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reaction database corrections in response to #174
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See issue #174 conversation for details.
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@Waschina
Waschina committed Sep 23, 2023
1 parent 139b3b4 commit fb3631d
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Showing 5 changed files with 22 additions and 10 deletions.
8 changes: 8 additions & 0 deletions dat/corrections_seed_reactionDB.tsv
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Expand Up @@ -2672,3 +2672,11 @@ rxn23817 TRUE [SW] duplicate reaction to rxn05733
rxn10448 TRUE [SW] duplicate reaction to rxn08188
rxn09688 TRUE [SW] duplicate reaction to rxn08323
rxn12416 TRUE [SW] duplicate reaction to rxn08323

rxn18552 [SW] ATP-dependent stachyose import TRUE
rxn90120 > -1:cpd00076:0:0:"sucrose";-1:cpd21648:0:0:"6-kestotriose";1:cpd25730:0:0:"6,6-kestotetraose";1:cpd00027:0:0:"D-Glucose" [SW] Reaction for EC 2.4.1.10 https://metacyc.org/compound?orgid=META&id=6-KESTOSE levansucrase levansucrase
rxn90121 > -1:cpd21648:0:0:"6-kestotriose";-1:cpd00001:0:0:"H2O";1:cpd00076:0:0:"sucrose";1:cpd00082:0:0:"D-Fructose" [SW] involved in levan degradation https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=3.2.1.154-RXN kestotriose fructosidase kestotriose fructosidase
rxn90122 > -1:cpd25730:0:0:"6,6-kestotetraose";-1:cpd00001:0:0:"H2O";1:cpd21648:0:0:"6-kestotriose";1:cpd00082:0:0:"D-Fructose" [SW] involved in levan degradation https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=3.2.1.154-RXN kestotetraose fructosidase kestotetraose fructosidase
rxn17933 TRUE [SW] highly unbalanced
rxn17983 TRUE [SW] highly unbalanced
rxn90123 > -1:cpd00155:1:0:"glycogen";-1:cpd00001:1:0:"H2O";1:cpd01262:1:0:"Amylotriose";1:cpd00179:1:0:"Maltose" [SW] A glycogen hydrolase that hydrolyses (1->6)-α-D-glucosidic branch linkages and releases shorter maltodextrins. Extracellular https://doi.org/10.1038/s41564-023-01447-2 isoamylase debranching enzyme, glycogen α-1,6-glucanohydrolase
1 change: 1 addition & 0 deletions dat/nutrients.tsv
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Expand Up @@ -737,6 +737,7 @@ cpd21755 1-4-alpha-D-galacturonosyl C18H23O19 -3 MNXM56632
cpd22614 sulfoquinovose C6H11O8S -1 MNXM83070
cpd23430 isocholate C24H39O5 -1 MNXM18754
cpd23431 3-dehydrocholate C24H37O5 -1 MNXM9997
cpd25730 6,6-kestotetraose C24H42O21 0 MNXM10354
cpd27289 indole-3-propionate C11H10NO2 -1 MNXM57347
cpd27519 Methylesterified-homogalacturonan C21H32O19 0 MNXM12261
cpd28763 (2,1-beta-D-fructan) C72H122O61 0 MNXM57547
