From 4b6b6f3f68b58a2add01ffb3ed8a93535464a8f0 Mon Sep 17 00:00:00 2001 From: jo Date: Wed, 22 Mar 2023 19:20:02 +0100 Subject: [PATCH] added ardinine degradation to custom pathways - identical to metacyc pathway ARGDEGRAD-PWY that is classified as superpathway (which are usually not considered) - without the pathway arginine deaminas 3.5.3.6 is not added if no in stickland pathways are found - thanks to Anna Burrichter for reporting the issue --- dat/custom_pwy.tbl | 1 + 1 file changed, 1 insertion(+) diff --git a/dat/custom_pwy.tbl b/dat/custom_pwy.tbl index 767590e0..c67d245e 100644 --- a/dat/custom_pwy.tbl +++ b/dat/custom_pwy.tbl @@ -48,3 +48,4 @@ THRBIOSYN-GS Threonine biosynthis from aspartate via homoserine (gapseq) L-threo ISOBILE-BIOSYN iso-bile acids biosynthesis (NADH or NADPH dependent) iso-bile acids biosynthesis (NADH or NADPH dependent) |Fatty-Acid-and-Lipid-Degradation|,|Steroids-Degradation|,|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Degradation|,|CARBOXYLATES-DEG|,|Bile-Acids-Degradation| |TAX-2| 3alpha-HSDH,3beta-HSDH , 3alpha-hydroxysteroid dehydrogenase;3beta-hydroxysteroid dehydrogenase False True |ARGDEGRAD-PWY2| L-arginine degradation V (arginine deiminase pathway) L-arginine degradation V (arginine deiminase pathway),L-arginine dihydrolase pathway,L-arginine deiminase degradation |THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Degradation|,|Amino-Acid-Degradation|,|Proteinogenic-Amino-Acids-Degradation|,|ARGININE-DEG| |TAX-2157|,|TAX-2759|,|TAX-2| ORNCARBAMTRANSFER-RXN,RXN-14196,RXN0-5222,ARGININE-DEIMINASE-RXN 2.1.3.3,2.7.2.2,,3.5.3.6 ORNCARBAMTRANSFER-RXN ornithine carbamoyltransferase, catabolic;carbamate kinase;cyanase;arginine deiminase 4 2 False True RXN0-5222 |PWY-8017-2| L-tryptophan degradation XIII (reductive Stickland reaction) L-tryptophan degradation XIII (reductive Stickland reaction),L-tryptophan reductive fermentation,L-tryptophan fermentation |Degradation|,|Amino-Acid-Degradation|,|Proteinogenic-Amino-Acids-Degradation|,|TRYPTOPHAN-DEG|,|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Energy-Metabolism|,|Fermentation|,|Amino-Acid-Fermentation|,|Stickland-Reductive| |TAX-2| RXN-19885,INDOLELACTATE-DEHYDROGENASE-RXN,TRYPTOPHAN-AMINOTRANSFERASE-RXN,RXN-19895,RXN-19896 1.3.8.15,1.1.1.110,2.6.1.1/2.6.1.27,2.8.3.17,4.2.1.175 (indolyl)propenoate reducatse;indole-3-pyruvate reductase;L-tryptophan transaminase;(indol-3-yl)-acryloyl-CoA:(indol-3-yl)-(R)-lactate CoA-transferase;(indol-3-yl)-(R)-lactoyl-CoA dehydratase False True +|ARGDEGRAD-PWY2| L-arginine degradation V (arginine deiminase pathway) L-arginine degradation V (arginine deiminase pathway),L-arginine dihydrolase pathway,L-arginine deiminase degradation |Super-Pathways|,|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Degradation|,|Amino-Acid-Degradation|,|Proteinogenic-Amino-Acids-Degradation|,|ARGININE-DEG| |TAX-2157|,|TAX-2759|,|TAX-2| ORNCARBAMTRANSFER-RXN,RXN-14196,RXN0-5222,ARGININE-DEIMINASE-RXN 2.1.3.3,,,3.5.3.6 ORNCARBAMTRANSFER-RXN ornithine carbamoyltransferase, catabolic;carbamate kinase;cyanase;arginine deiminase 4 2 False True RXN0-5222