Version 2 (o.a., Batch alignment)

README.md

@@ -33,11 +33,11 @@ For detailed use cases and full tutorials, see the [documentation](https://gapse
 
 Prediction of network candidate reactions, building of a draft model and gap filling:
 ```
-./gapseq doall toy/myb71.fna
+./gapseq doall toy/myb71.faa.gz
 ```
 Do the same but with a defined medium for gap filling:
 ```
-./gapseq doall toy/ecoli.fna.gz dat/media/MM_glu.csv
+./gapseq doall -m dat/media/MM_glu.csv toy/ecoli.faa.gz
 ```
 
 
@@ -53,7 +53,7 @@ GNU General Public License version 3.0 ([GPLv3](https://www.gnu.org/licenses/gpl
   Licensed under a Creative Commons Attribution 4.0 International License.
   Link to license: https://creativecommons.org/licenses/by/4.0/
   Website: https://www.metanetx.org/
-- **MetaCyc**: Copyright © SRI International 1999-2020, Marine Biological Laboratory  1998-2001, DoubleTwist Inc 1998-1999.  
+- **MetaCyc**: Copyright © SRI International 1999-2020, Marine Biological Laboratory  1998-2001, DoubleTwist Inc 1998-1999.
   Link to license: https://metacyc.org/ptools-academic-license.shtml .
   Website: https://metacyc.org/
 - **MODELSEED**: Copyright 2015 ModelSEED.

dat/SEED2VMH_translation_edited.csv

@@ -1920,7 +1920,7 @@ rxn10119,HYD2
 rxn10120,NO3R1
 rxn10121,NO3R2
 rxn10122,NADH6
-rxn10125,THD2
+rxn09295,THD2
 rxn10126,SUCD4
 rxn10127,TMAOR1e
 rxn10128,TMAOR2e

dat/altec.csv

@@ -3,6 +3,7 @@
 1.6.1.5,7.1.1.1
 1.6.5.3,7.1.1.2
 1.6.5.8,7.2.1.1
+1.9.3.1,7.1.1.9
 1.10.2.2,7.1.1.8
 1.10.3.10,7.1.1.3
 1.10.3.12,7.1.1.5

