Added new custom pathway for bacterial iso-bile acid biosynthesis

The new pathway is based on the recent study Paik et al. (2022, Nature), DOI: https://doi.org/10.1038/s41586-022-04480-z This pathway combines the two metacyc pathways: 1. iso-bile acids biosynthesis I [PWY-7755] 2. iso-bile acids biosynthesis II [PWY-7756] Their only difference is that (1) is NADH-dependent and (2) is NADPH-dependent.
jotech · Oct 30, 2022 · f715432 · f715432
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diff --git a/dat/custom_pwy.tbl b/dat/custom_pwy.tbl
@@ -45,3 +45,4 @@ QUERCETIN-ANAERO-DEG	Anaerobe quercetin degradation	Anaerobe quercetin degradati
 PHLOROGLUCINOL-DEG-PWY	phloroglucinol degradation (anaerobic)	phloroglucinol degradation (anaerobic)	|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Degradation|,|AROMATIC-COMPOUNDS-DEGRADATION|	|TAX-1239|	R5-RXN,R6-RXN,R8-RXN,R7-RXN	1.3.1.57,3.7.1,2.8.3.8,2.3.1	R5-RXN	phloroglucinol reductase;dihydrophloroglucinol hydrolase;acetate CoA-transferase;3-hydroxy-5-oxohexanoyl-CoA thiolase
 PWY-8086-GS	(S)-lactate fermentation to propanoate	(<i>S</i>)-lactate fermentation to propanoate	|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Energy-Metabolism|,|Fermentation|,|Fermentation-to-Acids|,|Fermentation-to-propanoate|	|TAX-2|	FUMHYDR-RXN,R601-RXN,RXN0-268,METHYLMALONYL-COA-EPIM-RXN,METHYLMALONYL-COA-MUT-RXN,MALATE-DEH-RXN,RXN-19738,PYRUVATE-CARBOXYLASE-RXN,L-LACTATE-DEHYDROGENASE-RXN	4.2.1.2,1.3.5.4,2.8.3.M4,5.1.99.1,5.4.99.2,1.1.1.37,7.2.4.3,6.4.1.1,1.1.1.27	RXN-19738	FUMHYDR-RXN;R601-RXN;RXN0-268;METHYLMALONYL-COA-EPIM-RXN;METHYLMALONYL-COA-MUT-RXN;MALATE-DEH-RXN;(S)-methylmalonyl-CoA decarboxylase;PYRUVATE-CARBOXYLASE-RXN;L-LACTATE-DEHYDROGENASE-RXN
 THRBIOSYN-GS	Threonine biosynthis from aspartate via homoserine (gapseq)	L-threonine biosynthesis from aspartate (gapseq)	|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Biosynthesis|,|Amino-Acid-Biosynthesis|,|IND-AMINO-ACID-SYN|,|THREONINE-BIOSYNTHESIS|	|TAX-2157|,|TAX-33090|,|TAX-4751|,|TAX-2|	HOMOSERKIN-RXN,THRESYN-RXN,ASPARTATEKIN-RXN,ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE-RXN,HOMOSERDEHYDROG-RXN	2.7.1.39,4.2.3.1,2.7.2.4,1.2.1.11,1.1.1.3		homoserine kinase;threonine synthase;aspartate kinase;aspartate-semialdehyde dehydrogenase;homoserine dehydrogenase
+ISOBILE-BIOSYN	iso-bile acids biosynthesis (NADH or NADPH dependent)	iso-bile acids biosynthesis (NADH or NADPH dependent)	|Fatty-Acid-and-Lipid-Degradation|,|Steroids-Degradation|,|THINGS|,|FRAMES|,|Generalized-Reactions|,|Pathways|,|Degradation|,|CARBOXYLATES-DEG|,|Bile-Acids-Degradation|	|TAX-2|	3alpha-HSDH,3beta-HSDH	,		3alpha-hydroxysteroid dehydrogenase;3beta-hydroxysteroid dehydrogenase
