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975e37f
getDBhit() function implemented in R
Waschina Mar 3, 2025
e1fe68c
getDBhit implementation in R
Waschina Mar 3, 2025
dee5da2
First steps towards reference sequence collate before batch alignment
Waschina Mar 4, 2025
dabdebf
Merge pull request #253 from jotech/master
Waschina Mar 4, 2025
052426c
More steps towards batch alignments
Waschina Mar 4, 2025
9f15d05
initial eggnog-mapper import scripts
jotech Mar 13, 2025
1fffb42
getting req seq files
Waschina Mar 21, 2025
c612763
Merge pull request #255 from jotech/master
Waschina Mar 25, 2025
cd5124b
Finished creating full fasta with all required reference seqs
Waschina Mar 28, 2025
e9cb4e5
first batch blast test
Waschina Mar 28, 2025
3be0cba
Merge pull request #256 from jotech/master
Waschina Mar 28, 2025
45dcb32
Supporting blast, diamond, and mmseq2 as aligners
Waschina Mar 28, 2025
c13d470
Analysing batch alignment statistics
Waschina Mar 28, 2025
c7ae8c8
First reaction output table with new batch alignments
Waschina Mar 28, 2025
f781473
Pathway prediction output table with new batch alignments
Waschina Mar 29, 2025
77fa1ac
Testing "-e <EC>" input
Waschina Mar 29, 2025
f4744f0
Corrected error in pathway presence/absence prediction
Waschina Mar 30, 2025
eabf8ef
Finalized pathway presence/absence inference from alignments
Waschina Mar 30, 2025
37545de
Small correction to threshold handling
Waschina Mar 30, 2025
1dc03b9
use 'strictCandidate' option
Waschina Mar 30, 2025
5a24d29
Speed improvements via 'parallel'
Waschina Mar 31, 2025
cc7cd53
Use vagueCutoff parameter in pathway completeness calculations
Waschina Mar 31, 2025
5108f08
Update Complex Detection and Vague Reaction Handling
Waschina Apr 1, 2025
2ef36d9
Translate genome when nucl genome input using pyrodigal
Waschina Apr 2, 2025
da3efef
Update installation instructions and conda env definition
Waschina Apr 2, 2025
0b9dd55
Add pathway prediction status to [...]-Reaction.tbl table
Waschina Apr 2, 2025
98892b4
New output table comment header
Waschina Apr 2, 2025
8435792
Allow different aligners in transporter prediction
Waschina Apr 2, 2025
111199c
getDBhit() function implemented in R
Waschina Mar 3, 2025
6cde2ef
getDBhit implementation in R
Waschina Mar 3, 2025
40483da
First steps towards reference sequence collate before batch alignment
Waschina Mar 4, 2025
58ef3e7
More steps towards batch alignments
Waschina Mar 4, 2025
5fc799d
initial eggnog-mapper import scripts
jotech Mar 13, 2025
254619f
getting req seq files
Waschina Mar 21, 2025
2212735
Finished creating full fasta with all required reference seqs
Waschina Mar 28, 2025
ae561de
first batch blast test
Waschina Mar 28, 2025
2eee085
Supporting blast, diamond, and mmseq2 as aligners
Waschina Mar 28, 2025
687c1cf
Analysing batch alignment statistics
Waschina Mar 28, 2025
a7e70f5
First reaction output table with new batch alignments
Waschina Mar 28, 2025
1351678
Pathway prediction output table with new batch alignments
Waschina Mar 29, 2025
6df5908
Testing "-e <EC>" input
Waschina Mar 29, 2025
371bf3c
Corrected error in pathway presence/absence prediction
Waschina Mar 30, 2025
e3edb89
Finalized pathway presence/absence inference from alignments
Waschina Mar 30, 2025
faba2ae
Small correction to threshold handling
Waschina Mar 30, 2025
c569176
use 'strictCandidate' option
Waschina Mar 30, 2025
43fb55d
Speed improvements via 'parallel'
Waschina Mar 31, 2025
c4a8b83
Use vagueCutoff parameter in pathway completeness calculations
Waschina Mar 31, 2025
551e782
Update Complex Detection and Vague Reaction Handling