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9 changes: 4 additions & 5 deletions dat/seed_Enzyme_Class_Reactions_Aliases_unique_edited.tsv
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Expand Up @@ -2060,7 +2060,7 @@ rxn08710|rxn26108|rxn26117|rxn28828|rxn28830|rxn28832|rxn28833|rxn28836|rxn28838
rxn28299|rxn37777|rxn37779|rxn37780 2.4.1 Enzyme Class
rxn02820|rxn03819|rxn04313|rxn04316|rxn04318|rxn04345|rxn04346|rxn04347|rxn04348|rxn04349|rxn04350|rxn04351|rxn04352|rxn04353|rxn04354|rxn04355|rxn04356|rxn04357|rxn04358|rxn04359|rxn04360|rxn04401|rxn04402|rxn04505|rxn04516|rxn04549|rxn04550|rxn04617|rxn04633|rxn05852|rxn05907|rxn06065|rxn06656|rxn06671|rxn07113|rxn07470|rxn07664|rxn07665|rxn07667|rxn07668|rxn07669|rxn07693|rxn07698|rxn07699|rxn07701|rxn07722|rxn07803|rxn07864|rxn07865|rxn08023|rxn11646|rxn13955|rxn13960|rxn13967|rxn13970|rxn13989|rxn14030|rxn14075|rxn14103|rxn14115|rxn14206|rxn14249|rxn14253|rxn15089|rxn15848|rxn15854|rxn16172|rxn16173|rxn16186|rxn16192|rxn16193|rxn16643|rxn16644|rxn16645|rxn16698|rxn21045|rxn21371|rxn21373|rxn21375|rxn21376|rxn21392|rxn22022|rxn22026|rxn22028|rxn22030|rxn22062|rxn22134|rxn22140|rxn22146|rxn22192|rxn22339|rxn22342|rxn22636|rxn23249|rxn23363|rxn23402|rxn23403|rxn23404|rxn23418|rxn23420|rxn23421|rxn23422|rxn23433|rxn23468|rxn23524|rxn23525|rxn23526|rxn23527|rxn23537|rxn23573|rxn23574|rxn23575|rxn23576|rxn23577|rxn23734|rxn23976|rxn23977|rxn23978|rxn23979|rxn23981|rxn23982|rxn23983|rxn23984|rxn23985|rxn23986|rxn23987|rxn23988|rxn23989|rxn23990|rxn23991|rxn23992|rxn23993|rxn23994|rxn23995|rxn23996|rxn23997|rxn23998|rxn23999|rxn24000|rxn24001|rxn24003|rxn24004|rxn24005|rxn24006|rxn24150|rxn24230|rxn24231|rxn24232|rxn24234|rxn24236|rxn24238|rxn24327|rxn24413|rxn24428|rxn24452|rxn24466|rxn24467|rxn24556|rxn24558|rxn24564|rxn24566|rxn24568|rxn24648|rxn24649|rxn24660|rxn24661|rxn24664|rxn24665|rxn24666|rxn24687|rxn24688|rxn24707|rxn24711|rxn24729|rxn24730|rxn24731|rxn24732|rxn24733|rxn24734|rxn24735|rxn24737|rxn24738|rxn24739|rxn24740|rxn24744|rxn24745|rxn24746|rxn24747|rxn24748|rxn24749|rxn24750|rxn24751|rxn24752|rxn24753|rxn24754|rxn24760|rxn24847|rxn24849|rxn24921|rxn24924|rxn24932|rxn24936|rxn24946|rxn24949|rxn24952|rxn24954|rxn24956|rxn24957|rxn24958|rxn25204|rxn25208|rxn25210|rxn25211|rxn25213|rxn25288|rxn25289|rxn25292|rxn25293|rxn25295|rxn25297|rxn25299|rxn25302|rxn25304|rxn25306|rxn25318|rxn25319|rxn25320|rxn25321|rxn25352|rxn25353|rxn25354|rxn25359|rxn25360|rxn25364|rxn25366|rxn25367|rxn25370|rxn25371|rxn25373|rxn25440|rxn25441|rxn25524|rxn25566|rxn25589|rxn25629|rxn25630|rxn25943