dat/custom_pwy.tbl

@@ -31,8 +31,8 @@ EXC-STARCH-N27	Extracellular starch(27n) degradation		|Polymer-Degradation|,|Deg
 EXO-GALACTAN_DEG	Extracellular galactan(2n) degradation		|Polymer-Degradation|,|Degradation|,|Carbohydrates-Degradation|,|POLYSACCHARIDES-DEG|,|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Glycan-Pathways|,|Glycan-Degradation|		galactanase	3.2.1.145		galactanase			False	True	
 FOLATE-SYN-GS1	Folate biosynthesis from GTP and 4-aminobenzoate via dihydropterin-3-triphosphate		|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Biosynthesis|,|Cofactor-Biosynthesis|,|Vitamin-Biosynthesis|,|Folate-Biosynthesis|	|TAX-2759|,|TAX-2|,|TAX-2157|	GTP-CYCLOHYDRO-I-RXN,ALKAPHOSPHA-RXN,H2NEOPTERINALDOL-RXN,H2PTEROATESYNTH-RXN,DIHYDROFOLATESYNTH-RXN,DHFR	3.5.4.16,3.1.3.1,4.1.2.25,2.5.1.15,6.3.2.12,1.5.1.3	H2PTEROATESYNTH-RXN	GTP cyclohydrolase;alkaline phosphatase;dihydroneopterin aldolase;dihydropteroate synthase;dihydrofolate synthase;dihydrofolate reductase			False	True	
 THIAZOLE-SYN-GS1	thiazole biosynthesis I (facultative anaerobic bacteria) with tautomerase	thiazole biosynthesis I (facultative anaerobic bacteria) with tautomerase	|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Biosynthesis|,|Cofactor-Biosynthesis|,|Vitamin-Biosynthesis|,|Thiamine-Biosynthesis|,|Thiazole-Biosynthesis|	|TAX-2|	RXN-12609,THIAZOLSYN2-RXN,DXS-RXN,RXN-9788,RXN-9789,RXN-11319,RXN-14382,RXN0-308	5.3.99.10,2.8.1.10,2.2.1.7,2.8.1,2.7.7.73,4.1.99.19,2.8.1.7,		thiazole tautomerase;1-deoxy-D-xylulose 5-phosphate:thiol sulfurtransferase;1-deoxy-D-xylulose-5-phosphate synthase;carboxy-adenylated-[ThiS sulfur-carrier-protein] sulfurtransferase;ThiS adenylyltransferase;2-iminoacetate synthase;cysteine :[Thil sulfur-protein cysteine] sulfurtransferase;L-cysteine:[protein cysteine] sulfurtransferase			False	True	
-F420-3-BIOSYN-ARCHAEA	F420 Biosynthesis until 3 glutamine residues		|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Biosynthesis|,|Cofactor-Biosynthesis|	|TAX-2157|	RXN-21088,RXN-19229,RXN-19230,RXN-21089,1.5.99.9-RXN,RXN-8080,RXN-8081,RXN-8087	2.7.7.68,2.5.1.147,4.3.1.32,2.7.2.28,1.5.98.1,6.3.2.31,6.3.2.34,6.3.2.32	RXN-21089	2-phospho-L-lactate guanylyltransferase;5-amino-6-(D-ribitylamino)uracil-L-tyrosine 4-hydroxyphenyl transferase;7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase;2-phospho-L-lactate transferase;methylenetetrahydromethanopterin dehydrogenase;coenzyme F420-0:L-glutamate ligase;coenzyme F420-1:gamma-L-glutamate ligase;coenzyme gamma-F420-2:alpha-L-glutamate ligase			False	True	
-LDH-ETF-PWY	Electron bifurcating LDH/Etf complex		|Pyruvate-Degradation|,|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Energy-Metabolism|,|Fermentation|,|Fermentation-to-Acids|,|Acetyl-CoA-Butyrate|	|TAX-2|	LDH-ETF	1.3.1.110		Electron bifurcating lactate dehydrogenase			False	True	