Waschina Apr 1, 2025
71d9162
Translate genome when nucl genome input using pyrodigal
Waschina Apr 2, 2025
2a28867
Update installation instructions and conda env definition
Waschina Apr 2, 2025
9575f4c
Add pathway prediction status to [...]-Reaction.tbl table
Waschina Apr 2, 2025
da6a822
New output table comment header
Waschina Apr 2, 2025
4941cd4
Allow different aligners in transporter prediction
Waschina Apr 3, 2025
41473b8
Merge branch 'batch_alignment_tests' of github.com:jotech/gapseq into…
Waschina Apr 3, 2025
6d7e597
Moved gram prediction to gapseq find
Waschina Apr 3, 2025
5209ec6
ORF Coverage calculation and pathway names in '-Pathways.tbl'
Waschina Apr 3, 2025
587e14d
First steps adjusting draft model generation
Waschina Apr 4, 2025
d9ac372
Merge pull request #261 from jotech/master
Waschina Apr 5, 2025
f584ca6
Adjustments in draft generation – bug fix in transporter.sh
Waschina Apr 7, 2025
a918010
Update tutorial
Waschina Apr 8, 2025
6c68a99
Draft script to process gapseq find-transport alignment results
Waschina Apr 10, 2025
6cadcb2
Adjust transport alignment analysis
Waschina Apr 10, 2025
7f45ecf
Renamed Neu5Ac to N-acetylneuraminate
Waschina Apr 11, 2025
23c42e1
Optimized transporter script finished
Waschina Apr 11, 2025
680c06d
Added ammonium channel to custom seed transporter table
Waschina Apr 11, 2025
62b2ee9
Update gapseq start script and moved 'doall' to separate script file
Waschina Apr 14, 2025
2c14f31
Smaller changes in docs and doall
Waschina Apr 14, 2025
6cbeab0
Small clean up
Waschina Apr 15, 2025
5b7476c
Allow custom aligner options to be proided to alignment tool
Waschina Apr 15, 2025
1c6cad7
Only list pathways matching key with option "-o" in 'gapseq find'
Waschina Apr 15, 2025
8f2736a
Respect option "-x" (no aligmnents) in 'gapseq find'
Waschina Apr 15, 2025
fffc635
'gapseq test' looks for optional dependencies
Waschina Apr 15, 2025
6450e4d
Modify installation instruction with opt dependencies info
Waschina Apr 15, 2025
b852169
Update documentation
Waschina Apr 15, 2025
1c45bca
Bug fix in pan draft (metabolite and reaction attributes)
Waschina Apr 15, 2025
7e4ed47
Added pyrodigal to conda environment definition
Waschina Apr 16, 2025
f170756
Bug fix when reading gff files
Waschina Apr 17, 2025
893eac1
File clean up
Waschina Apr 17, 2025
9227a56
Cleaning up options in find(-transport)
Waschina Apr 17, 2025
d9387be
Omit `-rxnWeights.RDS` and `-rxnXgenes.RDS` output files
Waschina Apr 21, 2025
5607729
Bug fix (when input file ends with other suffix than ".fna")
Waschina May 8, 2025
2477543
updated toy model files
jotech May 8, 2025
87cabee
updated toy data to work with usage example
jotech May 8, 2025
acc8c02
correct error with writing output files and quick test
jotech May 19, 2025
a24c7f9
Bug fix
Waschina May 23, 2025
31dfe42
Clean up and bug fix
Waschina May 23, 2025
641509d
updated toy files
jotech May 24, 2025
ac87dd2
updated gapseq test to check for cobrar version
jotech May 24, 2025
16dd870
Update Biochem-DB - Enabled dissimiliatory sulfite reduction
Waschina Jun 2, 2025
265f6ce
Update bile acid pathways
Waschina Jun 5, 2025
59df1e6
Update biochem-DB (HMO degradation)
Waschina Jun 30, 2025
a7d3f21
typo correction in usage instructions 'doall'
Waschina Aug 14, 2025
cebc2de
Bug fix (reaction names containing quotes)
Waschina Aug 19, 2025
6bc5242
gapseq adapt: added function to add/rm e donor
jotech Aug 19, 2025
8e203ac
Bug fix in pan-draft recon
Waschina Aug 20, 2025
9c076bb
Update documentation
Waschina Aug 21, 2025
5f6af7a
Added missing reaction for sulfur reduction
