From 72ff3e000d1522ee3e877376a145fb4dcd04d9be Mon Sep 17 00:00:00 2001 From: jo Date: Fri, 8 Dec 2023 14:27:03 +0100 Subject: [PATCH] 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 --- dat/corrections_seed_reactionDB.tsv | 5 +- dat/custom_pwy.tbl | 1 + dat/medium_prediction_rules.tsv | 2 +- dat/nutrients.tsv | 2 +- ..._Class_Reactions_Aliases_unique_edited.tsv | 2 +- dat/seed_Enzyme_Name_Reactions_Aliases.tsv | 1 + dat/seed_metabolites_edited.tsv | 2 +- dat/seed_reactions_corrected.tsv | 5 +- dat/seq/Bacteria/user/3.2.1.7.fasta | 53 +++++++++++++++++++ .../Bacteria/user/INULIN-ABC-TRANSPORT.fasta | 36 +++++++++++++ src/gapseq_find.sh | 14 ++--- 11 files changed, 109 insertions(+), 14 deletions(-) create mode 100644 dat/seq/Bacteria/user/3.2.1.7.fasta create mode 100644 dat/seq/Bacteria/user/INULIN-ABC-TRANSPORT.fasta diff --git a/dat/corrections_seed_reactionDB.tsv b/dat/corrections_seed_reactionDB.tsv index 3f69d222..9eae3816 100644 --- 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 index c67d245e..2e81b70d 100644 --- 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,CO2 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 index db891df8..8cc3fd06 100644 --- 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 index 780225d7..12442208 100644 --- 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 index 333155e2..f7e8fd12 100644 --- 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 index 60ead56a..c5d6fbd9 100644 --- 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 index 3228f2f8..54f46519 100644 --- 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 diff --git a/dat/seed_reactions_corrected.tsv b/dat/seed_reactions_corrected.tsv index d20dcaa5..a495ead8 100644 --- a/dat/seed_reactions_corrected.tsv +++ b/dat/seed_reactions_corrected.tsv @@ -25577,7 +25577,7 @@ rxn29772 TRANS-RXNAVI-26732.ce.brachyexp.L-ARABITOL_L-ARABITOL TRANS-RXNAVI-2673 rxn29773 TRANS-RXNAVI-26732.ce.brachyexp.L-SORBOSONE_L-SORBOSONE TRANS-RXNAVI-26732.ce.brachyexp.L-SORBOSONE_L-SORBOSONE (1) cpd00001[0] + (1) cpd00002[0] + (1) cpd20927[1] <=> (1) cpd00008[0] + (1) cpd00009[0] + (1) cpd20927[0] -1:cpd00001:0:0:"H2O";-1:cpd00002:0:0:"ATP";-1:cpd20927:1:0:"L-Sorbosone";1:cpd00008:0:0:"ADP";1:cpd00009:0:0:"Phosphate";1:cpd00067:0:0:"H+";1:cpd20927:0:0:"L-Sorbosone" 1 (1) cpd00001[0] + (1) cpd00002[0] + (1) cpd20927[1] => (1) cpd00008[0] + (1) cpd00009[0] + (1) cpd00067[0] + (1) cpd20927[0] (1) H2O[0] + (1) ATP[0] + (1) L-Sorbosone[1] => (1) ADP[0] + (1) Phosphate[0] + (1) H+[0] + (1) L-Sorbosone[0] > > -6.82 0.72 cpd00001;cpd00002;cpd00008;cpd00009;cpd00067;cpd20927 OK 0 not.assessed rxn29774 TRANS-RXNAVI-26732.ce.brachyexp.LINEAR-ALPHA-GLUCAN_LINEAR-ALPHA-GLUCAN