+F420-3-BIOSYN-ARCHAEA	F420 Biosynthesis until 3 glutamine residues		|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Biosynthesis|,|Cofactor-Biosynthesis|	|TAX-2157|	RXN-21088,RXN-19229,RXN-19230,RXN-21089,1.5.99.9-RXN,RXN-8080,RXN-8081,RXN-8087	2.7.7.68,2.5.1.147,4.3.1.32,2.7.8.28,1.5.98.1,6.3.2.31,6.3.2.34,6.3.2.32	RXN-21089	2-phospho-L-lactate guanylyltransferase;5-amino-6-(D-ribitylamino)uracil-L-tyrosine 4-hydroxyphenyl transferase;7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase;2-phospho-L-lactate transferase;methylenetetrahydromethanopterin dehydrogenase;coenzyme F420-0:L-glutamate ligase;coenzyme F420-1:gamma-L-glutamate ligase;coenzyme gamma-F420-2:alpha-L-glutamate ligase			False	True	
+LDH-ETF-PWY	Electron bifurcating LDH/Etf complex		|Pyruvate-Degradation|,|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Energy-Metabolism|,|Fermentation|,|Fermentation-to-Acids|,|Acetyl-CoA-Butyrate|	|TAX-2|	LDH-ETF	1.1.1.436		Electron bifurcating lactate dehydrogenase			False	True	
 H4SPT-SYN	H4SPT-SYN	Biosynthesis of tetrahydrosarcinapterin from tetrahydromethanopterin	|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Biosynthesis|,|Cofactor-Biosynthesis|	|TAX-2157|	RXN-11103	6.3.2.33		tetrahydrosarcinapterin synthase			False	True	
 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	
@@ -52,3 +52,7 @@ ISOBILE-BIOSYN	iso-bile acids biosynthesis (NADH or NADPH dependent)	iso-bile ac
 |PCEDEG-PWY2|	tetrachloroethene degradation II	tetrachloroethene degradation,PCE degradation,perchloroethene degradation	|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Degradation|,|CHLORINATED-COMPOUNDS-DEG|	|TAX-2|	TCEREDCHLOR-RXN,1.97.1.8-RXN	1.21.99.M1/1.21.99.5,1.21.99.5		trichloroethene-reductive dehalogenase;tetrachloroethene reductive dehalogenase	2	2	False	True	
 ARGSYN-SUCC-PWY	L-arginine biosynthesis via citrulline and succinylated intermediates	L-arginine biosynthesis via citrulline and succinylated intermediates	|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Biosynthesis|,|Amino-Acid-Biosynthesis|,|IND-AMINO-ACID-SYN|,|ARGININE-SYN|	|TAX-2|	NSUCCGLU-SYNKIN-NSUCCGLUP-REDUCTASE,SUCCORNTRANSAM-RXN,RXN-9778,NSUCCCITRULLINE-DESUCC,ARGSUCCINSYN-RXN,ARGSUCCINLYA-RXN,CARBPSYN-RXN	,2.6.1.81,2.1.3.11,,6.3.4.5,4.3.2.1,6.3.5.5	RXN-9778	aggregated reaction N-succinylglutamate synthase,N-succinylglutamate kinase, and N-succinylglutamylphosphate reductase;succinylornithine transaminase;N-succinylornithine carbamoyltransferase;N-succinylcitrulline desuccinylase;arginosuccinate synthetase;argininosuccinase;carbamoyl-phosphate synthase (glutamine-hydrolysing)	6	4	FALSE	True	
 CARBOX-HYDROX-BUT-CYC	Dicarboxylate-hydroxybutyrate cycle		|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Degradation|,|C1-COMPOUNDS|,|CO2-Fixation|,|Autotrophic-CO2-Fixation|	|TAX-2157|	PYRUFLAVREDUCT-RXN,PEPSYNTH-RXN,PEPCARBOX-RXN,MALATE-DEH-RXN,FUMHYDR-RXN,SUCCINATE-DEHYDROGENASE-UBIQUINONE-RXN,SUCCCOASYN-RXN,RXN-8891,RXN-11002,RXN-9092,RXN-8890,RXN-11667,RXN-1166,ACETYL-COA-ACETYLTRANSFER-RXN	1.2.7.1,2.7.9.2,4.1.1.31,1.1.1.37,4.2.1.2,1.3.5.1/1.3.5.4,6.2.1.5,1.2.1.76,1.1.1.co,6.2.1.40,4.2.1.120,4.2.1.17,1.1.1.35,2.3.1.9	RXN-8890	pyruvate ferredoxin oxidoreductase;pyruvate, water dikinase;phosphoenolpyruvate carboxylase;malate dehydrogenase;fumarate hydratase;succinate dehydrogenase / fumarate reductase;succinyl-CoA synthetase;succinyl-CoA reductase;succinate semialdehyde reductase (NADPH);4-hydroxybutyrate---CoA ligase (AMP-forming);4-hydroxybutyryl-CoA dehydratase;3-hydroxybutyryl-CoA dehydratase;3-hydroxyacyl-CoA dehydrogenase;acetyl-CoA C-acetyltransferase	14	14	FALSE	True	
