Tohama I
for which no corresponding enzyme has been identified in the genome.
The presence of those enzymes is suggested by the presence of the
pathway.
102 pathway holes (14.6%) are present in the 700 total reactions of 202 pathways
|
Reaction |
EC# |
Pathway(s) needing this reaction |
|
2-oxoglutarate + N-succinyl-L,L-2,6-diaminopimelate ← L-glutamate + N-succinyl-2-amino-6-ketopimelate |
2.6.1.17 |
L-lysine biosynthesis I |
|
3-oxo-5,6-didehydrosuberyl-CoA semialdehyde + NADP+ + H2O → 3-oxo-5,6-didehydrosuberyl-CoA + NADPH + 2 H+ |
1.2.1.91 |
phenylacetate degradation I (aerobic) |
|
2-oxepin-2(3H)-ylideneacetyl-CoA + H2O → 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde |
3.3.2.12 |
phenylacetate degradation I (aerobic) |
|
S-adenosyl-L-methionine + H+ → CO2 + S-adenosyl 3-(methylsulfanyl)propylamine |
4.1.1.50 |
spermidine biosynthesis I |
|
D-glucarate → 5-dehydro-4-deoxy-D-glucarate + H2O |
4.2.1.40 |
D-glucarate degradation I |
|
4-phospho-D-erythronate + NAD+ → (3R)-3-hydroxy-2-oxo-4 phosphooxybutanoate + NADH + H+ |
1.1.1.290 |
pyridoxal 5'-phosphate biosynthesis I |
|
D-erythrose 4-phosphate + NAD+ + H2O → 4-phospho-D-erythronate + NADH + 2 H+ |
1.2.1.72 |
pyridoxal 5'-phosphate biosynthesis I |
|
a [SoxY protein]-S-(2-sulfodisulfanyl)-L-cysteine + H2O → a [SoxY protein]-S-disulfanyl-L-cysteine + sulfate + 2 H+ |
3.1.6.20 |
thiosulfate oxidation III (multienzyme complex) |
|
a [SoxY protein]-S-sulfanyl-L-cysteine + thiosulfate + 2 oxidized c-type cytochrome → a [SoxY protein]-S-(2-sulfodisulfanyl)-L-cysteine + 2 reduced c-type cytochrome + 2 H+ |
2.8.5.2 |
thiosulfate oxidation III (multienzyme complex) |
|
a [SoxY protein]-S-sulfosulfanyl-L-cysteine + H2O → a [SoxY protein]-S-sulfanyl-L-cysteine + sulfate + H+ |
3.1.6.20 |
thiosulfate oxidation III (multienzyme complex) |
|
a [SoxY protein]-L-cysteine + thiosulfate + 2 oxidized c-type cytochrome → a [SoxY protein]-S-sulfosulfanyl-L-cysteine + 2 reduced c-type cytochrome + 2 H+ |
2.8.5.2 |
thiosulfate oxidation III (multienzyme complex) |
|
MCD cofactor chaperone + cytidylyl molybdenum cofactor (trioxo) → a [cytidylyl molybdenum cofactor chaperone]-cytidylyl MoO2(OH)-molybdopterin cofactor |
[none] |
cytidylyl molybdenum cofactor sulfurylation |
|
α-D-mannose 1-phosphate + GTP + H+ → GDP-α-D-mannose + diphosphate |
2.7.7.13 |
GDP-mannose biosynthesis |
|
5-amino-6-(5-phospho-D-ribitylamino)uracil + H2O → 5-amino-6-(D-ribitylamino)uracil + phosphate |
3.1.3.104 |
flavin biosynthesis I (bacteria and plants) |
|
adenosylcobinamide + ATP → adenosyl-cobinamide phosphate + ADP + H+ |
2.7.1.156 |
adenosylcobinamide-GDP salvage from cobinamide I |
|
adenosyl-cobinamide phosphate + GTP + H+ → adenosylcobinamide-GDP + diphosphate |
2.7.7.62 |
adenosylcobinamide-GDP salvage from cobinamide I |
|
(S)-3-hydroxy-3-methylglutaryl-CoA ← 3-methylglutaconyl-CoA + H2O |
4.2.1.18 |
L-leucine degradation I |
|
4-methyl-2-oxopentanoate + coenzyme A + NAD+ → 3-methylbutanoyl-CoA + CO2 + NADH |
1.2.1.25 |
L-leucine degradation I |
|
N-formimino-L-glutamate + H2O → ammonium + N-formyl-L-glutamate |
