-glutamate degradation V (via hydroxyglutarate),5.0,Acetate,P162-PWY,"Pellegrini-Toole A, Caspi R",7.2.4.5 (4.1.1.70),glutaconyl-CoA decarboxylase,"PTHR22855, IPR005661, PTHR45266, IPR005899",", PF03977, , PF04277","GcdA, GcdB, GcdC, GcdD (subunit)","Q06700, Q9ZAA6, Q9ZAA7, Q9ZAA8","PTHR22855, IPR005661, PTHR45266, IPR005899",", PF03977, , PF04277",,"IPR034733, IPR005661, IPR011053, IPR005899","PF01039, PF03977, PF00364, PF04277",IPR005661/IPR005899,PF03977 / PF04277,"Na+-transporting methylmalonyl-CoA/oxaloacetate decarboxylase, beta subunit / Sodium ion-translocating decarboxylase ",,,
20,7.0,L-glutamate degradation V (via hydroxyglutarate),6.0,Acetate,P162-PWY,"Pellegrini-Toole A, Caspi R",4.2.1.150,"3-hydroxybutyryl-CoA dehydratase, crotonase, 3-hydroxyacyl-CoA dehydrogenase FadJ, enoyl-CoA hydratase, fatty acid oxidation complex, α component ","IPR001753, IPR001753, IPR012802, , IPR012799","PF00378, PF00378, , , ,","crt, crt1, fadJ, ech, fadB","P52046, A5N5C7, P77399, , Q88L02 ","IPR001753, IPR001753, IPR012802, , IPR012799","PF00378, PF00378, , , ,",,"IPR001753, IPR014748, IPR018376, IPR029045; ",PF00378; ,IPR001753,PF00378 ,Enoyl-CoA hydratase/isomerase ,,,
21,7.0,L-glutamate degradation V (via hydroxyglutarate),7.0,Acetate,P162-PWY,"Pellegrini-Toole A, Caspi R",1.1.1.35,"3-hydroxybutyryl-CoA dehydrogenase, 3-hydroxyacyl-CoA dehydrogenase FadJ, (S)-3-hydroxybutanoyl-CoA dehydrogeanse, fatty acid oxidation complex, α component","IPR022694/PTHR43145, IPR012802, IPR022694, IPR012799",,"hbd, fadJ, mdpX, fadB","P52041, P77399, A2SP28, Q88L02","IPR022694/PTHR43145 (have more hits), IPR012802, IPR022694, IPR012799"," , , , ,",,"IPR006108, IPR006176, IPR006180, IPR008927, IPR013328, IPR022694, IPR036291","PF00725, PF02737",IPR012799,,"Fatty oxidation complex, alpha subunit FadB",checked,,
22,7.0,L-glutamate degradation V (via hydroxyglutarate),8.0,Acetate,P162-PWY,"Pellegrini-Toole A, Caspi R",2.3.1.9/2.3.1.16,acetyl-CoA C-acetyltransferase,IPR002155,,Entrez Gene ID 992613,"A2SL81, P45359 ",IPR002155,,,"IPR002155, IPR016039, IPR020610, IPR020615, IPR020616, IPR020617","PF00108, PF02803",IPR002155,,Thiolase,checked,,
23,7.0,L-glutamate degradation V (via hydroxyglutarate),9.0,Acetate,P162-PWY,"Pellegrini-Toole A, Caspi R",6.2.1.13,acetate-CoA ligase (ADP-forming),"PTHR43334, PF13549",PF13549,"acdA, acdB","E7FI45, E7FHP1","PTHR43334, PF13549",PF13549,,"IPR032875, IPR003781, IPR014089, IPR016102, IPR036291; IPR011761, IPR013815","PF13380, PF13607; PF08442",non_predicted,,,,,
