added new inulin degradation pathway

- inulinase (3.2.1.7) + abc transporter - intracellular pathway defined by two new reactions: - rxn90124 inulinase - rxn29776 abc transporter - cpd28763 (11 x fructose + 1 glucose) is used as default inulin - sequences for inulinase from uniprot by EC number - sequences for abc transporter - abc inulin transporter in Lactobacillus inuABCDEF https://doi.org/10.1038/s41598-021-95356-1 - SusC-like TonB-dependent inulin transporter in Bacteroides ovatus (BACOVA_04505) https://doi.org/10.1128%2FmBio.01762-19 - inulin ABC transporter complex FusABC-MsmK (Streptococcus) https://www.uniprot.org/uniprotkb/A0A0H2URD6/entry
jotech · Dec 8, 2023 · 72ff3e0 · 72ff3e0
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diff --git a/dat/corrections_seed_reactionDB.tsv b/dat/corrections_seed_reactionDB.tsv
@@ -2240,7 +2240,7 @@ rxn90057	=		-4:cpd00067:0:0:"H+";-2:cpd11620:0:0:"Reducedferredoxin";2:cpd11621:
 rxn90058	=		-3:cpd00067:0:0:"H+";-1:cpd02935:0:0:"CoM-S-S-CoB";-1:cpd08702:0:0:"Dihydromethanophenazine";1:cpd02246:0:0:"CoM";1:cpd02817:0:0:"HTP";1:cpd08701:0:0:"Methanophenazine";2:cpd00067:1:0:"H+"	[JZ] rxn03126 can be reversible when linked to membrane potential	http://dx.doi.org/10.1038/nrmicro1931			Coenzyme B:coenzyme M:methanophenazine oxidoreductase (chemiosmosis)	
 rxn90059	<		-2:cpd00067:0:0:"H+";-1:cpd08701:0:0:"Methanophenazine";-1:cpd11640:0:0:"H2";1:cpd08702:0:0:"Dihydromethanophenazine";2:cpd00067:1:0:"H+"	[JZ] rxn16961 can be reversible when linked to membrane potential	http://dx.doi.org/10.1038/nrmicro1931			hydrogen:2-(2,3-dihydropentaprenyloxy)phenazine oxidoreductase  (chemiosmosis)	
 rxn15961	>			[JZ] direction changed according to MetaCyc + Thauer2008	https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=RXN-7733 http://dx.doi.org/10.1038/nrmicro1931				
-rxn90060	>		-1:cpd28763:1:0:"(2,1-beta-D-fructan)";-9:cpd00001:1:0:"H2O";9:cpd00082:1:0:"D-Fructose";1:cpd02298:1:0:"1F-beta-D-Fructosylsucrose"	[SW] New reaction for inulin/fructan degradation step 1	https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=3.2.1.153-RXN		inulinase	fructan beta-(2,1)-fructosidase (extracellular)	
+rxn90060	>		-1:cpd28763:1:0:"Inulin";-9:cpd00001:1:0:"H2O";9:cpd00082:1:0:"D-Fructose";1:cpd02298:1:0:"1F-beta-D-Fructosylsucrose"	[SW] New reaction for inulin/fructan degradation step 1	https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=3.2.1.153-RXN		inulinase	fructan beta-(2,1)-fructosidase (extracellular)	
 rxn23749	>		-1:cpd00001:0:0:"H2O";-1:cpd02298:0:0:"1F-beta-D-Fructosylsucrose";1:cpd00076:0:0:"Sucrose";1:cpd00082:0:0:"D-Fructose"	[SW] Reaction needed for 1-Kestotriose degradation	https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=RXN-1841				