+|PWY-7754|	bile acid 7α-dehydroxylation	bile acid 7α-dehydroxylation,secondary bile acid biosynthesis,bile acids degradation	|Fatty-Acid-and-Lipid-Degradation|,|Steroids-Degradation|,|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Degradation|,|CARBOXYLATES-DEG|,|Bile-Acids-Degradation|	|TAX-2|	CHOLATE—COA-LIGASE-RXN,BAIAEUBSP-RXN,BAI3OXO-OXRED-RXN,RXN-17398,RXN-17399,RXN-17400,RXN-21335,RXN-21336,RXN-19429,RXN-19428,RXN-21338,RXN-21339,RXN-21340,RXN-21341	6.2.1.7,1.1.1.395,1.3.1.115,6.2.1.7,1.1.1.395,1.3.1.115,2.8.3.25,4.2.1.106,1.3.1.114,1.3.1.114,2.8.3.25,4.2.1.106,1.3.1.114,1.3.1.114		cholate-CoA ligase;choloyl-CoA 3-dehydrogenase;3-oxo-choloyl-CoA dehydrogenase;chenodeoxycholate-CoA ligase;chenodeoxycholoyl-CoA 3-dehydrogenase;7alpha-hydroxy-3-oxochol-4-en-24-oyl-CoA dehydrogenase;bile acid coenzyme A transferase;7alpha,12alpha-dihydroxy-3-oxochol-4-enoate dehydratase;12-alpha-hydroxy-3 oxochola-4,6-dienoate 6-reductase;12-alpha-hydroxy-3 oxochol-4-enoate 4-reductase;bile acid coenzyme A transferase;7alpha-hydroxy-3-oxochol-4-enoate dehydratase;3-oxochol-4,6-dienoate 6-reductase;3-oxochol-4-enoate 4-reductase	14	14	False	True	
+|PWY-8134|	bile acid 7β-dehydroxylation	bile acid 7β-dehydroxylation,ursodeoxycholate 7-dehydroxylation	|Fatty-Acid-and-Lipid-Degradation|,|Steroids-Degradation|,|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Degradation|,|CARBOXYLATES-DEG|,|Bile-Acids-Degradation|	|TAX-2|	RXN-21342,RXN-21343,RXN-17416,RXN-17419,RXN-21344,RXN-21340,RXN-21341	6.2.1.7,1.1.1.395,1.3.1.116,4.2.1.M3,2.8.3.25,1.3.1.114,1.3.1.114		ursodeoxycholate-CoA ligase;ursodeoxycholoyl-CoA 3-dehydrogenase;7beta-dihydroxy-3-oxo-5beta-cholanoyl-CoA 4-oxidoreductase;7beta-hydroxy-3-oxochol-4-en-24-oyl-CoA 7beta-dehydratase;bile acid coenzyme A transferase;3-oxochol-4,6-dienoate 6-reductase;3-oxochol-4-enoate 4-reductase	7	7	False	True	
+|ASPARAGINE-BIOSYNTHESIS|	L-asparagine biosynthesis I	L-asparagine biosynthesis I	|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Biosynthesis|,|Amino-Acid-Biosynthesis|,|IND-AMINO-ACID-SYN|,|ASPARAGINE-SYN|	|TAX-2|,|TAX-2759|,|TAX-2157|	ASNSYNB-RXN	6.3.5.4		asparagine synthetase	1	1	False	True	
+|ARGSYN-PWY|	L-arginine biosynthesis I (via L-ornithine)	L-arginine biosynthesis I (via L-ornithine)	|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Biosynthesis|,|Amino-Acid-Biosynthesis|,|IND-AMINO-ACID-SYN|,|ARGININE-SYN|	|TAX-2157|,|TAX-33090|,|TAX-2|	ARGSUCCINSYN-RXN,ARGSUCCINLYA-RXN,ORNCARBAMTRANSFER-RXN,CARBPSYN-RXN,N-ACETYLTRANSFER-RXN,ACETYLGLUTKIN-RXN,N-ACETYLGLUTPREDUCT-RXN,ACETYLORNTRANSAM-RXN,ACETYLORNDEACET-RXN	6.3.4.5,4.3.2.1,2.1.3.3,6.3.5.5,2.3.1.1,2.7.2.8,1.2.1.38,2.6.1.11,3.5.1.16	ACETYLORNDEACET-RXN,ACETYLORNDEACET-RXN	ARGSUCCINSYN-RXN;argininosuccinate lyase;ornithine carbamoyltransferase;carbamoyl phosphate synthetase;N-acetylglutamate synthase;acetylglutamate kinase;N-acetylglutamylphosphate reductase;N-acetylornithine aminotransferase;acetylornithine deacetylase	9	9	False	True	