25,7.0,L-glutamate degradation V (via hydroxyglutarate),1.0,Butanoate,P162-PWY,"Pellegrini-Toole A, Caspi R",1.4.1.2,glutamate dehydrogenase (NAD-dependent),"IPR006095, IPR014362, PTHR11606 ",,gdhA,P28997,"IPR006095, IPR014362, PTHR11606 (hit more specific enzymes)",,,,,IPR014362,,Glutamate dehydrogenase,,,
26,7.0,L-glutamate degradation V (via hydroxyglutarate),2.0,Butanoate,P162-PWY,"Pellegrini-Toole A, Caspi R",1.1.1.399,2-oxoglutarate reductase,,,,,,,,,,IPR006236,,D-3-phosphoglycerate dehydrogenase ,,,
27,7.0,L-glutamate degradation V (via hydroxyglutarate),3.0,Butanoate,P162-PWY,"Pellegrini-Toole A, Caspi R",2.8.3.12,glutaconate CoA-transferase,"IPR004165, PTHR43293",,"Af-gctA, Af-gctB (subunit)","Q59111, Q59112","IPR004165, PTHR43293 (may contain some useful info)",,,IPR037171,PF01144,IPR004165,PF01144 ,Coenzyme A transferase family I ,checked,,
28,7.0,L-glutamate degradation V (via hydroxyglutarate),4.0,Butanoate,P162-PWY,"Pellegrini-Toole A, Caspi R",4.2.1.167,active (R)-2-hydroxyglutaryl-CoA dehydratase,IPR010327,,"HgdA, HgdB (subunit)","P11569, P11570",IPR010327,,,IPR010327,PF06050,IPR010327,PF06050,FldB/FldC dehydratase alpha/beta subunit,,,
29,7.0,L-glutamate degradation V (via hydroxyglutarate),5.0,Butanoate,P162-PWY,"Pellegrini-Toole A, Caspi R",7.2.4.5 (4.1.1.70),glutaconyl-CoA decarboxylase,"PTHR22855, IPR005661, PTHR45266, IPR005899",", PF03977, , PF04277","GcdA, GcdB, GcdC, GcdD (subunit)","Q06700, Q9ZAA6, Q9ZAA7, Q9ZAA8","PTHR22855, IPR005661, PTHR45266, IPR005899",", PF03977, , PF04277",,"IPR034733, IPR005661, IPR011053, IPR005899","PF01039, PF03977, PF00364, PF04277",IPR005661/IPR005899,PF03977 / PF04277,"Na+-transporting methylmalonyl-CoA/oxaloacetate decarboxylase, beta subunit / Sodium ion-translocating decarboxylase ",,,
30,7.0,L-glutamate degradation V (via hydroxyglutarate),6.0,Butanoate,P162-PWY,"Pellegrini-Toole A, Caspi R",1.3.8.1,"butyryl-CoA dehydrogenase, acyl-CoA dehydrogenase",PIRSF016578,,"bcd, fadE","P52042, Q47146 ","PTHR43884, PTHR43835, PTHR43292 (added by another fadE protein from uniprot)",,1. which one to integrate,"IPR006089, IPR006091, IPR009075, IPR009100, IPR013786, IPR036250, IPR037069; IPR006091, IPR009075, IPR009100, IPR013786, IPR015396, IPR036250, IPR037069","PF00441, PF02770, PF02771; PF00441, PF02770, PF02771, PF09317",non_predicted,,,,,
31,7.0,L-glutamate degradation V (via hydroxyglutarate),7.0,Butanoate,P162-PWY,"Pellegrini-Toole A, Caspi R",2.8.3.1/2.8.3.8,propinoate CoA-transferase / acetate CoA-transferase ,IPR003702,PF02550,cat3,A5N390,IPR003702,PF02550,,"IPR003702, IPR026888, IPR037171, IPR038460","PF02550, PF13336",IPR014388/IPR004165,NA / PF01144,3-oxoacid CoA-transferase / Coenzyme A transferase family I ,? / checked,,