3.5.3.13 |
L-histidine degradation II |
|
4-imidazolone-5-propanoate + H2O → N-formimino-L-glutamate |
3.5.2.7 |
L-histidine degradation II |
|
4-imidazolone-5-propanoate ← urocanate + H2O |
4.2.1.49 |
L-histidine degradation II |
|
L-histidine → ammonium + urocanate |
4.3.1.3 |
L-histidine degradation II |
|
(2R,3S)-2-methylisocitrate → succinate + pyruvate |
4.1.3.30 |
2-methylcitrate cycle II |
|
aldehydo-D-arabinose 5-phosphate ← D-ribulose 5-phosphate |
5.3.1.13 |
CMP-3-deoxy-D-manno-octulosonate biosynthesis |
|
3-deoxy-D-manno-octulosonate 8-phosphate + H2O → 3-deoxy-α-D-manno-2-octulosonate + phosphate |
3.1.3.45 |
CMP-3-deoxy-D-manno-octulosonate biosynthesis |
|
squalene + reduced [NADPH-hemoprotein reductase] + dioxygen → (3S)-2,3-epoxy-2,3-dihydrosqualene + oxidized [NADPH-hemoprotein reductase] + H2O |
1.14.14.17 |
epoxysqualene biosynthesis |
|
arsenic triglutathione + [ArsD arsenite metallochaperone] → arsenite-[ArsD arsenite metallochaperone] complex + 3 glutathione |
[none] |
arsenate detoxification I |
|
D-glucopyranose 6-phosphate → 1D-myo-inositol 3-monophosphate |
5.5.1.4 |
myo-inositol biosynthesis |
|
L-tyrosine + S-adenosyl-L-methionine + NADPH → 2-iminoacetate + 4-methylphenol + 5'-deoxyadenosine + L-methionine + NADP+ + H+ |
4.1.99.19 |
thiazole component of thiamine diphosphate biosynthesis I |
|
[ThiI sulfur-carrier protein]-S-sulfanyl-L-cysteine + carboxy-adenylated-[ThiS sulfur-carrier protein] + 2 reduced ferredoxin [iron-sulfur] cluster → thiocarboxylated-[ThiS sulfur-carrier protein] + [ThiI sulfur-carrier protein]-L-cysteine + AMP + 2 oxidized ferredoxin [iron-sulfur] cluster |
2.8.1.- |
thiazole component of thiamine diphosphate biosynthesis I |
|
bis-MGD cofactor chaperone + bis(guanylyl molybdopterin) cofactor → [bis-MGD cofactor chaperone]-bis-MGD |
[none] |
bis(guanylyl molybdopterin) cofactor sulfurylation |
|
[bis-MGD cofactor chaperone]-bis-MGD + a [bis(guanylyl molybdopterin) cofactor chaperone]-S-sulfanyl-L-cysteine + reduced two electron carrier → a [bis(guanylyl molybdopterin) cofactor chaperone]-L-cysteine + sulfo-bis(guanylyl molybdopterin) cofactor + oxidized electron carrier + H2O |
2.8.1.- |
bis(guanylyl molybdopterin) cofactor sulfurylation |
|
ammonium + NAD+ + H2O ← hydroxylamine + NADH + 2 H+ |
1.7.1.10 |
protein S-nitrosylation and denitrosylation |
|
a [protein]-L-cysteine + nitric oxide + dioxygen → a [protein] 3-nitrosothio-L-alanine + superoxide + H+ |
[none] |
protein S-nitrosylation and denitrosylation |
|
(3R)-3-hydroxyhexadecanoyl-[acp] + UDP-2-acetamido-3-amino-2,3-dideoxy-α-D-glucopyranose → UDP-2-acetamido-2,3-dideoxy-3-{[(3R)-3-hydroxyhexadecanoyl]amino}-α-D-glucopyranose + acyl-carrier protein |
2.3.1.- |
lipid IVA biosynthesis (2,3-diamino-2,3-dideoxy-D-glucopyranose-containing) |
|
[ThiS sulfur-carrier protein] + ATP + H+ → carboxy-adenylated-[ThiS sulfur-carrier protein] + diphosphate |
2.7.7.73 |
thiazole component of thiamine diphosphate biosynthesis II,
thiazole component of thiamine diphosphate biosynthesis I |
|
glycine + dioxygen → 2-iminoacetate + hydrogen peroxide + H+ |