dat/exception.tbl

@@ -14,3 +14,9 @@ D-ribulose-1,5-bisphosphate cleaving dioxygenase	RuBisCo
 1.1.1.244	methanol dehydrogenase (high similarity to EC 1.1.1.1)
 1.1.1.26	glycolate dehydrogenase
 2.6.1.19	4-aminobutyrate aminotransferase
+1.1.1.52	3alphaHSDH
+1.1.1.391	3betaHSDH (high similarity to EC 1.1.1.21)
+1.1.1.159	7alphaHSDH
+1.1.1.201	7betaHSDH
+1.1.1.176	12alphaHSDH
+1.1.1.238	12betaHSDH

dat/medium_prediction_rules.tsv

@@ -20,7 +20,7 @@ N2	cpd00528	"N2FIX-PWY" | "PWY-7576"	25	FALSE	Nitrogen fixation	Inorganics
 O2	cpd00007	"PWY-3781" | "PWY1YI0-3" | "PWY-7279" | "PWY1YI0-6"	12.5	FALSE	aerobic respiration (1 - I (cytochrome c); 2- NDH-1 to cytochrome c oxidase via plastocyanin; 3 - II (cytochrome c); 3 - ;4- in cyanobacteria)	Inorganics
 O2	cpd00007	"PWY0-1565" | "PWY0-1561" | "PWY0-1544" | "PWY-7545" | "PWY-7544" | "PWY0-1353" | "PWY0-1329"	12.5	FALSE	1 - D-Lactate to Cytochrome bo; 2 - glyc3p to cytochrome bo; 3 - Pro to Cytochom bo; 4 - Pyr to cytochrome bd; 5  - Pyr to cytochrome bo; 6 - Succ to cytochrome bd; 7  - Succ to cytochrome bo	Inorganics
 O2	cpd00007	"PWY0-1334" | "PWY0-1568" | "PWY0-1335" | "PWY0-1567"	12.5	FALSE	NADH to cytochrome	Inorganics
-O2	cpd00007	rxn05747 | rxn09272 | rxn08288 | rxn00145	12.5	FALSE	Reactions from respiration chain (complex I + II), a quinol oxidases and a lactate dehydrogenase (cytochrome) 	Inorganics
+O2	cpd00007	(rxn05747 | rxn09272) & rxn12494	12.5	FALSE	Reactions from respiration chain (complex I + II)	Inorganics
 CO2	cpd00011	"CALVIN-PWY" | "CODH-PWY" | "PWY-5789" | "PWY-7784" | "LWP-GS" | "METHANOGENESIS-PWY"	25	FALSE	CO2 fixation, methanogenesis	Inorganics
 H2	cpd11640	"CODH-PWY" | "LWP-GS" | "METHANOGENESIS-PWY" | "PWY-7867"	100	FALSE	Ljungdahl-Wood pathway, methanogenesis	Inorganics
 Photons	cpd11632	"PWY-101"	50	FALSE	photosynthesis light reactions	Inorganics
@@ -31,22 +31,22 @@ D-Glucose	cpd00027	rxn05226 | rxn08612	5	TRUE	D-glucose transport via PEP:Pyr PT
 D-Glucose	cpd00027	rxn05573 | rxn08616	5	TRUE	D-glucose transport in via proton symport	Saccharides
 D-Glucose	cpd00027	rxn05147 | rxn08606	5	TRUE	D-Glucose-ABC transport	Saccharides
 D-Fructose	cpd00082	rxn05560 | rxn08536	5	TRUE	D-Fructose-specific PTS-System	Saccharides