 rxn29739				[SW] Needed for 1-Kestotriose uptake					TRUE
 rxn23769	>		-3:cpd00001:0:0:"H2O";-1:cpd27519:0:0:"Methylesterified-homogalacturonan";3:cpd00116:0:0:"Methanol";1:cpd21755:0:0:"1-4-alpha-D-galacturonosyl";3:cpd00067:0:0:"H+"	[SW] Reaction for first step pectin degradation	https://metacyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-7248				
@@ -2682,3 +2682,6 @@ 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	
 
 rxn20665									TRUE
+
+rxn29776	>		-1:cpd00001:0:0:"H2O";-1:cpd00002:0:0:"ATP";-1:cpd28763:1:0:"Inulin";1:cpd00008:0:0:"ADP";1:cpd00009:0:0:"Phosphate";1:cpd00067:0:0:"H+";1:cpd28763:0:0:"Inulin"	[JZ] inulin abc transporter					TRUE
+rxn90124	>		-1:cpd28763:0:0:"Inulin";-11:cpd00001:0:0:"H2O";11:cpd00082:0:0:"D-Fructose";1:cpd00027:0:0:"D-Glucose"	[JZ] inulinase, intracellular	https://www.vmh.life/#reaction/INULINASE		inulinase	inulinase, intracellular	
diff --git a/dat/custom_pwy.tbl b/dat/custom_pwy.tbl
@@ -37,6 +37,7 @@ H4SPT-SYN	H4SPT-SYN	Biosynthesis of tetrahydrosarcinapterin from tetrahydrometha
 NA-TRANSLOCATING-RNF	Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex		|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Transport|	|TAX-2157|,|TAX-2|	NA-TRANSLOCATING-RNF			Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex			False	True	
 NA-F0F1ATPSYN	Na(+)-translocating ATPase		|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Transport|	|TAX-2759|,|TAX-2|,|TAX-2157|	NA-F0F1ATPSYNTHASE	7.2.2.1		Na(+)-translocating ATPase			False	True	
 INULIN-DEGRADATION-EXO	Inulin degradation(11xFru,1xGlc) (extracellular)		|Polymer-Degradation|,|Degradation|,|Carbohydrates-Degradation|,|POLYSACCHARIDES-DEG|,|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Glycan-Pathways|,|Glycan-Degradation|		3.2.1.153-RXN,1-KESTOTRIOSE-ABC-TRANSPORT,RXN-1841	3.2.1.153,,3.2.1.80	3.2.1.153	fructan beta-(2,1)-fructosidase;1-Kestotriose ABC-Transporter;fructan beta-fructosidase 			False	True	
+INULIN-DEGRADATION	Inulin degradation(11xFru,1xGlc) (intracellular)		|Polymer-Degradation|,|Degradation|,|Carbohydrates-Degradation|,|POLYSACCHARIDES-DEG|,|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Glycan-Pathways|,|Glycan-Degradation|		3.2.1.7-RXN,INULIN-ABC-TRANSPORT	3.2.1.7,	3.2.1.7-RXN	Inulinase;Inuline ABC-Transporter 			False	True	
 TYR-DEG-4HPAC	L-Tyrosine degradation to 4-hydroxyphenylacetate via tyramine		|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Degradation|	|TAX-2|	TYROSINE-DECARBOXYLASE-RXN,RXN-5821,1.2.1.53-RXN	4.1.1.25,1.4.3.4,1.2.1.53		tyrosine decarboxylase;monoamine oxidase;4-hydroxyphenylacetaldehyde dehydrogenase			False	True	