[none] |
thiazole component of thiamine diphosphate biosynthesis II |
|
2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate → 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate |
5.3.99.10 |
thiazole component of thiamine diphosphate biosynthesis II |
|
L-histidinol phosphate + H2O → histidinol + phosphate |
3.1.3.15 |
L-histidine biosynthesis |
|
isopentenyl diphosphate ↔ prenyl diphosphate |
5.3.3.2 |
methylerythritol phosphate pathway I |
|
oxidized thioredoxin + reduced two electron carrier ← reduced thioredoxin + oxidized electron carrier |
[none] |
thioredoxin pathway |
|
glutathione → L-cysteinylglycine + 5-oxo-L-proline |
4.3.2.7 |
5-oxo-L-proline metabolism |
|
[protein] with an N-terminal 5-oxo-L-proline + H2O → 5-oxo-L-proline + peptide |
3.4.19.3 |
5-oxo-L-proline metabolism |
|
oxaloacetate + ATP → CO2 + phosphoenolpyruvate + ADP |
4.1.1.49 |
gluconeogenesis I |
|
dodecanoyl-[acp] + H2O → acyl-carrier protein + laurate + H+ |
3.1.2.21 |
palmitate biosynthesis (type II fatty acid synthase) |
|
palmitoyl-[acp] + H2O → palmitate + acyl-carrier protein + H+ |
3.1.2.14 |
palmitate biosynthesis (type II fatty acid synthase) |
|
ATP + β-D-fructofuranose 6-phosphate → ADP + β-D-fructose 1,6-bisphosphate + H+ |
2.7.1.11 |
glycolysis I (from glucose 6-phosphate) |
|
2-phospho-D-glycerate ↔ 3-phospho-D-glycerate |
5.4.2.12 |
glycolysis I (from glucose 6-phosphate),
gluconeogenesis I |
|
an apo-[hydroxymethylbilane synthase]-L-cysteine + preuroporphyrinogen → a [hydroxymethylbilane synthase] ES2 intermediate + H2O |
[none] |
dipyrromethane cofactor biosynthesis |
|
selenodiglutathione + NADPH + H+ → glutathioselenol + glutathione + NADP+ |
1.8.1.- |
selenate reduction |
|
hydrogen selenide + glutathione + NADP+ ← glutathioselenol + NADPH + H+ |
1.8.1.- |
selenate reduction |
|
selenite + AMP + glutathione disulfide + 2 H+ ← adenosine 5'-phosphoselenate + 2 glutathione |
1.8.4.9 |
selenate reduction |
|
stearoyl-[acp] + H2O → stearate + acyl-carrier protein + H+ |
3.1.2.14 |
stearate biosynthesis II (bacteria and plants) |
|
β-nicotinamide D-ribonucleotide + H2O → ammonium + β-nicotinate D-ribonucleotide |
3.5.1.42 |
NAD salvage pathway II (PNC IV cycle) |
|
carboxy-adenylated [molybdopterin-synthase sulfur-carrier protein subunit] + an [L-cysteine desulfurase]-S-sulfanyl-L-cysteine + reduced two electron carrier → thiocarboxylated [molybdopterin-synthase sulfur-carrier protein subunit] + an [L-cysteine desulfurase]-L-cysteine + AMP + oxidized electron carrier + H+ |
2.8.1.11 |
molybdopterin biosynthesis |
|
protoporphyrinogen IX + 3 dioxygen → protoporphyrin IX + 3 hydrogen peroxide |
1.3.3.4 |
heme b biosynthesis I (aerobic) |
|
[cysteine desulfurase]-[scaffold protein-(2Fe-2S)] complex + [Fe-S cluster biosynthesis co-chaperone] → [co-chaperone]-[scaffold protein-(2Fe-2S)] complex + [L-cysteine desulfurase] |
[none] |
[2Fe-2S] iron-sulfur cluster biosynthesis |
|
[cysteine desulfurase]-(S-sulfanyl)2-[disordered-form scaffold protein] complex + 2 Fe3+ → [cysteine desulfurase]-[scaffold protein-(2Fe-2S)] complex |
[none] |