TRANS-RXNAVI-26732.ce.brachyexp.LINEAR-ALPHA-GLUCAN_LINEAR-ALPHA-GLUCAN (1) cpd00001[0] + (1) cpd00002[0] + (1) cpd29323[1] <=> (1) cpd00008[0] + (1) cpd00009[0] + (1) cpd29323[0] -1:cpd00001:0:0:"H2O";-1:cpd00002:0:0:"ATP";-1:cpd29323:1:0:"linear alpha-glucan";1:cpd00008:0:0:"ADP";1:cpd00009:0:0:"Phosphate";1:cpd00067:0:0:"H+";1:cpd29323:0:0:"linear alpha-glucan" 1 (1) cpd00001[0] + (1) cpd00002[0] + (1) cpd29323[1] => (1) cpd00008[0] + (1) cpd00009[0] + (1) cpd00067[0] + (1) cpd29323[0] (1) H2O[0] + (1) ATP[0] + (1) linear alpha-glucan[1] => (1) ADP[0] + (1) Phosphate[0] + (1) H+[0] + (1) linear alpha-glucan[0] > > -6.82 0.72 cpd00001;cpd00002;cpd00008;cpd00009;cpd00067;cpd29323 OK 0 not.assessed rxn29775 TRANS-RXNAVI-26732.ce.brachyexp.N-ACETYLNEURAMINATE_N-ACETYLNEURAMINATE TRANS-RXNAVI-26732.ce.brachyexp.N-ACETYLNEURAMINATE_N-ACETYLNEURAMINATE (1) cpd00001[0] + (1) cpd00002[0] + (1) cpd27569[1] <=> (1) cpd00008[0] + (1) cpd00009[0] + (1) cpd27569[0] -1:cpd00001:0:0:"H2O";-1:cpd00002:0:0:"ATP";-1:cpd27569:1:0:"N-ACETYLNEURAMINATE";1:cpd00008:0:0:"ADP";1:cpd00009:0:0:"Phosphate";1:cpd00067:0:0:"H+";1:cpd27569:0:0:"N-ACETYLNEURAMINATE" 1 (1) cpd00001[0] + (1) cpd00002[0] + (1) cpd27569[1] => (1) cpd00008[0] + (1) cpd00009[0] + (1) cpd00067[0] + (1) cpd27569[0] (1) H2O[0] + (1) ATP[0] + (1) N-ACETYLNEURAMINATE[1] => (1) ADP[0] + (1) Phosphate[0] + (1) H+[0] + (1) N-ACETYLNEURAMINATE[0] > > -6.82 0.72 cpd00001;cpd00002;cpd00008;cpd00009;cpd00067;cpd27569 OK 0 not.assessed -rxn29776 TRANS-RXNAVI-26732.ce.brachyexp.NYSTOSE_NYSTOSE TRANS-RXNAVI-26732.ce.brachyexp.NYSTOSE_NYSTOSE (1) cpd00001[0] + (1) cpd00002[0] + (1) cpd11602[1] <=> (1) cpd00008[0] + (1) cpd00009[0] + (1) cpd11602[0] -1:cpd00001:0:0:"H2O";-1:cpd00002:0:0:"ATP";-1:cpd11602:1:0:"Inulin";1:cpd00008:0:0:"ADP";1:cpd00009:0:0:"Phosphate";1:cpd00067:0:0:"H+";1:cpd11602:0:0:"Inulin" 1 (1) cpd00001[0] + (1) cpd00002[0] + (1) cpd11602[1] => (1) cpd00008[0] + (1) cpd00009[0] + (1) cpd00067[0] + (1) cpd11602[0] (1) H2O[0] + (1) ATP[0] + (1) Inulin[1] => (1) ADP[0] + (1) Phosphate[0] + (1) H+[0] + (1) Inulin[0] > > -6.82 0.72 cpd00001;cpd00002;cpd00008;cpd00009;cpd00067;cpd11602 OK 0 not.assessed +rxn29776 TRANS-RXNAVI-26732.ce.brachyexp.NYSTOSE_NYSTOSE TRANS-RXNAVI-26732.ce.brachyexp.NYSTOSE_NYSTOSE (1) cpd00001[0] + (1) cpd00002[0] + (1) cpd11602[1] <=> (1) cpd00008[0] + (1) cpd00009[0] + (1) cpd11602[0] -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" 1 (1) cpd00001[0] + (1) cpd00002[0] + (1) cpd11602[1] => (1) cpd00008[0] + (1) cpd00009[0] + (1) cpd00067[0] + (1) cpd11602[0] (1) H2O[0] + (1) ATP[0] + (1) Inulin[1] => (1) ADP[0] + (1) Phosphate[0] + (1) H+[0] + (1) Inulin[0] > > -6.82 0.72 cpd00001;cpd00002;cpd00008;cpd00009;cpd00067;cpd11602 OK 