 PYR-ACCOA-FROX	Pyruvate-ferredoxin oxidorectase to acetyl-CoA		|Pyruvate-Degradation|,|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Energy-Metabolism|,|Fermentation|,|Fermentation-to-Acids|,|Acetyl-CoA-Butyrate|	|TAX-2|	pyr.ferredoxin-OXIDO			pyruvate:ferredoxin oxidoreductase			False	True	
 LWP-GS	Ljungdahl-Wood pathway (gapseq)	reductive acetyl coenzyme A pathway I (homoacetogenic bacteria),Wood pathway,acetate synthesis,acetyl-CoA pathway,carbon monoxide dehydrogenase pathway,carbon fixation,CO<SUB>2</SUB> fixation,Ljungdahl-Wood pathway,Wood-Ljungdahl pathway,reductive acetyl CoA pathway	|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Degradation|,|C1-COMPOUNDS|,|CO2-Fixation|,|Autotrophic-CO2-Fixation|	|TAX-2157|,|TAX-2|	FORMATE-DEHYDROGENASE-FRDX,METHCOCLTH-RXN,ACETYLSYNCLTH-RXN,RXN-5061,1.5.1.20-RXN,METHENYLTHFCYCLOHYDRO-RXN,FORMATETHFLIG-RXN,METHYLENETHFDEHYDROG-NADP-RXN,1.2.7.4-RXN,RXN-21797	1.17.99.7,2.1.1.258,2.3.1.169,1.5.7.1,1.5.1.20,3.5.4.9,6.3.4.3,1.5.1.5,1.2.7.4,1.5.1.M4	1.2.7.4-RXN,FORMATE-DEHYDROGENASE-FRDX	formate dehydrogenase (ferredoxin);methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase;CO-methylating acetyl-CoA synthase;methylenetetrahydrofolate reductase;5,10-methylenetetrahydrofolate reductase;methenyltetrahydrofolate cyclohydrolase;formyltetrahydrofolate synthetase;NADP+-dependent methylenetetrahydrofolate dehydrogenase;carbon monoxide dehydrogenase (ferredoxin);methylene tetrahydrofolate reductase (bifurcating)			False	True	

diff --git a/dat/medium_prediction_rules.tsv b/dat/medium_prediction_rules.tsv
@@ -37,7 +37,7 @@ Maltose	cpd00179	"MALTOSECAT-PWY"	2.5	TRUE		Saccharides
 Pectin	cpd27519	"PWY-7246" | "PWY-7248"	1.67	TRUE		Saccharides
 Melitose/Raffinose	cpd00382	rxn05643 & (rxn00818 | rxn34781)	1.67	TRUE	Raffinose transporter AND galactohydrolase	Saccharides
 Sucrose	cpd00076	"SUCUTIL-PWY" | "PWY-621" | "PWY-5384" | "SUCROSEUTIL2-PWY"	2.5	TRUE		Saccharides
-Inulin	cpd28763	"INULIN-DEGRADATION-EXO"	0.42	TRUE		Saccharides
+Inulin	cpd28763	"INULIN-DEGRADATION-EXO" | "INULIN-DEGRADATION"	0.42	TRUE		Saccharides
 N-acetylneuraminate	cpd00232	"PWY0-1324" & "GLUAMCAT-PWY"	5	TRUE		Saccharides
 N-Acetyl-D-glucosamine	cpd00122	"GLUAMCAT-PWY" & (rxn05485 | rxn08041)	5	TRUE	Including PTS for uptake	Saccharides
 Xylan-b-1-4	cpd90021	"PWY-6717"	0.01	TRUE	1,4-D-beta-Xylan (n=500) degradation, extracellular	Saccharides

diff --git a/dat/nutrients.tsv b/dat/nutrients.tsv
@@ -740,7 +740,7 @@ 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
+cpd28763	Inulin (2,1-beta-D-fructan)	C72H122O61	0	MNXM57547
 cpd31356	(S)-2,3-Dihydroxypropane-1-sulfonate	C3H7O5S	-1	MNXM13761
 cpd35610	3alpha-hydroxy-7-oxo-5beta-cholan-24-oate	C24H37O4	-1	""
 cpd90001	2-fucosyllactose	C18H32O15	0	""