[2Fe-2S] iron-sulfur cluster biosynthesis |
|
demethylated methyl acceptor + S-adenosyl-L-methionine ← S-adenosyl-L-homocysteine + methylated methyl acceptor + H+ |
2.1.1.- |
L-methionine degradation I (to L-homocysteine) |
|
all-trans-heptaprenyl diphosphate + 1,4-dihydroxy-2-naphthoate + H+ → CO2 + demethylmenaquinol-7 + diphosphate |
2.5.1.74 |
menaquinol-7 biosynthesis |
|
pppGpp + H2O → ppGpp + phosphate + H+ |
3.6.1.40 |
ppGpp metabolism |
|
3-hydroxyanthranilate + dioxygen → 2-amino-3-carboxymuconate-6-semialdehyde |
1.13.11.6 |
L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde |
|
L-kynurenine + NADPH + dioxygen + H+ → 3-hydroxy-L-kynurenine + NADP+ + H2O |
1.14.13.9 |
L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde |
|
O-acetyl-L-homoserine + hydrogen sulfide → L-homocysteine + acetate + H+ |
2.5.1.49 |
L-homocysteine biosynthesis |
|
galactarate → 5-dehydro-4-deoxy-D-glucarate + H2O |
4.2.1.42 |
D-galactarate degradation I |
|
D-glycerate + NAD(P)+ ← tartronate semialdehyde + NAD(P)H + H+ |
1.1.1.60 |
D-glucarate degradation I,
D-galactarate degradation I |
|
2-octaprenylphenol + NADPH + dioxygen + H+ → 3-(all-trans-octaprenyl)benzene-1,2-diol + NADP+ + H2O |
1.14.13.240 |
ubiquinol-8 biosynthesis (early decarboxylation) |
|
2-methoxy-6-(all-trans-octaprenyl)phenol + NADPH + dioxygen + H+ → 2-methoxy-6-all trans-octaprenyl-1,4-benzoquinol + NADP+ + H2O |
1.14.13.- |
ubiquinol-8 biosynthesis (early decarboxylation) |
|
2-iminosuccinate + glycerone phosphate → quinolinate + phosphate + 2 H2O |
2.5.1.72 |
NAD de novo biosynthesis I (from aspartate) |
|
propanoyl-CoA + phosphate → propanoyl phosphate + coenzyme A |
2.3.1.222 |
L-threonine degradation I |
|
2-oxobutanoate + coenzyme A → propanoyl-CoA + formate |
2.3.1.- |
L-threonine degradation I |
|
dTTP + α-D-glucopyranose 1-phosphate + H+ → dTDP-α-D-glucose + diphosphate |
2.7.7.24 |
dTDP-beta-L-rhamnose biosynthesis |
|
a nascent peptidoglycan with (L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-glycine) tetrapeptide → a mature peptidoglycan with (L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-glycine) tetrapeptide + di-trans,octa-cis-undecaprenyl diphosphate + H+ |
[none] |
peptidoglycan maturation (meso-diaminopimelate containing) |
|
a nascent peptidoglycan with (L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanine) tetrapeptide → a mature peptidoglycan with (L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanine) tetrapeptide + di-trans,octa-cis-undecaprenyl diphosphate + H+ |
[none] |
peptidoglycan maturation (meso-diaminopimelate containing) |
|
a nascent peptidoglycan with L,D cross links (meso-diaminopimelate containing) → a mature peptidoglycan with L,D cross-links (meso-diaminopimelate containing) + di-trans,octa-cis-undecaprenyl diphosphate + H+ |
[none] |
peptidoglycan maturation (meso-diaminopimelate containing) |
|
a nascent peptidoglycan with D,D cross-links (meso-diaminopimelate containing) → a mature peptidoglycan with D,D cross-links (meso-diaminopimelate containing) + di-trans,octa-cis-undecaprenyl diphosphate + H+ |
[none] |
