From 27a3cc7e5f28227009bdd7dbb6d3320719120628 Mon Sep 17 00:00:00 2001 From: Sven Thiele Date: Thu, 28 Apr 2022 06:22:47 +0200 Subject: [PATCH] Update Report example --- Report_example.md | 481 +++++++++++++++++++++++++++++----------------- 1 file changed, 303 insertions(+), 178 deletions(-) diff --git a/Report_example.md b/Report_example.md index d5cbb3d..39a721f 100644 --- a/Report_example.md +++ b/Report_example.md @@ -58,288 +58,413 @@ Targets file: Ectodata/targets.sbml Repair db file: Ectodata/metacyc_16-5.sbml 4 unreconstructable targets + CPD__45__13814 CPD__45__14292 - DOCOSANOATE CPD__45__8119 - CPD__45__13814 + DOCOSANOATE 47 reconstructable targets - SUC - OLEATE__45__CPD - TRP - CPD__45__8121 - MET + ARACHIDIC_ACID + ARACHIDONIC_ACID + ARG ASN - L__45__ORNITHINE - CPD__45__9247 + CIT CPD__45__7836 + CPD__45__8117 + CPD__45__8120 + CPD__45__8121 + CPD__45__9245 + CPD__45__9247 + CYS + D__45__ALANINE GLC - CIT - PHE + GLN + GLT + GLUTATHIONE + GLY GLYCERATE + GLYCEROL + GLYCOLLATE + HIS + HOMO__45__SER ILE - TYR - LYS - CYS - LINOLEIC_ACID - GLY LEU - ARACHIDIC_ACID - THR - ARG - CPD__45__8117 - HOMO__45__SER - GLYCEROL + LINOLEIC_ACID LINOLENIC_ACID - SER - _5Z8Z11Z14Z17Z__45__EICOSAPENTAENOATE - D__45__ALANINE - CPD__45__8120 - GLYCOLLATE + LYS L__45__ALPHA__45__ALANINE + L__45__ASPARTATE + L__45__ORNITHINE MANNITOL + MET + OLEATE__45__CPD PALMITATE - _4__45__AMINO__45__BUTYRATE - GLUTATHIONE - GLT - HIS - GLN - THREO__45__DS__45__ISO__45__CITRATE - ARACHIDONIC_ACID - VAL - CPD__45__9245 + PHE PRO - L__45__ASPARTATE + SER STEARIC_ACID + SUC + THR + THREO__45__DS__45__ISO__45__CITRATE + TRP + TYR + VAL + _4__45__AMINO__45__BUTYRATE + _5Z8Z11Z14Z17Z__45__EICOSAPENTAENOATE -0 essential reactions for target SUC +3 essential reactions for target ARACHIDIC_ACID + RXN__45__9520 + RXN__45__9655 + _4__46__2__46__1__46__59__45__RXN -5 essential reactions for target OLEATE__45__CPD - _3__46__1__46__2__46__14__45__RXN +11 essential reactions for target ARACHIDONIC_ACID + RXN__45__12777 + RXN__45__12968 + RXN__45__12969 + RXN__45__12971 + RXN__45__13435 + RXN__45__8346 + RXN__45__9520 + RXN__45__9655 _1__46__14__46__19__46__2__45__RXN + _3__46__1__46__2__46__14__45__RXN + _4__46__2__46__1__46__59__45__RXN + +0 essential reactions for target ARG + +0 essential reactions for target ASN + +0 essential reactions for target CIT + +6 essential reactions for target CPD__45__7836 + RXN__45__10727 + RXN__45__9520 + RXN__45__9533 + RXN__45__9537 RXN__45__9655 + _4__46__2__46__1__46__59__45__RXN + +5 essential reactions for target CPD__45__8117 RXN__45__9520 + RXN__45__9655 + _1__46__14__46__19__46__2__45__RXN + _3__46__1__46__2__46__14__45__RXN _4__46__2__46__1__46__59__45__RXN -0 essential reactions for target TRP +10 essential reactions for target CPD__45__8120 + RXN__45__12777 + RXN__45__12968 + RXN__45__12969 + RXN__45__12971 + RXN__45__13435 + RXN__45__9520 + RXN__45__9655 + _1__46__14__46__19__46__2__45__RXN + _3__46__1__46__2__46__14__45__RXN + _4__46__2__46__1__46__59__45__RXN 0 essential reactions for target CPD__45__8121 -0 essential reactions for target MET - -0 essential reactions for target ASN - -0 essential reactions for target L__45__ORNITHINE +4 essential reactions for target CPD__45__9245 + RXN__45__9520 + RXN__45__9550 + RXN__45__9655 + _4__46__2__46__1__46__59__45__RXN 6 essential reactions for target CPD__45__9247 - RXN__45__9655 RXN__45__9520 RXN__45__9555 - RXN__45__9558 RXN__45__9557 - _4__46__2__46__1__46__59__45__RXN - -6 essential reactions for target CPD__45__7836 - RXN__45__9537 - RXN__45__9533 - RXN__45__10727 + RXN__45__9558 RXN__45__9655 - RXN__45__9520 _4__46__2__46__1__46__59__45__RXN -0 essential reactions for target GLC +0 essential reactions for target CYS -0 essential reactions for target CIT +0 essential reactions for target D__45__ALANINE -0 essential reactions for target PHE +0 essential reactions for target GLC -0 essential reactions for target GLYCERATE +0 essential reactions for target GLN -0 essential reactions for target ILE +0 essential reactions for target GLT -0 essential reactions for target TYR +0 essential reactions for target GLUTATHIONE -0 essential reactions for target LYS +0 essential reactions for target GLY -0 essential reactions for target CYS +0 essential reactions for target GLYCERATE -5 essential reactions for target LINOLEIC_ACID - _3__46__1__46__2__46__14__45__RXN - _1__46__14__46__19__46__2__45__RXN - RXN__45__9655 - RXN__45__9520 - _4__46__2__46__1__46__59__45__RXN +0 essential reactions for target GLYCEROL -0 essential reactions for target GLY +0 essential reactions for target GLYCOLLATE -0 essential reactions for target LEU +2 essential reactions for target HIS + HISTCYCLOHYD__45__RXN + HISTIDPHOS__45__RXN -3 essential reactions for target ARACHIDIC_ACID - RXN__45__9655 - RXN__45__9520 - _4__46__2__46__1__46__59__45__RXN +0 essential reactions for target HOMO__45__SER -0 essential reactions for target THR +0 essential reactions for target ILE -0 essential reactions for target ARG +0 essential reactions for target LEU -5 essential reactions for target CPD__45__8117 - _3__46__1__46__2__46__14__45__RXN - _1__46__14__46__19__46__2__45__RXN - RXN__45__9655 +5 essential reactions for target LINOLEIC_ACID RXN__45__9520 + RXN__45__9655 + _1__46__14__46__19__46__2__45__RXN + _3__46__1__46__2__46__14__45__RXN _4__46__2__46__1__46__59__45__RXN -0 essential reactions for target HOMO__45__SER - -0 essential reactions for target GLYCEROL - 0 essential reactions for target LINOLENIC_ACID -0 essential reactions for target SER +0 essential reactions for target LYS -0 essential reactions for target _5Z8Z11Z14Z17Z__45__EICOSAPENTAENOATE +0 essential reactions for target