-Lactose	cpd00208	"LACTOSECAT-PWY" | "LACTOSEUTIL-PWY" | "BGALACT-PWY"	2.5	TRUE		Saccharides
-Starch (n=27)	cpd90003	rxn90043 & rxn90034	0.18	TRUE	Pullulanase-type debranching enzyme and alpha-amylase	Saccharides
-Starch (n=27)	cpd90003	"METHANOGENESIS-PWY" | "PWY-7867"	NA	TRUE	Do not add starch for methanogens, can stop methanogenesis to be predicted	Saccharides
-Maltose	cpd00179	"MALTOSECAT-PWY"	2.5	TRUE		Saccharides
-2'-Fucosyllactose	cpd90001	"2FLHYD"	1.67	TRUE	Alpha-fucosidase & ABC transport	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" | "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
-Trehalose	cpd00794	"PWY0-1182" | "PWY0-1466" | "PWY-2721" | "PWY-2722" | "PWY-2723" | "TREDEGLOW-PWY"	2.5	TRUE		Saccharides
 Xylose	cpd00154	"XYLCAT-PWY" | "PWY-5516" | "PWY-6760" | "PWY-7294" | "PWY-7178" | "PWY-8020" | "PWY-8330"	5	TRUE		Saccharides
 Fucose	cpd00751	"FUCCAT-PWY" | "PWY-8444" | "PWY-8318"	5	TRUE		Saccharides
 Rhamnose	cpd00396	"RHAMCAT-PWY" | "PWY-6713" | "PWY-6714"	5	TRUE		Saccharides
+Maltose	cpd00179	"MALTOSECAT-PWY"	2.5	TRUE		Saccharides
+Lactose	cpd00208	"LACTOSECAT-PWY" | "LACTOSEUTIL-PWY" | "BGALACT-PWY"	2.5	TRUE		Saccharides
+Sucrose	cpd00076	"SUCUTIL-PWY" | "PWY-621" | "PWY-5384" | "SUCROSEUTIL2-PWY"	2.5	TRUE		Saccharides
+Trehalose	cpd00794	"PWY0-1182" | "PWY0-1466" | "PWY-2721" | "PWY-2722" | "PWY-2723" | "TREDEGLOW-PWY"	2.5	TRUE		Saccharides
+Melitose/Raffinose	cpd00382	rxn05643 & (rxn00818 | rxn34781)	1.67	TRUE	Raffinose transporter AND galactohydrolase	Saccharides
+Starch (n=27)	cpd90003	rxn90043 & rxn90034 & !("METHANOGENESIS-PWY") & !("PWY-7867")	0.18	TRUE	Pullulanase-type debranching enzyme and alpha-amylase and Do not add starch for methanogens, can stop methanogenesis to be predicted	Saccharides
+Pectin	cpd27519	"PWY-7246" | "PWY-7248"	1.67	TRUE		Saccharides
+Inulin	cpd28763	"INULIN-DEGRADATION-EXO" | "INULIN-DEGRADATION"	0.42	TRUE		Saccharides
+Xylan-b-1-4	cpd90021	"PWY-6717"	0.01	TRUE	1,4-D-beta-Xylan (n=500) degradation, extracellular	Saccharides
+2'-Fucosyllactose	cpd90001	"2FLHYD"	1.67	TRUE	Alpha-fucosidase & ABC transport	Saccharides
+sulfoquinovose	cpd22614	"PWY-7446" | "PWY-7722"	10	TRUE		Saccharides
 
