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Merge Duplicate Lipoic Acid Biosynthesis Pathways #707

Merged
merged 10 commits into from
Oct 17, 2023
Merged

Merge Duplicate Lipoic Acid Biosynthesis Pathways #707

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ce1c33c
fix: remove MAR06400 for being a less accurate duplicate of MAR06403
Devlin-Moyer Jul 28, 2023
83aab80
fix: remove MAR06401 for being a duplicate of MAR06402
Devlin-Moyer Jul 28, 2023
a9e732a
fix: remove MAM02397c
Devlin-Moyer Jul 28, 2023
a171e17
fix: update metabolite annotation files
Devlin-Moyer Jul 28, 2023
4e4cfe7
chore: merge in latest develop branch
Devlin-Moyer Aug 22, 2023
d00cb22
chore: merge in latest develop branch
Devlin-Moyer Oct 14, 2023
4dcfc78
feat: added direction-specific RHEA IDs for MAR06402 and MAR06403
Devlin-Moyer Oct 14, 2023
4e7dad2
Merge branch 'develop' into fix/dupe_lipoate_biosynth
feiranl Oct 16, 2023
7ca9471
Merge branch 'develop' into fix/dupe_lipoate_biosynth
haowang-bioinfo Oct 16, 2023
01a5d1e
doc: update Rhea ids for MAR01706
haowang-bioinfo Oct 16, 2023
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1 change: 1 addition & 0 deletions data/deprecatedIdentifiers/deprecatedMetabolites.tsv
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Expand Up @@ -2237,6 +2237,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM01445m" "MAM01445" "cholate" "C00695" "HMDB0000619" "CHEBI:16359" "221493" "LMST04010001" "" "HC00502" "cholate" "MNXM450" "m01445m" "m01445m"
"MAM01514m" "MAM01514" "cholcoa" "C01794" "HMDB0001374" "CHEBI:15519" "439573" "" "" "HC00844" "cholcoa" "MNXM162468;MNXM431" "m01514m" "m01514m"
"MAM00759c" "MAM00759" "" "C13712" "" "" "" "LMST02030130" "" "" "M00759" "MNXM3494" "m00759c" "m00759c"
"MAM02397c" "MAM02397" "" "C16239" "" "" "" "" "" "" "M02397" "MNXM19093" "m02397c" "m02397c"
"MAM01268c" "MAM01268" "" "" "" "" "" "PROTEIN" "" "" "M01268" "" "m01268c" "m01268c"
"MAM01268m" "MAM01268" "" "" "" "" "" "PROTEIN" "" "" "M01268" "" "m01268m" "m01268m"
"MAM01268n" "MAM01268" "" "" "" "" "" "PROTEIN" "" "" "M01268" "" "m01268n" "m01268n"
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4 changes: 3 additions & 1 deletion data/deprecatedIdentifiers/deprecatedReactions.tsv
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Expand Up @@ -230,6 +230,8 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR00096" "" "BUP2" "" "" "" "BUP2" "MNXR96346" "" "" "" 0 "" "" "BUP2"
"MAR02027" "" "r0193" "" "" "" "r0193" "MNXR105313" "" "" "" 0 "" "" "r0193"
"MAR02006" "" "CPS_m" "" "" "" "r0034" "" "" "" "" 0 "" "" "r0034"
"MAR06400" "R07768" "" "R07768C" "" "" "HMR_6400" "MNXR111356" "HMR_6400" "RCR11944" "" 0 "" "" "HMR_6400"
"MAR06401" "R07769" "" "R07769C" "" "" "HMR_6401" "MNXR111357" "HMR_6401" "RCR11945" "" 0 "" "" "HMR_6401"
"MAR03940" "R01795" "PHETHPTOX" "R01795C" "r0399" "" "r0399" "MNXR102632;MNXR107174" "HMR_3940" "RCR11388" "" 0 "" "RHEA:30787" "HMR_3940"
"MAR07785" "" "ATPtx" "" "" "" "ATPtx" "MNXR96140" "HMR_7785" "RCR20040" "" 0 "" "" "HMR_7785"
"MAR07775" "" "NADHtpu" "" "" "" "NADHtpu;NADtpu" "MNXR101881" "HMR_7775" "RCR20024" "" 0 "" "" "HMR_7775"
Expand All @@ -238,4 +240,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR07771" "" "NADtpu" "" "" "" "NADtx" "MNXR101881" "HMR_7771" "RCR20023" "" 0 "" "" "HMR_7771"
"MAR07782" "" "ADPtx" "" "" "" "ADPtx" "MNXR95484" "HMR_7782" "RCR20201" "" 0 "" "" "HMR_7782"
"MAR07783" "" "AMPtp" "" "" "" "AMPtp" "MNXR95830" "HMR_7783" "RCR20046" "" 0 "" "" "HMR_7783"
"MAR07790" "" "FADtx" "" "" "" "FADtx" "MNXR99217" "HMR_7790" "RCR20203" "" 0 "" "" "HMR_7790"
"MAR07790" "" "FADtx" "" "" "" "FADtx" "MNXR99217" "HMR_7790" "RCR20203" "" 0 "" "" "HMR_7790"
51 changes: 0 additions & 51 deletions model/Human-GEM.yml
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Expand Up @@ -32665,14 +32665,6 @@
- charge: -1
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM02397c"
- name: "lipoyl-[ACP]"