L__45__ALPHA__45__ALANINE -0 essential reactions for target D__45__ALANINE +0 essential reactions for target L__45__ASPARTATE -10 essential reactions for target CPD__45__8120 - RXN__45__12971 - RXN__45__12968 - _3__46__1__46__2__46__14__45__RXN - RXN__45__12969 - _1__46__14__46__19__46__2__45__RXN - RXN__45__9655 - RXN__45__9520 - RXN__45__12777 - RXN__45__13435 - _4__46__2__46__1__46__59__45__RXN +0 essential reactions for target L__45__ORNITHINE -0 essential reactions for target GLYCOLLATE +0 essential reactions for target MANNITOL -0 essential reactions for target L__45__ALPHA__45__ALANINE +0 essential reactions for target MET -0 essential reactions for target MANNITOL +5 essential reactions for target OLEATE__45__CPD + RXN__45__9520 + RXN__45__9655 + _1__46__14__46__19__46__2__45__RXN + _3__46__1__46__2__46__14__45__RXN + _4__46__2__46__1__46__59__45__RXN 4 essential reactions for target PALMITATE - RXN__45__9655 RXN__45__9520 - _4__46__2__46__1__46__59__45__RXN RXN__45__9549 + RXN__45__9655 + _4__46__2__46__1__46__59__45__RXN -0 essential reactions for target _4__45__AMINO__45__BUTYRATE +0 essential reactions for target PHE -0 essential reactions for target GLUTATHIONE +0 essential reactions for target PRO -0 essential reactions for target GLT +0 essential reactions for target SER -2 essential reactions for target HIS - HISTIDPHOS__45__RXN - HISTCYCLOHYD__45__RXN +3 essential reactions for target STEARIC_ACID + RXN__45__9520 + RXN__45__9655 + _4__46__2__46__1__46__59__45__RXN -0 essential reactions for target GLN +0 essential reactions for target SUC -0 essential reactions for target THREO__45__DS__45__ISO__45__CITRATE +0 essential reactions for target THR -11 essential reactions for target ARACHIDONIC_ACID - RXN__45__12971 - RXN__45__12968 - _3__46__1__46__2__46__14__45__RXN - RXN__45__8346 - RXN__45__12969 - _1__46__14__46__19__46__2__45__RXN - RXN__45__9655 - RXN__45__9520 - RXN__45__12777 - RXN__45__13435 - _4__46__2__46__1__46__59__45__RXN +0 essential reactions for target THREO__45__DS__45__ISO__45__CITRATE -0 essential reactions for target VAL +0 essential reactions for target TRP -4 essential reactions for target CPD__45__9245 - RXN__45__9655 - RXN__45__9520 - _4__46__2__46__1__46__59__45__RXN - RXN__45__9550 +0 essential reactions for target TYR -0 essential reactions for target PRO +0 essential reactions for target VAL -0 essential reactions for target L__45__ASPARTATE +0 essential reactions for target _4__45__AMINO__45__BUTYRATE -3 essential reactions for target STEARIC_ACID - RXN__45__9655 - RXN__45__9520 - _4__46__2__46__1__46__59__45__RXN +0 essential reactions for target _5Z8Z11Z14Z17Z__45__EICOSAPENTAENOATE Overall 21 essential reactions found - RXN__45__9550 RXN__45__12968 - RXN__45__9533 - _3__46__1__46__2__46__14__45__RXN - RXN__45__8346 - RXN__45__12969 - RXN__45__9655 - RXN__45__9520 