|rxn26143|rxn26345|rxn26521|rxn26526|rxn26748|rxn26749|rxn26750|rxn27011|rxn27012|rxn27090|rxn27092|rxn28835|rxn31283|rxn31284|rxn31294|rxn31303|rxn31304|rxn31305|rxn31306|rxn31307|rxn31308|rxn31311|rxn31672|rxn37028|rxn37085|rxn37086|rxn37087|rxn37088|rxn37091|rxn37094|rxn37097|rxn37102|rxn37183|rxn37277|rxn37278|rxn37279|rxn37280|rxn37342|rxn37343|rxn37344|rxn37345|rxn37346|rxn37350|rxn37353|rxn37354|rxn37355|rxn37356|rxn37357|rxn37358|rxn37359|rxn37360|rxn37376|rxn37377|rxn37387|rxn37388|rxn37389|rxn37390|rxn37391|rxn37392|rxn37393|rxn37394|rxn37395|rxn37396|rxn37397|rxn37398|rxn37399|rxn37400|rxn37401|rxn37402|rxn37403|rxn37411|rxn37420|rxn37544|rxn37545|rxn08711|rxn26102 rxn02408|rxn02820|rxn04401|rxn04402|rxn04633|rxn05907|rxn06656|rxn06671|rxn07113|rxn07405|rxn07470|rxn07664|rxn07665|rxn07667|rxn07668|rxn07669|rxn07693|rxn07698|rxn07699|rxn07701|rxn07704|rxn07722|rxn07803|rxn07864|rxn07865|rxn08583|rxn08618|rxn08619|rxn08620|rxn08710|rxn08711|rxn08712|rxn13955|rxn13960|rxn13967|rxn13970|rxn13989|rxn14030|rxn14075|rxn14103|rxn14206|rxn14249|rxn14253|rxn14324 2.4.1.- Enzyme Class
rxn06049|rxn06096|rxn08611|rxn10363|rxn13299|rxn15563|rxn15594|rxn19864|rxn19869|rxn25316|rxn26127|rxn27912|rxn27981|rxn28262|rxn38470 rxn05740|rxn06049|rxn06096|rxn08611|rxn10363 2.4.1.1 Enzyme Class
rxn15452|rxn20032|rxn23736|rxn23739 rxn06618 2.4.1.10 Enzyme Class
rxn15452|rxn20032|rxn23736|rxn23739|rxn90120 rxn06618 2.4.1.10 Enzyme Class
rxn23732 2.4.1.100 Enzyme Class
rxn17492|rxn31291 2.4.1.101 Enzyme Class
rxn06731|rxn17493 rxn06731 2.4.1.102 Enzyme Class
Expand Down Expand Up @@ -3390,7 +3390,7 @@ rxn05973|rxn17917|rxn35562|rxn35563 rxn05973 3.2.1.137 Enzyme Class
rxn01078|rxn15211|rxn17918 rxn01078 3.2.1.139 Enzyme Class
rxn05941|rxn06152|rxn15160|rxn15578|rxn15579|rxn15580|rxn17919|rxn23051|rxn23053 rxn05941|rxn06152 3.2.1.14 Enzyme Class
rxn03502|rxn15525|rxn90004 rxn03502 3.2.1.140 Enzyme Class
rxn17922|rxn27554 3.2.1.141 Enzyme Class
rxn17922|rxn27554|rxn10817 3.2.1.141 Enzyme Class
rxn17923 3.2.1.142 Enzyme Class
rxn17924 3.2.1.143 Enzyme Class
rxn07021|rxn17925 rxn07021 3.2.1.144 Enzyme Class
Expand All @@ -3403,7 +3403,7 @@ rxn17928|rxn17929 3.2.1.150 Enzyme Class
rxn17930 3.2.1.151 Enzyme Class
rxn17931 3.2.1.152 Enzyme Class
rxn17932|rxn90060 3.2.1.153 Enzyme Class
rxn17933 3.2.1.154 Enzyme Class
rxn17933|rxn90121|rxn90122 3.2.1.154 Enzyme Class
rxn22866 3.2.1.155 Enzyme Class
rxn17934 3.2.1.156 Enzyme Class
rxn17935 3.2.1.157 Enzyme Class
Expand Down Expand Up @@ -3479,8 +3479,7 @@ rxn17981 3.2.1.64 Enzyme Class
rxn06945|rxn15543|rxn17982 rxn06945 3.2.1.65 Enzyme Class