diff --git a/dat/seq/Bacteria/user/44c3c97f35dad7fa14516d2165a895a1.fasta b/dat/seq/Bacteria/user/44c3c97f35dad7fa14516d2165a895a1.fasta
@@ -0,0 +1,48 @@
+>sp|P19337|BAIA2_CLOSV 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 OS=Clostridium scindens (strain JCM 10418 / VPI 12708) OX=29347 GN=baiA2 PE=1 SV=1
+MNLVQDKVTIITGGTRGIGFAAAKIFIDNGAKVSIFGETQEEVDTALAQLKELYPEEEVL
+GFAPDLTSRDAVMAAVGQVAQKYGRLDVMINNAGITSNNVFSRVSEEEFKHIMDINVTGV
+FNGAWCAYQCMKDAKKGVIINTASVTGIFGSLSGVGYPASKASVIGLTHGLGREIIRKNI
+RVVGVAPGVVNTDMTNGNPPEIMEGYLKALPMKRMLEPEEIANVYLFLASDLASGITATT
+VSVDGAYRP
+>tr|B0NAQ3|B0NAQ3_CLOS5 Uncharacterized protein OS=Clostridium scindens (strain ATCC 35704 / DSM 5676 / VPI 13733 / 19) OX=411468 GN=CLOSCI_00522 PE=4 SV=1
+MISMIRINQLKLNIKHSEADLKEKILKTLCISEDSLLSYEIKKQSLDARRKPELYYVYAV
+DVKVKNVSSIKKRVRNQNVQFKDKPLSYQIQANGTEVLHHRPVVIGTGPAGLFCGYQLAV
+LGYRPILLERGACVEERMQAVERFWATGELDQNCNVQFGEGGAGTFSDGKLNTLVHDSNG
+RSQKVLELFVKYGAPKEILYQHKPHIGTDVLSRVVKNIREAILSYGGEVRFLTRVTDILS
+ESAGEGRRLTALQVYDHAAGKEYALETEIAVLAIGHSARDTFSMLLKNEIPMESKSFAVG
+VRIEHPQAMIDEFQYGMKNDGSLPPASYKLTENFACGRGVYTFCMCPGGYVVNASSEPGR
+LAVNGMSYHDRDGFNANSAVIVTVTPQDYGGTGVLAGMEFQRRLEEAAYRLGKGRIPVQL
+FEDFCKNRPSKGPGDILPQMKGAYAWSNVREIFPPELSRALEEGIRSFDRKIKGYPRPDA
+LVSGVESRTSSPVRISRDESMQSTLFGLYPCGEGAGYAGGITSAAMDGLKTAESIVKKYQ
+SLDKLPKGLRNF
+>sp|C8WMP0|3AHD_EGGLE 3alpha-hydroxysteroid dehydrogenase OS=Eggerthella lenta (strain ATCC 25559 / DSM 2243 / JCM 9979 / NCTC 11813 / VPI 0255) OX=479437 GN=Elen_0690 PE=1 SV=1
+MGIYVITGATSGIGAKTAEILRERGHEVVNIDLNGGDINANLATKEGRAGAIAELHERFP
+EGIDAMICNAGVSGGKVPISLIISLNYFGATEMARGVFDLLEKKGGSCVVTSSNSIAQGA
+ARMDVAGMLNNHADEDRILELVKDVDPAIGHVYYASTKYALARWVRRMSPDWGSRGVRLN
+AIAPGNVRTAMTANMLPEQRAAMEAIPVPTHFGEEPLMDPVEIANAMAFIASPEASGING
+VVLFVDGGTDALLNSEKVY
+>sp|C8WMP0|3AHD_EGGLE 3alpha-hydroxysteroid dehydrogenase OS=Eggerthella lenta (strain ATCC 25559 / DSM 2243 / CCUG 17323 / JCM 9979 / KCTC 3265 / NCTC 11813 / VPI 0255 / 1899 B) OX=479437 GN=Elen_0690 PE=1 SV=1
+MGIYVITGATSGIGAKTAEILRERGHEVVNIDLNGGDINANLATKEGRAGAIAELHERFP
+EGIDAMICNAGVSGGKVPISLIISLNYFGATEMARGVFDLLEKKGGSCVVTSSNSIAQGA
+ARMDVAGMLNNHADEDRILELVKDVDPAIGHVYYASTKYALARWVRRMSPDWGSRGVRLN
+AIAPGNVRTAMTANMLPEQRAAMEAIPVPTHFGEEPLMDPVEIANAMAFIASPEASGING
+VVLFVDGGTDALLNSEKVY
+>sp|A7B3K3|3AHDP_RUMGV 3alpha-hydroxysteroid dehydrogenase OS=Ruminococcus gnavus (strain ATCC 29149 / VPI C7-9) OX=411470 GN=baiA PE=1 SV=1
+MFMMLKNKVAIVTGGTRGIGFAVVKKFIENGAAVSLWGSRQETVDQALEQLKELYPDAKI
+SGKYPSLKDTAQVTAMINQVKEEFGAVDILVNNAGISQSTSFYNYQPEEFQKIVDLNVTA
+VFNCSQAAAKIMKEQGGGVILNTSSMVSIYGQPSGCGYPASKFAVNGLTKSLARELGCDN
+IRVNAVAPGITRTDMVAALPEAVIKPLIATIPLGRVGEPEDIANAFLFLASDMASYVTGE
+ILSVDGAARS
+>sp|P07914|BAIA1_CLOSV 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 1/3 OS=Clostridium scindens (strain JCM 10418 / VPI 12708) OX=29347 GN=baiA3 PE=1 SV=3