 L-Tryptophan	cpd00065	!("TRPSYN-PWY2" | "TRPSYN-PWY")	0.1	TRUE		Amino acids
 L-Histidine	cpd00119	!"HISTSYN-PWY"	0.1	TRUE		Amino acids
@@ -62,7 +62,7 @@ L-Leucine	cpd00107	!("LEUSYN-PWY" & (rxn00003 | rxn33164) & rxn02186 & rxn00898)
 L-Lysine	cpd00039	!("DAPLYSINESYN-PWY" | "PWY-2941" | "PWY-2942" | "PWY-3081" | "PWY-5097")	0.1	TRUE		Amino acids
 L-Methionine	cpd00060	!("HOMOSER-METSYN-PWY" | "PWY-702" | "HSERMETANA-PWY" | "PWY-7977")	0.1	TRUE		Amino acids
 L-Phenylalanine	cpd00066	!((rxn01256 & rxn01000 & (rxn00493 | rxn21134 | rxn28060 | rxn38254)) | "PWY-3462" | "PWY-7432")	0.1	TRUE		Amino acids
-L-Proline	cpd00129	!("PROSYN-PWY" | "PWY-3341")	0.1	TRUE		Amino acids
+L-Proline	cpd00129	!("PROSYN-PWY" | "PWY-3341" | rxn00471)	0.1	TRUE	Either one of the metacyc pathways "PROSYN-PWY”, "PWY-3341" or the biosynthesis from ornithine via EC 4.3.1.12 (ornithine cyclodeaminase)	Amino acids
 L-Threonine	cpd00161	!("HOMOSER-THRESYN-PWY" | "THRBIOSYN-GS")	0.1	TRUE	Either MetaCycs HOMOSER-THRESYN-PWY (from L-homoserine to Thr) or gapseq connected pathway of the same route but together with L-Homoserine synthesis.	Amino acids
 L-Tyrosine	cpd00069	!("TYRSYN" | "PWY-3461" | "PWY-6120" | "PWY-6134")	0.1	TRUE		Amino acids
 L-Valine	cpd00156	!"VALSYN-PWY"	0.1	TRUE		Amino acids
@@ -74,12 +74,13 @@ Riboflavin	cpd00220	!("RIBOSYN2-PWY" | "PWY-6167")	0.025	TRUE		Vitamins
 L-Lactate	cpd00159	rxn90054	15	TRUE	Electron-bifurcating lactate dehydrogenase forming pyruvate (EC 1.3.1.110)	Organic acids
 L-Lactate	cpd00159	"PWY-5494" | "PWY-8086" | "PWY-8086-GS"	15	TRUE	acrylate pathway or lactate fermentation to propionate, acetate and h2	Organic acids
 Acetate	cpd00029	rxn00875 & rxn00225 & rxn00173 & rxn90001	20	TRUE	EC 2.8.3.8, EC 2.7.2.1, EC 2.3.1.8, EC 1.3.1.109	Organic acids
+Acetate	cpd00029	rxn05488 & "PWY0-1313"	20	TRUE		Organic acids
 Acetate	cpd00029	"METH-ACETATE-PWY"	25	TRUE	Methanogenisis from acetate	Organic acids
 Succinate	cpd00036	"PWY-5677"	10	TRUE	Succinate fermentation to butyrate	Organic acids
 Succinate	cpd00036	(rxn00602 | rxn01996) & rxn90096 & rxn09174	10	TRUE	Succinate transformation to propionate (Na+ exporting). Part of PWY-8086	Organic acids
 Formate	cpd00047	"PWY-7868"	20	TRUE	coenzyme B/coenzyme M regeneration V (formate-dependent) involved in methanogenesis	Organic acids
+Pyruvate	cpd00020	rxn05469 & ("PWY-8274" | "P108-PWY" | "PWY-5480" | "PWY-5481" | "PWY-5482" | "PWY-5486" | "PWY-5938" | "PWY-5939" | "PWY-6389" | "PWY-6583" | "PWY-6587" | "PWY-6588" | "PWY3O-440" | "PYRUVDEHYD-PWY" | "CENTFERM-PWY")	10	TRUE		Organic acids
 
-sulfoquinovose	cpd22614	"PWY-7446" | "PWY-7722"	10	TRUE		Secondary plant metabolites
 Gallate	cpd01020	"GALLATE-DEGRADATION-II-PWY" | "GALLATE-DEGRADATION-I-PWY" | "P3-PWY"	10	TRUE		Secondary plant metabolites
 Quercetin	cpd00313	"QUERCETIN-ANAERO-DEG"	10	TRUE	Key-reaction: Taxifolin isomerase (EC 5.5.1.6)	Secondary plant metabolites
 Genistein	cpd03971	rxn90097	10	TRUE	Genistein reductase	Secondary plant metabolites