0 approved rxn29777 TRANS-RXNAVI-26732.ce.brachyexp.RIBITOL_RIBITOL TRANS-RXNAVI-26732.ce.brachyexp.RIBITOL_RIBITOL (1) cpd00001[0] + (1) cpd00002[0] + (1) cpd00366[1] <=> (1) cpd00008[0] + (1) cpd00009[0] + (1) cpd00366[0] -1:cpd00001:0:0:"H2O";-1:cpd00002:0:0:"ATP";-1:cpd00366:1:0:"Ribitol";1:cpd00008:0:0:"ADP";1:cpd00009:0:0:"Phosphate";1:cpd00067:0:0:"H+";1:cpd00366:0:0:"Ribitol" 1 (1) cpd00001[0] + (1) cpd00002[0] + (1) cpd00366[1] => (1) cpd00008[0] + (1) cpd00009[0] + (1) cpd00067[0] + (1) cpd00366[0] (1) H2O[0] + (1) ATP[0] + (1) Ribitol[1] => (1) ADP[0] + (1) Phosphate[0] + (1) H+[0] + (1) Ribitol[0] > > -6.82 0.72 cpd00001;cpd00002;cpd00008;cpd00009;cpd00067;cpd00366 OK 0 not.assessed rxn29778 TRANS-RXNAVI-26732.ce.brachyexp.RIBULOSE_RIBULOSE TRANS-RXNAVI-26732.ce.brachyexp.RIBULOSE_RIBULOSE (1) cpd00001[0] + (1) cpd00002[0] + (1) cpd29557[1] <=> (1) cpd00008[0] + (1) cpd00009[0] + (1) cpd29557[0] -1:cpd00001:0:0:"H2O";-1:cpd00002:0:0:"ATP";-1:cpd29557:1:0:"D-erythro-pentulose";1:cpd00008:0:0:"ADP";1:cpd00009:0:0:"Phosphate";1:cpd00067:0:0:"H+";1:cpd29557:0:0:"D-erythro-pentulose" 1 (1) cpd00001[0] + (1) cpd00002[0] + (1) cpd29557[1] => (1) cpd00008[0] + (1) cpd00009[0] + (1) cpd00067[0] + (1) cpd29557[0] (1) H2O[0] + (1) ATP[0] + (1) D-erythro-pentulose[1] => (1) ADP[0] + (1) Phosphate[0] + (1) H+[0] + (1) D-erythro-pentulose[0] > > -6.82 0.72 cpd00001;cpd00002;cpd00008;cpd00009;cpd00067;cpd29557 OK 0 not.assessed rxn29779 TRANS-RXNAVI-26732.ce.brachyexp.SORBITOL_SORBITOL TRANS-RXNAVI-26732.ce.brachyexp.SORBITOL_SORBITOL (1) cpd00001[0] + (1) cpd00002[0] + (1) cpd00588[1] <=> (1) cpd00008[0] + (1) cpd00009[0] + (1) cpd00588[0] -1:cpd00001:0:0:"H2O";-1:cpd00002:0:0:"ATP";-1:cpd00588:1:0:"Sorbitol";1:cpd00008:0:0:"ADP";1:cpd00009:0:0:"Phosphate";1:cpd00067:0:0:"H+";1:cpd00588:0:0:"Sorbitol" 1 (1) cpd00001[0] + (1) cpd00002[0] + (1) cpd00588[1] => (1) cpd00008[0] + (1) cpd00009[0] + (1) cpd00067[0] + (1) cpd00588[0] (1) H2O[0] + (1) ATP[0] + (1) Sorbitol[1] => (1) ADP[0] + (1) Phosphate[0] + (1) H+[0] + (1) Sorbitol[0] > > -6.82 0.72 cpd00001;cpd00002;cpd00008;cpd00009;cpd00067;cpd00588 OK 0 not.assessed @@ -34785,7 +34785,7 @@ rxn90055 Na-F0F1ATPase Na+ F1FO ATP synthase -1:cpd00008:0:0:"ADP";-1:cpd00009: rxn90057 ECHAF ferredoxin hydrogenase (chemiosmosis) -4:cpd00067:0:0:"H+";-2:cpd11620:0:0:"Reducedferredoxin";2:cpd11621:0:0:"Oxidizedferredoxin";1:cpd11640:0:0:"H2";2:cpd00067:1:0:"H+" 0 (4) cpd00067[0] + (2) cpd11620[0] <=> (2) cpd11621[0] + (1) cpd11640[0] + (2) cpd00067[1] (4) H+[0] + (2) Reducedferredoxin[0] <=> (2) Oxidizedferredoxin[0] + (1) H2[0] + (2) H+[1] = = 1e+07 1e+07 OK 0 Gapseq new corrected rxn90058 Coenzyme B:coenzyme M:methanophenazine oxidoreductase (chemiosmosis) -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+" 0 (3) cpd00067[0] + (1) cpd02935[0] + (1) cpd08702[0] <=> (1) cpd02246[0] + (1) cpd02817[0] + (1) cpd08701[0] + (2) cpd00067[1] (3) H+[0] + (1) CoM-S-S-CoB[0] + (1) Dihydromethanophenazine[0] <=> (1) CoM[0] + (1) HTP[0] + (1) Methanophenazine[0] + (2) H+[1] = = 1e+07 1e+07 OK 0 Gapseq new corrected rxn90059 hydrogen:2-(2,3-dihydropentaprenyloxy)phenazine oxidoreductase (chemiosmosis) -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+" 0 (2) cpd00067[0] + (1) cpd08701[0] + (1) cpd11640[0] <= (1) cpd08702[0] + (2) cpd00067[1] (2) H+[0] + (1) Methanophenazine[0] + (1) H2[0] <= (1) Dihydromethanophenazine[0] + (2) H+[1] < < 1e+07 1e+07 OK 0 Gapseq new corrected -rxn90060 inulinase fructan beta-(2,1)-fructosidase (extracellular) -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" 0 (1) cpd28763[1] + (9) cpd00001[1] => (9) cpd00082[1] + (1) cpd02298[1] (1) (2,1-beta-D-fructan)[1] + (9) H2O[1] => (9) D-Fructose[1] + (1) 1F-beta-D-Fructosylsucrose[1] > > 1e+07 1e+07 OK 0 Gapseq new corrected +rxn90060 inulinase fructan beta-(2,1)-fructosidase (extracellular) -1:cpd28763:1:0:"Inulin";-9:cpd00001:1:0:"H2O";9:cpd00082:1:0:"D-Fructose";1:cpd02298:1:0:"1F-beta-D-Fructosylsucrose" 0 (1) cpd28763[1] + (9) cpd00001[1] => (9) cpd00082[1] + (1) cpd02298[1] (1) Inulin[1] + (9) H2O[1] => (9) D-Fructose[1] + (1) 1F-beta-D-Fructosylsucrose[1] > > 1e+07 1e+07 OK 0 Gapseq new corrected rxn90062 exopolygalacturonase galacturonan 1,4-alpha-galacturonidase -1:cpd21755:0:0:"1-4-alpha-D-galacturonosyl";-2:cpd00001:0:0:"H2O";3:cpd00280:0:0:"D-Galacturonate" 0 (1) cpd21755[0] + (2) cpd00001[0] => (3) cpd00280[0] (1) 1-4-alpha-D-galacturonosyl[0] + (2) H2O[0] => (3) D-Galacturonate[0] > > 1e+07 1e+07 OK 0 Gapseq new corrected rxn90063 tagaturonate epimerase tagaturonate epimerase -1:cpd00437:0:0:"D-Tagaturonate";1:cpd00672:0:0:"D-Fructuronate" 0 (1) cpd00437[0] <=> (1) cpd00672[0] (1) D-Tagaturonate[0] <=> (1) D-Fructuronate[0] = = 1e+07 1e+07 OK 0 Gapseq new corrected rxn90064 homogalacturonate ABC transporter homogalacturonate ABC transporter -1:cpd00001:0:0:"H2O";-1:cpd00002:0:0:"ATP";-1:cpd21755:1:0:"1-4-alpha-D-galacturonosyl";1:cpd00008:0:0:"ADP";1:cpd00009:0:0:"Phosphate";1:cpd21755:0:0:"1-4-alpha-D-galacturonosyl";1:cpd00067:0:0:"H+" 0 (1) cpd00001[0] + (1) cpd00002[0] + (1) cpd21755[1] => (1) cpd00008[0] + (1) cpd00009[0] + (1) cpd21755[0] + (1) cpd00067[0] (1) H2O[0] + (1) ATP[0] + (1) 1-4-alpha-D-galacturonosyl[1] => (1) ADP[0] + (1) Phosphate[0] + (1) 1-4-alpha-D-galacturonosyl[0] + (1) H+[0] > > 1e+07 1e+07 OK 0 Gapseq new corrected @@ -34884,3 +34884,4 @@ rxn90120 levansucrase levansucrase -1:cpd00076:0:0:"sucrose";-1:cpd21648:0:0:"6 