rxn01760|rxn15335|rxn15336|rxn20659|rxn33476 rxn01760 3.2.1.66 Enzyme Class
rxn05122|rxn06064|rxn15598|rxn15677|rxn90062 rxn05122|rxn06064 3.2.1.67 Enzyme Class
rxn17983|rxn22743|rxn23920|rxn28284 3.2.1.68 Enzyme Class
rxn30585 3.2.1.68- Enzyme Class
rxn17983|rxn22743|rxn23920|rxn28284|rxn90123 rxn10817 3.2.1.68 Enzyme Class
rxn17984 3.2.1.7 Enzyme Class
rxn17985 3.2.1.70 Enzyme Class
rxn17986 3.2.1.71 Enzyme Class
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2 changes: 1 addition & 1 deletion dat/seed_metabolites_edited.tsv
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Expand Up @@ -18931,7 +18931,7 @@ cpd21644 MNXM2842 (GlcNAc)2(Man)9(Asn)1 (GlcNAc)2(Man)9(Asn)1 null 10000000 Mode
cpd21645 MNXM174019 (Gal)2(GlcNAc)2(S)3 (Gal)2(GlcNAc)2(S)3 null 10000000 ModelSEED 0 1 0 null 0 10000000 10000000 null null null null
cpd21646 MNXM174018 (Gal)2(GlcNAc)2(S)2 (Gal)2(GlcNAc)2(S)2 null 10000000 ModelSEED 0 1 0 null 0 10000000 10000000 null null null null
cpd21647 MNXM174003 (Gal)2(GalNAc)1(GlcNAc)1 (Gal)2(GalNAc)1(GlcNAc)1 null 10000000 ModelSEED 0 1 0 null 0 10000000 10000000 null null null null
cpd21648 MNXM8193 (Fruf)2(Glc)1 (Fruf)2(Glc)1 null 10000000 ModelSEED 0 1 0 null 0 10000000 10000000 null null null null ODEHMIGXGLNAKK-OESPXIITSA-N HMDB33673 64833 InChI=1S/C18H32O16/c19-1-6-9(23)12(26)13(27)16(31-6)34-18(5-22)15(29)11(25)8(33-18)3-30-17(4-21)14(28)10(24)7(2-20)32-17/h6-16,19-29H,1-5H2/t6-,7-,8-,9-,10-,11-,12+,13-,14+,15+,16-,17-,18+/m1/s1 6-KESTOSE
cpd21648 MNXM8193 (Fruf)2(Glc)1 6-kestotriose C18H32O16 10000000 ModelSEED 0 1 0 null 0 10000000 10000000 null null null null ODEHMIGXGLNAKK-OESPXIITSA-N HMDB33673 64833 InChI=1S/C18H32O16/c19-1-6-9(23)12(26)13(27)16(31-6)34-18(5-22)15(29)11(25)8(33-18)3-30-17(4-21)14(28)10(24)7(2-20)32-17/h6-16,19-29H,1-5H2/t6-,7-,8-,9-,10-,11-,12+,13-,14+,15+,16-,17-,18+/m1/s1 6-KESTOSE
cpd21649 MNXM174031 (GalA)2 (GalA)2 null 10000000 ModelSEED 0 1 0 null 0 10000000 10000000 null null null null
cpd21650 MNXM174050 (GlcA)1(GlcNAc)1 (GlcA)1(GlcNAc)1 null 10000000 ModelSEED 0 1 0 null 0 10000000 10000000 null null null null
cpd21651 MNXM43850 nLc4 nLc4 null 10000000 ModelSEED 0 1 0 null 0 10000000 10000000 null null null null IEQCXFNWPAHHQR-YKLSGRGUSA-N 60239 InChI=1S/C26H45NO21/c1-6(32)27-11-14(35)20(46-25-18(39)15(36)12(33)7(2-28)43-25)10(5-31)45-24(11)48-22-13(34)8(3-29)44-26(19(22)40)47-21-9(4-30)42-23(41)17(38)16(21)37/h7-26,28-31,33-41H,2-5H2,1H3,(H,27,32)/t7-,8-,9-,10-,11-,12+,13+,14-,15+,16-,17-,18-,19-,20-,21-,22+,23?,24+,25+,26+/m1/s1 CPD-16472
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