diff --git a/dat/seed_Enzyme_Class_Reactions_Aliases_unique_edited.tsv b/dat/seed_Enzyme_Class_Reactions_Aliases_unique_edited.tsv
@@ -3481,7 +3481,7 @@ 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|rxn90123	rxn10817	3.2.1.68	Enzyme Class
-rxn17984		3.2.1.7	Enzyme Class
+rxn17984|rxn90124		3.2.1.7	Enzyme Class
 rxn17985		3.2.1.70	Enzyme Class
 rxn17986		3.2.1.71	Enzyme Class
 rxn17987		3.2.1.72	Enzyme Class

diff --git a/dat/seed_Enzyme_Name_Reactions_Aliases.tsv b/dat/seed_Enzyme_Name_Reactions_Aliases.tsv
@@ -52,3 +52,4 @@ rxn48035	3beta-hydroxysteroid dehydrogenase
 rxn03097	R107-RXN
 rxn21189	protocatechuate 2,3-dioxygenase
 rxn21190	5-carboxy-2-hydroxymuconate-6-semialdehyde decarboxylase
+rxn29776	Inuline ABC-Transporter
diff --git a/dat/seed_metabolites_edited.tsv b/dat/seed_metabolites_edited.tsv
@@ -26029,7 +26029,7 @@ cpd28759	MNXM13490	(+)-bornane-2,5-dione	(+)-bornane-2,5-dione	C10H14O2	166	Mode
 cpd28760	MNXM97093	1-butanone, 4-(methylamino)-1-(3-pyridinyl)-	1-butanone, 4-(methylamino)-1-(3-pyridinyl)-	C10H15N2O	178	ModelSEED	1	1	0	null	0	10000000	10000000			null	null	null	null	SGDIDUFQYHRMPR-UHFFFAOYSA-O	HMDB01240		37753;66878	InChI=1S/C10H14N2O/c1-11-6-3-5-10(13)9-4-2-7-12-8-9/h2,4,7-8,11H,3,5-6H2,1H3/p+1	C20361		CPD-14092
 cpd28761	MNXM97045	3-succinoylpyridine	3-succinoylpyridine	C9H8NO3	179	ModelSEED	-1	1	0	null	0	10000000	10000000			null	null	null	null	JGSUNMCABQUBOY-UHFFFAOYSA-M	HMDB00992		66942;66951	InChI=1S/C9H9NO3/c11-8(3-4-9(12)13)7-2-1-5-10-6-7/h1-2,5-6H,3-4H2,(H,12,13)/p-1	C19569		CPD-14094
 cpd28762	MNXM507032	CPD-3401	CPD-3401	C16H14O5	286.284	ModelSEED	0	1	0	null	0	10000000	10000000			null	null	null	null								
-cpd28763	MNXM57547	(2,1-beta-D-fructan)	(2,1-beta-D-fructan)	C72H122O61	1999.73	ModelSEED	0	1	0	null	0	10000000	10000000			null	null	null	null		HMDB14776		15443;10799;10845;169;18519;24854				Inulin
+cpd28763	MNXM57547	Inulin	Inulin (2,1-beta-D-fructan)	C72H122O61	1999.73	ModelSEED	0	1	0	null	0	10000000	10000000			null	null	null	null		HMDB14776		15443;10799;10845;169;18519;24854				Inulin
 cpd28764	MNXM527666	ketoconazol	ketoconazol	C26H31N4O4	463	ModelSEED	1	1	0	null	0	10000000	10000000			null	null	null	null								
 cpd28765	MNXM3626	5-hydroxy-1,4-naphthoquinone	5-hydroxy-1,4-naphthoquinone	C10H3O3	171.132	ModelSEED	0	1	0	null	0	10000000	10000000			null	null	null	null	KQPYUDDGWXQXHS-UHFFFAOYSA-N	HMDB30773		15794;12130;20574;2062	InChI=1S/C10H6O3/c11-7-4-5-9(13)10-6(7)2-1-3-8(10)12/h1-5,12H	C03840		HYDROXYNAPHTHOQUINONE
 cpd28766	MNXM489188	7,2'-dihydroxy-4'-methoxy-isoflavanol carbocation intermediate 1	7,2'-dihydroxy-4'-methoxy-isoflavanol carbocation intermediate 1	C16H17O5	289.307	ModelSEED	0	1	0	null	0	10000000	10000000			null	null	null	null