rxn90121 kestotriose fructosidase kestotriose fructosidase -1:cpd21648:0:0:"6-kestotriose";-1:cpd00001:0:0:"H2O";1:cpd00076:0:0:"sucrose";1:cpd00082:0:0:"D-Fructose" 0 (1) cpd21648[0] + (1) cpd00001[0] => (1) cpd00076[0] + (1) cpd00082[0] (1) 6-kestotriose[0] + (1) H2O[0] => (1) sucrose[0] + (1) D-Fructose[0] > > 1e+07 1e+07 OK 0 Gapseq new corrected rxn90122 kestotetraose fructosidase kestotetraose fructosidase -1:cpd25730:0:0:"6,6-kestotetraose";-1:cpd00001:0:0:"H2O";1:cpd21648:0:0:"6-kestotriose";1:cpd00082:0:0:"D-Fructose" 0 (1) cpd25730[0] + (1) cpd00001[0] => (1) cpd21648[0] + (1) cpd00082[0] (1) 6,6-kestotetraose[0] + (1) H2O[0] => (1) 6-kestotriose[0] + (1) D-Fructose[0] > > 1e+07 1e+07 OK 0 Gapseq new corrected rxn90123 isoamylase debranching enzyme, glycogen α-1,6-glucanohydrolase -1:cpd00155:1:0:"glycogen";-1:cpd00001:1:0:"H2O";1:cpd01262:1:0:"Amylotriose";1:cpd00179:1:0:"Maltose" 0 (1) cpd00155[1] + (1) cpd00001[1] => (1) cpd01262[1] + (1) cpd00179[1] (1) glycogen[1] + (1) H2O[1] => (1) Amylotriose[1] + (1) Maltose[1] > > 1e+07 1e+07 OK 0 Gapseq new corrected +rxn90124 inulinase inulinase, intracellular -1:cpd28763:0:0:"Inulin";-11:cpd00001:0:0:"H2O";11:cpd00082:0:0:"D-Fructose";1:cpd00027:0:0:"D-Glucose" 0 (1) cpd28763[0] + (11) cpd00001[0] => (11) cpd00082[0] + (1) cpd00027[0] (1) Inulin[0] + (11) H2O[0] => (11) D-Fructose[0] + (1) D-Glucose[0] > > 1e+07 1e+07 OK 0 Gapseq new corrected diff --git a/dat/seq/Bacteria/user/3.2.1.7.fasta b/dat/seq/Bacteria/user/3.2.1.7.fasta new file mode 100644 index 00000000..f2fa7da4 --- /dev/null +++ b/dat/seq/Bacteria/user/3.2.1.7.fasta @@ -0,0 +1,53 @@ +>tr|A0A0F6MTX2|A0A0F6MTX2_9SPHN Inulinase OS=Sphingomonas sp. JB13 OX=1163478 GN=inuA PE=3 SV=1 +MKRTLAAFIGAGLLASGAQAQRPDIRPTYHFAPQRNWMNDPNGLVYYDGEYHLFFQYNPY +GDRWGHMSWGHAVSRDLVHWQQLPVAIPETDVMAFSGSAVVDWDNTSGFGQGGKPPMVAI +YTGQNVKTGNQSQFVAYSNDHGRHWTVHGKVLDIGSTAFRDPKVFWHAATRRWVMVAVMA +DENRAVIYTSPNLKDWRFASSFGPAGRRGKNWECPDLFELPVEGGAPGEKRWVLSINLGD +NAVAGGSGGQYFVGDFDGTTFKTVPGWGDQPRWLDYGADFYATVSWNDLPKSDPRRIWIG +WANNWRYANDIPTYPSRGLMTVPRAVTLHKTADGYRLAQAPVKEIEALRGAPQVRHGLTL +GETPVPLPVSGGSDELAVDLDTGSARQIALTLTDGEGYQTVIGVNPAVDEVFIDRTRSGP +HFFDGFEDRHIAPVDLGSGKVRLHVLVDQSIIELFINNGSRTITDRFFRGGGALRWSASA +LGGTATMDVTAWPLGPERNTAMLMP +>tr|A0A410R7T9|A0A410R7T9_PAEPO Endoinulinase OS=Paenibacillus polymyxa OX=1406 PE=3 SV=1 +MSHATDNRGLIMYWAFNEGTGTSALESVSQVQDNIQYVFNQAEFTKPCPPRWRQGVIGNG +LLFDGYSTYIAHSFDEGNQNTEPEYRSALSIGVWVAPRSYEWGDDGKLSAIVNRYNLDRK +QGYLLGMFRHGSWSFQVGLEGGDWKELWSPDGHELPKNEWSYVNAVFDGNQGEIKLYLNG +SEIASAALPCGSRLAEATDSELLIGKNNHSSLLAEVFSLHMLSGIIDELKIYNRALSAEE +VAASYRHVLDTFHEGVRPQLNYDEIKLDRTPLLLDRHRPQYHVSPPAHWMNEPHASIYFD +GQYHLFYQHNPHGPFFHQIHWGHWVSQDLVHWRDLPVALAPEKDQLAPDGIWSGSATYDA +DGLPVLFFTAGNDSASPNQSVALARSTYTLDGNPDLVHWVKHPEPLIVQKKGMGAFGDFR +DPFVWKDDDGWYALVGSGIEGGAALAFASQDMLNWTYKGPFFKADIQKFPYLGPIWELPV +LLPLGSDKQGVNKHLLLVSPVGKGADVEVFYWIGQLDKQNLSFIPDQEEPQLIDVGDFHF +TGPSGMVDPKTGRNIVFTIAQGDRTSEMEYKSGWAHNGGLPLSVYLRDDGRLGIEPIQEL +QSLRSAKRLSLRDQSLAETNVRLRDVHGDMLEIQLELEPGSAKQFGIKVRCTPDGEEETL +LYYDWNQAMLMVDRSKTTLHPGEKCGGIQGGKLELLGENLKLRIYLDRSMVETYANGLKS +LTTRVYPSRMDALGLEIWGDGEPFVKSLEIWDMQSIW +>tr|H7CE76|H7CE76_9GAMM Endo-inulinase OS=Microbulbifer sp. JAM-3301 OX=1081041 GN=inu PE=3 SV=1 +MGMPVLHRLFGFLFLAFPAPLLVAAEEPPAYRQDFERLDTEALAPLRIHTQFSAPDSVPG +VAGKAWRSDGFSSWAELPYETGEKFSLTVWLALESYPSDLEVPVSELSPSAIVHQWDGRG +GFNIHVDTFGRWGARLQTESGETDLVVETPFPLYRWVQLALSVNEREAALYLDGEMVARE +VLPAPLRPADAPIRLARAVDEAEILNFTVNRLNGVFDELRLYRRGLPAAEIQAIRRRYPD +TVPVEPSLAVPESRFAGDHLRPRLHAMPPANWTNEPHGLVKVGDLWHLFYQRTPNGPYKT +QMHWGHMVSRDLLRWENLPDALWPELQDDEFGFDMKGIWSGDVIYEGGRAFAYYTSVNHG +DRLGAANPGVSMAVSEDPELRHWRKLGPIINTRYVRDFRDPYLFKDGDTWHMLIGAAQKD +GGGLDYYILEKEENKWRHRRRFSSIPFHKMDIGSEIWEMPVFEPISVDAHVLVVNPIGGR +ISKYGEPATRAVYWVGRWRNGLFHPYESEPKNLDLLPGHLAPAVERGEDGSLRAIGIVDE +RRSPQAQEDAGWAHTFSFPRRWRLLEDGRTLGQSPAPELVRLRGEPLDTPPVPALLEKPL +WLAEPDGAYELVLESSGAGGLAIGVDLLVSSAGGEYTRLMFDGESDTVILDKRNSWHGGG +GEGPDLLQAAYDSAAFGEIRELRVFVDGSVVEVFVNDSAAFSFRSYPEDPGARGLRIFPL +RKKAVLAGATLWPLRIPAE +>tr|Q9RBA5|Q9RBA5_9MICC Endo-inulinase OS=Arthrobacter sp. S37 OX=85703 GN=inu1 PE=3 SV=1 +MTTATRKVVPMTELRQTQPTTNLPGLGRRTFLQGAAVSAAVIATGALFRPAAAATGDPVL +RLTYDQPNGSTTVLDEVGRSNFTVHVSNNPAERVPGVRGNAFRTDGFSTWATGQFATPLT +TQMTIQTWIALESYPSDSEQPYDALTPSSIIYQRTNDAGFDIAINTYGEWWFTAHVGGQW +RTVKAPWLFPLYEWVQIAAVVDGDAGQLRLHLDDAAGPKVASVAIPTGSRFTQAAGAPLV +VGKASKDVTTGVFLINALNAAYDDTRIYDIARGAAALTGEYTSGIAGASPAHDVALQVTG +LRFADDILRPRYHAMPPANWTNEPHGLVRHDCSYHMFYQRTPNGPFKWQMNWGHMTSTDL +VHWTNMPDALRPELNDREARLGAVAGSGLSGQGSKGIWSGDVVSVDGTAHAFFTTVNFGG +PFDPGITRASSTDPDLLTWTKASTGVIDKNAPAHVADFRDPYLWQEGGTWHMIIGAATDA +GGALEHYTTQDIQGQWTRASRPFSTVSFASMDIGSAIWEMPVFEKIGTHAGRDKYVLVVS +PIGRSVSKLSEPYTRSVYWTGTWNGSQFTPDYARPKSLDLIHGHLSPTVAHGPDGKLVAI +GIVDERSSSKMQLDLGWAHTFSAPREWRLLEDGQTLGQRPIAQLMTLRAGSAQTATNVAV +TGEHNLAAAGNQVEILAKVDPASTGARYGLCIGASPDGSEITRIYYDGNDIVIDKTRSSR +NFENEEAVLLRGAYDEAVFGKPHTFHVFVDHSVIDVFINDAAAFSNRIYPTSRGADGAAA +STGLRLYSEGGQTRFTQTDVWQLQSAWPTPAF diff --git a/dat/seq/Bacteria/user/INULIN-ABC-TRANSPORT.fasta b/dat/seq/Bacteria/user/INULIN-ABC-TRANSPORT.fasta new file mode 100644 index 00000000..88a6afb0 --- /dev/null +++ b/dat/seq/Bacteria/user/INULIN-ABC-TRANSPORT.fasta @@ -0,0 +1,36 @@ +>tr|Q1G9K3|Q1G9K3_LACDA Oligopeptide ABC transporter, permease protein OS=Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14) OX=390333 GN=oppB PE=3 SV=1 +MWKTVLRRVLIMIPQLILLSIIVFMLAKMMPGDPFTGLINPNSSPKEIARLKQAYGLNDP +VPVQYVRWIKNLLHGDLGQSYIQHVPVASLIADRAQNTFWLSLLSTIILYGIAIPMGISA +GKHEGEWQDRAISIFNYVTYAIPGFVFYLLGLWLFGFTLGWFPISGTVAANASGFWGVFF +SRLQHMILPAILFAIIATTGTVQYLRTGIIDNKVEDYVKTARSKGVPEKVVFNKHILRNS +FLPIAAFMGNTITGLLGGSLIIETVFSFPGMGKLFLDSISQRDYTTLTALIMIYGTLTLL +GNLLSDIIMSLVDPRIRVK +>sp|A0A0H2URD6|FUSA_STRPN Fructooligosaccharide ABC transporter substrate-binding protein FusA OS=Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) OX=170187 GN=fusA PE=1 SV=1 +MKFKTFSKSAVLLTASLAVLAACGSKNTASSPDYKLEGVTFPLQEKKTLKFMTASSPLSP +KDPNEKLILQRLEKETGVHIDWTNYQSDFAEKRNLDISSGDLPDAIHNDGASDVDLMNWA +KKGVIIPVEDLIDKYMPNLKKILDEKPEYKALMTAPDGHIYSFPWIEELGDGKESIHSVN +DMAWINKDWLKKLGLEMPKTTDDLIKVLEAFKNGDPNGNGEADEIPFSFISGNGNEDFKF +LFAAFGIGDNDDHLVVGNDGKVDFTADNDNYKEGVKFIRQLQEKGLIDKEAFEHDWNSYI +AKGHDQKFGVYFTWDKNNVTGSNESYDVLPVLAGPSGQKHVARTNGMGFARDKMVITSVN +KNLELTAKWIDAQYAPLQSVQNNWGTYGDDKQQNIFELDQASNSLKHLPLNGTAPAELRQ +KTEVGGPLAILDSYYGKVTTMPDDAKWRLDLIKEYYVPYMSNVNNYPRVFMTQEDLDKIA +HIEADMNDYIYRKRAEWIVNGNIDTEWDDYKKELEKYGLSDYLAIKQKYYDQYQANKN +>tr|A7M317|A7M317_BACO1 TonB-linked outer membrane protein, SusC/RagA family OS=Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / BCRC 10623 / CCUG 4943 / NCTC 11153) OX=411476 GN=BACOVA_04505 PE=3 SV=1 +MLSIMKNKKLLCSVCFLFTFMSVLWGQNITVKGNVTSKTDGQPIIGASVVQNDSKSTGTI +TDLDGNFTLSVPTNALLAISYIGYKEVIIAAKPSLKIVMEEDAKMIDEVVVTGYMAEKKA +SLTGSVAVVKMKEVADIPTGNVMSGLQGRVAGMNVTTDGKPGGGNTDTKLRGITTINNSS +PLYVIDGVQTHDNVASIISSNDVESIQVLKDAASAAIYGAQAANGVIIITTKRAKEGDVK +VSFDMSLTAQTFTGGIDMLDAYQWGDVYWQAYKNTFGTNPNSVVYGNGEKAQLQEYYFDQ +NGVKIKSGNTDWAKEIFGTALMQNYNLSLSKGFKDGNVALTLNYMNQDGLCRNTDYERFN +SRLASNFRFVDGKVRVGESISVNHWLEHLNPAGIEELVIAQHPAIPVYDENGGYAGGYVD +ILGDKPNAIRLTDNEANNRHKSWRIFGNVYLEVEPIKNLVLKSQFGLNYTTGFNSTFVPK +WSEADRKVDVNELTVRQDNSVQWVWSNTANYSIDFGKNNISAVIGTEAKKENGEHLQGYG +RGLVIEDLDYRYLDTVTEGKSVSNNASTYAMVSYFGKVNYAFDDKYLISGTVRRDASSRF +GKGNNSAIFPSVSAGWRVSREKFMECTQNWLSDLKLRASWGINGNDQIDNNATYNLYYTN +MSNGSYNFNGDGTTVLPGVQKDRSGNNDLKWEETKQLNFGIDAAFFDNRLGLTLDYFQKK +TTGMLIQKPYIGVIGEGGYKWYNAASMDNSGVEATFTWRDEIKDFKYDISFNLSYYKNEI +TELPDVIKYTWGGGNGVDKTIVGQPYGSWMSYKADGVFKTKQEVYEYLSKYDVQIGAPGV +GRIRYKDLNGDNIINTADMDWQGSDQPRFIGGLNIGASYKGFDLSVFFNGMIRDAWNNSK +FYTDLFQGWTGNHSVRLMDAMHAWNAYEQTGVYNCDIPALTVVDNNVETRSSTFFIEDGS +YVKLKTLTVGYTFPDKWIKKAHLSNLRLYLQAQNVFTLTNYTGADPEGLGYPYPQPRTYT +FGLSLGF diff --git a/src/gapseq_find.sh b/src/gapseq_find.sh index b7b1b8c7..418226ab 100755 --- a/src/gapseq_find.sh +++ b/src/gapseq_find.sh @@ -35,9 +35,9 @@ input_mode="auto" output_dir=. OS=$(uname -s) if [ "$OS" = "Darwin" -o "$OS" = "FreeBSD" ]; then - n_threads=$(sysctl hw.ncpu|cut -f2 -d' ') + n_threads=$(sysctl hw.ncpu|cut -f2 -d' ') else - n_threads=`grep -c ^processor /proc/cpuinfo` + n_threads=`grep -c ^processor /proc/cpuinfo` fi usage() @@ -624,14 +624,14 @@ do #echo test: ${ec[i]} ${EC_test[i]} if [[ -n "${EC_test[i]}" ]]; then # check if sequence is not available => try to download - if [[ (! -f $seqpath/rev/${ec[i]}.fasta || "$update_manually" = true) && "$force_offline" = false ]]; then + if [[ (! -f $seqpath/rev/${ec[i]}.fasta || "$update_manually" = true) && "$force_offline" = false ]]; then if ! already_downloaded "$seqpath/rev/${ec[i]}.fasta"; then [[ verbose -ge 1 ]] && echo -e '\t\t'Downloading reviewed sequences for: ${ec[i]} $dir/uniprot.sh -e "${ec[i]}" -t "$taxonomy" -i $uniprotIdentity -o >/dev/null echo $seqpath/rev/${ec[i]}.fasta >> $download_log fi fi - if [[ ((! -f $seqpath/unrev/${ec[i]}.fasta && $seqSrc -gt 1) || "$update_manually" = true) && "$force_offline" = false ]]; then + if [[ ((! -f $seqpath/unrev/${ec[i]}.fasta && $seqSrc -gt 1) || "$update_manually" = true) && "$force_offline" = false ]]; then if ! already_downloaded "$seqpath/unrev/${ec[i]}.fasta"; then [[ verbose -ge 1 ]] && echo -e '\t\t'Downloading unreviewed sequences for: ${ec[i]} $dir/uniprot.sh -u -e "${ec[i]}" -t "$taxonomy" -i $uniprotIdentity -o >/dev/null @@ -670,14 +670,14 @@ do if [[ -n "$reaName" ]] && ( [[ "$EC_test_bool" = false ]] || [[ ! -s "$query" ]] );then reaNameHash=$(echo -n "$reaName" | md5sum | awk '{print $1}') # check if sequence is not available => try to download - if [[ (! -f $seqpath/rev/$reaNameHash.fasta || "$update_manually" = true) && "$force_offline" = false ]]; then + if [[ (! -f $seqpath/rev/$reaNameHash.fasta || "$update_manually" = true) && "$force_offline" = false ]]; then if ! already_downloaded "$seqpath/rev/$reaNameHash.fasta"; then [[ verbose -ge 1 ]] && echo -e '\t\t'Downloading reviewed sequences for: $reaName "\n\t\t(hash: $reaNameHash)" $dir/uniprot.sh -r "$reaName" -t "$taxonomy" -i $uniprotIdentity -o >/dev/null echo $seqpath/rev/$reaNameHash.fasta >> $download_log fi fi - if [[ ((! -f $seqpath/unrev/$reaNameHash.fasta && $seqSrc -gt 1) || "$update_manually" = true) && "$force_offline" = false ]]; then + if [[ ((! -f $seqpath/unrev/$reaNameHash.fasta && $seqSrc -gt 1) || "$update_manually" = true) && "$force_offline" = false ]]; then if ! already_downloaded "$seqpath/unrev/$reaNameHash.fasta"; then [[ verbose -ge 1 ]] && echo -e '\t\t'Downloading unreviewed sequences for: $reaName "\n\t\t(hash: $reaNameHash)" $dir/uniprot.sh -u -r "$reaName" -t "$taxonomy" -i $uniprotIdentity -o >/dev/null @@ -708,7 +708,7 @@ do # sequence by gene name if [[ -n "$geneName" ]] && [[ -n "$geneRef" ]] && [[ "$use_gene_seq" = true ]]; then - if [[ (! -f $seqpath/rxn/$rea.fasta || "$update_manually" = true) && "$force_offline" = false ]]; then + if [[ (! -f $seqpath/rxn/$rea.fasta || "$update_manually" = true) && "$force_offline" = false ]]; then reaSeqTmp=$(mktemp -p $tmpdir) for gr in $geneRef do