+MKLVQDKITIITGGTRGIGFAAAKLFIENGAKVSIFGETQEEVDTALAQLKELYPEEEVL
+GFAPDLTSRDAVMAAVGTVAQKYGRLDVMINNAGITMNSVFSRVSEEDFKNIMDINVNGV
+FNGAWSAYQCMKDAKQGVIINTASVTGIYGSLSGIGYPTSKAGVIGLTHGLGREIIRKNI
+RVVGVAPGVVDTDMTKGLPPEILEDYLKTLPMKRMLKPEEIANVYLFLASDLASGITATT
+ISVDGAYRP
+>sp|P80702|DIDH_COMTE 3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase OS=Comamonas testosteroni OX=285 GN=hsdA PE=1 SV=2
+MSIIVISGCATGIGAATRKVLEAAGHQIVGIDIRDAEVIADLSTAEGRKQAIADVLAKCS
+KGMDGLVLCAGLGPQTKVLGNVVSVNYFGATELMDAFLPALKKGHQPAAVVISSVASAHL
+AFDKNPLALALEAGEEAKARAIVEHAGEQGGNLAYAGSKNALTVAVRKRAAAWGEAGVRL
+NTIAPGATETPLLQAGLQDPRYGESIAKFVPPMGRRAEPSEMASVIAFLMSPAASYVHGA
+QIVIDGGIDAVMRPTQF
+
diff --git a/dat/seq/Bacteria/user/cef7d61a04f14b663c3e4b457bca44f3.fasta b/dat/seq/Bacteria/user/cef7d61a04f14b663c3e4b457bca44f3.fasta
@@ -0,0 +1,27 @@
+>sp|P9WQP7|3BHS_MYCTU 3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase OS=Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) OX=83332 GN=Rv1106c PE=1 SV=1
+MLRRMGDASLTTELGRVLVTGGAGFVGANLVTTLLDRGHWVRSFDRAPSLLPAHPQLEVL
+QGDITDADVCAAAVDGIDTIFHTAAIIELMGGASVTDEYRQRSFAVNVGGTENLLHAGQR
+AGVQRFVYTSSNSVVMGGQNIAGGDETLPYTDRFNDLYTETKVVAERFVLAQNGVDGMLT
+CAIRPSGIWGNGDQTMFRKLFESVLKGHVKVLVGRKSARLDNSYVHNLIHGFILAAAHLV
+PDGTAPGQAYFINDAEPINMFEFARPVLEACGQRWPKMRISGPAVRWVMTGWQRLHFRFG
+FPAPLLEPLAVERLYLDNYFSIAKARRDLGYEPLFTTQQALTECLPYYVSLFEQMKNEAR
+AEKTAATVKP
+>sp|A7AZH2|3BHDP_RUMGV 3beta-hydroxysteroid dehydrogenase OS=Ruminococcus gnavus (strain ATCC 29149 / VPI C7-9) OX=411470 GN=RUMGNA_00694 PE=1 SV=1
+MNFGGFIMGRFDEKIMLVTGATSGIGRAVAIRAAKEGATVVAVGRNEERGAAVVAAMEEA
+GGKGEFMKCDVSNKDAVKALFAEIQEKYGKLDVAVNNAGIVGASKTVEELEDDDWFQVID
+ANLNSCFFCCREEVKLMQPSGGAIVNVSSVAGMRGFPSAAAYVASKHAVSGLTKAVAVDY
+ATKGITCNAICPAGTDTPLTERSSADIKTRMAEIAAQGKDPMEWLKNSMLSGKTETLQKK
+NATPEEQAATILYFASDEARHITGSIVASDGGFTTY
+>sp|C8WGQ3|3BHD2_EGGLE 3beta-hydroxysteroid dehydrogenase 2 OS=Eggerthella lenta (strain ATCC 25559 / DSM 2243 / CCUG 17323 / JCM 9979 / KCTC 3265 / NCTC 11813 / VPI 0255 / 1899 B) OX=479437 GN=Elen_1325 PE=1 SV=1
+MSEARHNPVLAGQTAVITGGASGIGKSIVQRFLEAGASCLAADLNEEALAALKQELAEYG
+DKLDVVKVDVSNRDDVEGMVDRAVQTFGQMDIIVNNAGIMDNLLPIAEMDDDVWERLMKV
+NLNSVMYGTRKAVRYFMERGEGGVIINTASLSGLCAGRGGCAYTASKFAVVGLTKNVAFM
+YADTGIRCNAICPGNTQTNIGVGMRQPSERGMAKATTGYAGATRSGTPEEISAAAAFLAS
+DQAGFINGETLTIDGGWSAY
+>tr|A0A388QR12|A0A388QR12_9BACT 3beta-hydroxysteroid-dehydrogenase/ decarboxylase isoform 1 OS=Verrucomicrobia bacterium OX=2026799 GN=EMGBD4_03880 PE=4 SV=1
+MSHPTVLVTGGGGFLGRAVVERCLTRGYTVRVYGRSALATDLAARVEFHRGDLADAAMLT
+AAVKGCDYVFHVAAKAGVWGKWEDYVRSNITGTETVVQACRDHGVTALVYTSTPSVVFNG
+ESFRGADESLPYGTEFLCAYAETKATAERRALEAASERLKVCALRPHLIWGPGDHHLFPR
+VLAAARAGKLRIVGDGANLVDVTHVDTAANAHLGALDALLAGRANGKAYFLSQGQPVKLW
+DFINRLVVGAGLLPITKRMPLRRAYALGALMEGLWTLLPLKGEPPMTRFVAVELAKDHWF
+DVSAAHRDLGLKPAVDTWTELDRLAATFRAKG