HISTCYCLOHYD__45__RXN - RXN__45__13435 - RXN__45__12971 - RXN__45__9537 _1__46__14__46__19__46__2__45__RXN - RXN__45__10727 - HISTIDPHOS__45__RXN + RXN__45__9655 + RXN__45__9533 + _4__46__2__46__1__46__59__45__RXN + RXN__45__13435 + RXN__45__12969 RXN__45__9555 + HISTIDPHOS__45__RXN + RXN__45__8346 + RXN__45__12777 + RXN__45__10727 + RXN__45__9550 RXN__45__9558 + _3__46__1__46__2__46__14__45__RXN + RXN__45__9520 RXN__45__9549 - RXN__45__12777 RXN__45__9557 - _4__46__2__46__1__46__59__45__RXN + RXN__45__12971 + RXN__45__9537 One minimal completion of size 48 + FATTY__45__ACYL__45__COA__45__SYNTHASE__45__RXN FORMYLMETHIONINE__45__DEFORMYLASE__45__RXN - _3__46__4__46__14__46__1__45__RXN - RXN__45__9550 - RXN__45__9533 - _3__46__1__46__2__46__14__45__RXN - RXN__45__8346 - RXN__45__12969 - RXN__45__9655 - SHIKIMATE__45__5__45__DEHYDROGENASE__45__RXN - HISTCYCLOHYD__45__RXN - RXN__45__13435 - RXN__45__10663 - RXN__45__13431 GDPMANMANHYDRO__45__RXN - RIB5PISOM__45__RXN - RXN__45__13261 - RXN__45__12971 - PREPHENATEDEHYDROG__45__RXN + GLUC1PURIDYLTRANS__45__RXN GLUTDECARBOX__45__RXN - _3__46__4__46__19__46__7__45__RXN - _3__46__4__46__13__46__4__45__RXN + HISTCYCLOHYD__45__RXN HISTIDPHOS__45__RXN + MALONYL__45__ACPDECARBOX__45__RXN + PHOSPHOGLYCERATE__45__PHOSPHATASE__45__RXN + PREPHENATEDEHYDROG__45__RXN + RIB5PISOM__45__RXN + RXN__45__10663 + RXN__45__10727 + RXN__45__12487 + RXN__45__12766 + RXN__45__12777 + RXN__45__12793 + RXN__45__12794 + RXN__45__12968 + RXN__45__12969 + RXN__45__12971 + RXN__45__13242 + RXN__45__13261 + RXN__45__13431 + RXN__45__13435 + RXN__45__7968 + RXN__45__8346 + RXN__45__9520 + RXN__45__9533 + RXN__45__9537 + RXN__45__9548 RXN__45__9549 + RXN__45__9550 RXN__45__9555 + RXN__45__9557 RXN__45__9558 - RXN__45__12777 + RXN__45__9634 + RXN__45__9655 + RXN__45__9673 + _1__46__14__46__19__46__2__45__RXN + _1__46__1__46__3__46__40__45__RXN + _3__46__1__46__2__46__14__45__RXN + _3__46__4__46__13__46__17__45__RXN + _3__46__4__46__14__46__1__45__RXN + _3__46__4__46__19__46__7__45__RXN + _4__46__2__46__1__46__58__45__RXN _4__46__2__46__1__46__59__45__RXN _4__46__2__46__1__46__61__45__RXN - RXN__45__12793 - RXN__45__9634 - RXN__45__12968 + +Intersection of cardinality minimal completions + FORMYLMETHIONINE__45__DEFORMYLASE__45__RXN + GLUTDECARBOX__45__RXN + HISTCYCLOHYD__45__RXN + HISTIDPHOS__45__RXN + RIB5PISOM__45__RXN + RXN__45__10727 RXN__45__12766 - _2__46__7__46__1__46__142__45__RXN + RXN__45__12777 + RXN__45__12968 + RXN__45__12969 + RXN__45__12971 RXN__45__13242 + RXN__45__13261 + RXN__45__13435 + RXN__45__8346 RXN__45__9520 - FATTY__45__ACYL__45__COA__45__SYNTHASE__45__RXN - PHOSPHOGLYCERATE__45__PHOSPHATASE__45__RXN - _2__46__3__46__1__46__180__45__RXN + RXN__45__9533 RXN__45__9537 + RXN__45__9548 + RXN__45__9549 + RXN__45__9550 + RXN__45__9555 + RXN__45__9557 + RXN__45__9558 + RXN__45__9634 + RXN__45__9655 RXN__45__9673 _1__46__14__46__19__46__2__45__RXN + _3__46__1__46__2__46__14__45__RXN + _3__46__4__46__14__46__1__45__RXN + _3__46__4__46__19__46__7__45__RXN + _4__46__2__46__1__46__58__45__RXN + _4__46__2__46__1__46__59__45__RXN + _4__46__2__46__1__46__61__45__RXN + +Union of cardinality minimal completions + ACP__45__S__45__ACETYLTRANSFER__45__RXN + CYCLOHEXADIENYL__45__DEHYDROGENASE__45__RXN + FATTY__45__ACID__45__SYNTHASE__45__RXN + FATTY__45__ACYL__45__COA__45__SYNTHASE__45__RXN + FORMYLMETHIONINE__45__DEFORMYLASE__45__RXN + GDPMANMANHYDRO__45__RXN + GLUC1PADENYLTRANS__45__RXN + GLUC1PURIDYLTRANS__45__RXN + GLUCISOM__45__RXN + GLUCOKIN__45__RXN + GLUCOSE__45__1__45__PHOSPHATE__45__PHOSPHODISMUTASE__45__RXN + GLUCOSE__45__6__45__PHOSPHATASE__45__RXN + GLUTDECARBOX__45__RXN + HISTCYCLOHYD__45__RXN + HISTIDPHOS__45__RXN + MALONYL__45__ACPDECARBOX__45__RXN + MANNITOL__45__1__45__PHOSPHATASE__45__RXN + MANNITOL__45__2__45__DEHYDROGENASE__45__NADP__43____45__RXN + MANNITOL__45__2__45__DEHYDROGENASE__45__RXN + MANNOSE__45__6__45__PHOSPHATE__45__6__45__REDUCTASE__45__RXN + MANNPDEHYDROG__45__RXN + PHOSPHOGLYCERATE__45__PHOSPHATASE__45__RXN + PREPHENATEDEHYDROG__45__RXN + PREPHENATE__45__ASP__45__TRANSAMINE__45__RXN + PREPHENATE__45__DEHYDROGENASE__45__NADP__43____45__RXN + PREPHENATE__45__TRANSAMINE__45__RXN + RIB5PISOM__45__RXN + RXN__45__10663 RXN__45__10727 + RXN__45__10770 + RXN__45__11508 + RXN__45__12361 + RXN__45__12486 RXN__45__12487 + RXN__45__12755 + RXN__45__12766 + RXN__45__12777 + RXN__45__12793 + RXN__45__12794 + RXN__45__12968 + RXN__45__12969 + RXN__45__12971 + RXN__45__13242 + RXN__45__13261 + RXN__45__13431 + RXN__45__13435 + RXN__45__5682 + RXN__45__7968 + RXN__45__8346 + RXN__45__8347 + RXN__45__8349 + RXN__45__8350 + RXN__45__8389 + RXN__45__9520 + RXN__45__9533 + RXN__45__9537 RXN__45__9548 - _4__46__2__46__1__46__58__45__RXN + RXN__45__9549 + RXN__45__9550 + RXN__45__9555 RXN__45__9557 + RXN__45__9558 + RXN__45__9634 + RXN__45__9655 + RXN__45__9673 + SHIKIMATE__45__5__45__DEHYDROGENASE__45__RXN + SUGAR__45__TERMINAL__45__PHOSPHATASE__45__RXN + TYRAMINOTRANS__45__RXN + TYROSINE__45__AMINOTRANSFERASE__45__RXN + _1__46__14__46__19__46__2__45__RXN + _1__46__1__46__1__46__255__45__RXN _1__46__1__46__3__46__40__45__RXN - RXN__45__12794 + _2__46__3__46__1__46__180__45__RXN + _2__46__4__46__1__46__216__45__RXN + _2__46__7__46__1__46__142__45__RXN + _2__46__7__46__7__46__34__45__RXN + _3__45__PHOSPHOGLYCERATE__45__PHOSPHATASE__45__RXN + _3__46__1__46__2__46__14__45__RXN + _3__46__4__46__13__46__17__45__RXN + _3__46__4__46__13__46__19__45__RXN + _3__46__4__46__13__46__4__45__RXN + _3__46__4__46__13__46__5__45__RXN + _3__46__4__46__14__46__1__45__RXN + _3__46__4__46__19__46__7__45__RXN + _4__46__2__46__1__46__58__45__RXN + _4__46__2__46__1__46__59__45__RXN + _4__46__2__46__1__46__61__45__RXN