Waschina Aug 22, 2025
d5a4a86
Fix of small bug in script for DB corrections
Waschina Aug 22, 2025
e3ad402
Biochem DB update
Waschina Aug 22, 2025
5db6657
Corrected EC number in custom pathway
Waschina Aug 22, 2025
db0c656
Added missing reaction in archael CoA-biosynthesis
Waschina Aug 23, 2025
a661322
Biochemistry DB update (some archaeal pathways)
Waschina Aug 24, 2025
47d72fd
Biochemistry DB Update - Methanofuran Biosynthesis
Waschina Aug 25, 2025
12c8bc0
Updated custom pwy DB and medium prediction
Waschina Aug 26, 2025
d322e97
Enabling option for offline mode in 'doall'
Waschina Aug 26, 2025
e4c8db6
Omit option "-a" in gapseq find
Waschina Aug 27, 2025
9b90aca
EC 1.3.1.110 transferred to EC 1.1.1.436
Waschina Aug 28, 2025
2733b48
Small addition to previous commit
Waschina Aug 28, 2025
943dc9b
Option to specify custom directory for ref. sequence database
Waschina Aug 29, 2025
663a177
Updated install docs
Waschina Aug 29, 2025
0100c3b
Update medium prediction
Waschina Aug 29, 2025
a546fa2
Database corrections for reactions of the EC 7.1.1 group
Waschina Aug 29, 2025
e5c8866
Removing cross-feeding tutorial for now
Waschina Aug 29, 2025
6f41551
Added lactate oxidase (EC 1.1.3.2) to biochemistry DB
Waschina Sep 1, 2025
3a8044b
Moving ARGSYN-PWY to custom pathways
Waschina Oct 2, 2025
8551e59
Tag Sulfoquinovose as Saccharide in medium prediction
Waschina Oct 2, 2025
b7f59e7
Handle potential EC conflict between 1.1.2.3 and 1.1.3.2
Waschina Oct 2, 2025
5a1fb11
Merge branch 'batch_alignment_tests' of github.com:jotech/gapseq into…
jotech Oct 15, 2025
61bd341
Update gapseq environment yaml
Waschina Oct 20, 2025
5e8bf5b
Bug fix in enumerating candidate reactions linked to complexes
Waschina Oct 23, 2025
e157524
No DB download when updating manually
Waschina Oct 24, 2025
193865a
Merge branch 'batch_alignment_tests' of github.com:jotech/gapseq into…
jotech Nov 5, 2025
54757d5
added pyruvate to medium prediction
jotech Nov 5, 2025
4ab4dc1
added acetate medium prediction rule
jotech Nov 5, 2025
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6 changes: 3 additions & 3 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -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
```


Expand All @@ -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.
Expand Down
2 changes: 1 addition & 1 deletion dat/SEED2VMH_translation_edited.csv
Original file line number Diff line number Diff line change
Expand Up @@ -1920,7 +1920,7 @@ rxn10119,HYD2
rxn10120,NO3R1
rxn10121,NO3R2
rxn10122,NADH6
rxn10125,THD2
rxn09295,THD2
rxn10126,SUCD4
rxn10127,TMAOR1e
rxn10128,TMAOR2e
Expand Down
1 change: 1 addition & 0 deletions dat/altec.csv
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
76 changes: 69 additions & 7 deletions dat/corrections_seed_reactionDB.tsv

Large diffs are not rendered by default.

8 changes: 6 additions & 2 deletions dat/custom_pwy.tbl
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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 7&alpha;-dehydroxylation bile acid 7&alpha;-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 7&beta;-dehydroxylation bile acid 7&beta;-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
6 changes: 6 additions & 0 deletions dat/exception.tbl
Original file line number Diff line number Diff line change
Expand Up @@ -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
29 changes: 15 additions & 14 deletions dat/medium_prediction_rules.tsv
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
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