- compartment: "c"
- formula: "C19H33N2O8PRS3"
- charge: -1
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM02398c"
- name: "lipoyl-AMP"
Expand Down Expand Up @@ -100756,49 +100748,6 @@
- subsystem:
- "Lipoic acid metabolism"
- confidence_score: 0
- !!omap
- id: "MAR06400"
- name: ""
- metabolites: !!omap
- MAM01098c: 2
- MAM02039c: -5
- MAM02040c: 6
- MAM02397c: 1
- MAM02471c: 2
- MAM02554c: 7
- MAM02555c: -7
- MAM02643c: -1
- MAM02681c: 2
- MAM02682c: -2
- MAM02877c: -2
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000121897 or ENSG00000175536"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.8.1.8;2.3.1.181"
- references: ""
- subsystem:
- "Lipoic acid metabolism"
- confidence_score: 0
- !!omap
- id: "MAR06401"
- name: "lipoyl-[acp]:protein N6-lipoyltransferase"
- metabolites: !!omap
- MAM00184c: 1
- MAM00209c: 1
- MAM01350c: -1
- MAM02397c: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000175536"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.3.1.181"
- references: ""
- subsystem:
- "Lipoic acid metabolism"
- confidence_score: 0
- !!omap
- id: "MAR06402"
- name: "octanoyl-[acp]:protein N6-octanoyltransferase"
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1 change: 0 additions & 1 deletion model/metabolites.tsv
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Expand Up @@ -4081,7 +4081,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM02396n" "MAM02396" "" "C06315" "HMDB0005082" "CHEBI:6499" "5280915" "LMFA03040002" "" "" "C06315" "MNXM12130" "m02396n" "m02396n"
"MAM02396x" "MAM02396" "" "C06315" "HMDB0005082" "CHEBI:6499" "5280915" "LMFA03040002" "" "" "C06315" "MNXM12130" "m02396p" "m02396p"
"MAM02396r" "MAM02396" "" "C06315" "HMDB0005082" "CHEBI:6499" "5280915" "LMFA03040002" "" "" "C06315" "MNXM12130" "m02396r" "m02396r"
"MAM02397c" "MAM02397" "" "C16239" "" "" "" "" "" "" "M02397" "MNXM19093" "m02397c" "m02397c"
"MAM02398c" "MAM02398" "" "C16238" "" "" "23724672" "" "CE5656" "" "CE5656" "MNXM2392" "m02398c" "m02398c"
"MAM02399c" "MAM02399" "" "" "" "" "53481572" "" "CE2102" "" "CE2102" "MNXM60228" "m02399c" "m02399c"
"MAM02401c" "MAM02401" "" "C03127" "" "CHEBI:29160" "" "" "" "" "M02401" "MNXM89832" "m02401c" "m02401c"
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6 changes: 2 additions & 4 deletions model/reactions.tsv
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Expand Up @@ -1668,10 +1668,8 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR06397" "" "" "RE2882C" "" "" "HMR_6397" "" "HMR_6397" "RCR10619" "" 0 "" "" "HMR_6397"
"MAR06398" "R07770" "" "R07770C" "" "" "RE1944C" "MNXR101081" "HMR_6398" "RCR14489" "" 0 "" "RHEA:12913" "HMR_6398"
"MAR06399" "R07771" "" "R07771C" "" "" "HMR_6399" "MNXR111358" "HMR_6399" "RCR14490" "" 0 "" "RHEA:20473" "HMR_6399"
"MAR06400" "R07768" "" "R07768C" "" "" "HMR_6400" "MNXR111356" "HMR_6400" "RCR11944" "" 0 "" "" "HMR_6400"
"MAR06401" "R07769" "" "R07769C" "" "" "HMR_6401" "MNXR111357" "HMR_6401" "RCR11945" "" 0 "" "" "HMR_6401"
"MAR06402" "R07766" "" "R07766C" "" "" "HMR_6402" "MNXR111354" "HMR_6402" "RCR11946" "" 0 "" "RHEA:17665" "HMR_6402"
"MAR06403" "R07767" "" "R07767C" "" "" "HMR_6403" "MNXR111355" "HMR_6403" "RCR11947" "" 0 "" "RHEA:16585" "HMR_6403"
"MAR06402" "R07766;R07769" "" "R07766C;R07769C" "" "" "HMR_6402;HMR_6401" "MNXR111354" "HMR_6402;HMR_6401" "RCR11946;RCR11945" "" 0 "RHEA:17666" "RHEA:17665" "HMR_6402;HMR_6401;MAR06401"
"MAR06403" "R07767;R07768" "" "R07767C;R07768C" "" "" "HMR_6403;HMR_6400" "MNXR111355" "HMR_6403;HMR_6400" "RCR11947;RCR11948" "" 0 "RHEA:16586" "RHEA:16585" "HMR_6403;HMR_6400;MAR06400"
"MAR06404" "R08550" "" "R08550C" "" "" "HMR_6404" "MNXR112089" "HMR_6404" "RCR14491" "" 0 "" "" "HMR_6404"
"MAR02472" "" "HMR_2472" "RE3109C" "" "" "HMR_2472" "" "HMR_2472" "RCR11948" "" 0 "" "" "HMR_2472"
"MAR02475" "" "RE3110C" "RE3110C" "" "" "RE3110C" "MNXR103792" "HMR_2475" "RCR11949" "" 0 "" "" "HMR_2475"
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