peptidoglycan maturation (meso-diaminopimelate containing) |
|
a nascent peptidoglycan with (L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimelate) tripeptide → a mature peptidoglycan with (L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimelate) tripeptide + di-trans,octa-cis-undecaprenyl diphosphate + H+ |
[none] |
peptidoglycan maturation (meso-diaminopimelate containing) |
|
a nascent peptidoglycan with (L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine) pentapeptide → a mature peptidoglycan with (L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine) pentapeptide + di-trans,octa-cis-undecaprenyl diphosphate + H+ |
[none] |
peptidoglycan maturation (meso-diaminopimelate containing) |
|
a nascent peptidoglycan with (L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanine) tetrapeptide + glycine → a nascent peptidoglycan with (L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-glycine) tetrapeptide + D-alanine |
[none] |
peptidoglycan maturation (meso-diaminopimelate containing) |
|
a nascent peptidoglycan with (L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanine) tetrapeptide + a peptidoglycan internal segment with (L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanine) tetrapeptide → a nascent peptidoglycan with L,D cross links (meso-diaminopimelate containing) + D-alanine |
[none] |
peptidoglycan maturation (meso-diaminopimelate containing) |
|
a hydroperoxy-fatty-acyl-[lipid] + 2 glutathione → glutathione disulfide + a hydroxy-fatty-acyl-[lipid] + H2O |
1.11.1.12 |
glutathione-peroxide redox reactions |
|
hydrogen peroxide + 2 glutathione → glutathione disulfide + 2 H2O |
1.11.1.9 |
glutathione-peroxide redox reactions |
|
an (S-diacyl-sn-glyceryl)-L-cysteinyl-[apolipoprotein] + a phosphoglyceride → an N-acyl-(S-diacyl-sn-glyceryl)-L-cysteinyl-[lipoprotein] + a 1-lysophospholipid + H+ |
2.3.1.269 |
lipoprotein posttranslational modification |
|
a 5-methylaminomethyl-2-(Se-phospho)selenouridine34 in tRNA + H2O → a 5-methylaminomethyl-2-selenouridine34 in tRNA + phosphate |
[none] |
tRNA-uridine 2-thiolation and selenation (bacteria) |
|
selenophosphate + a 5-methylaminomethyl-2-(S-geranyl)thiouridine34 in tRNA → a 5-methylaminomethyl-2-(Se-phospho)selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol |
[none] |
tRNA-uridine 2-thiolation and selenation (bacteria) |
|
geranyl diphosphate + a 5-[(methylamino)methyl]-2-thiouridine34 in tRNA → a 5-methylaminomethyl-2-(S-geranyl)thiouridine34 in tRNA + diphosphate |
[none] |
tRNA-uridine 2-thiolation and selenation (bacteria) |
|
a [TusA sulfur-carrier protein]-S-sulfanyl-L-cysteine + a [TusD]-L-cysteine → a [TusA]-L-cysteine + a [TusD sulfur-carrier protein]-S-sulfanyl-L-cysteine |
2.8.1.- |
tRNA-uridine 2-thiolation and selenation (bacteria) |
|
a [TusD sulfur-carrier protein]-S-sulfanyl-L-cysteine + a [TusE sulfur carrier protein]-L-cysteine → a [TusD]-L-cysteine + a [TusE sulfur carrier protein]-S-sulfanylcysteine |
2.8.1.- |
tRNA-uridine 2-thiolation and selenation (bacteria) |
|
an [L-cysteine desulfurase]-S-sulfanyl-L-cysteine + a [TusA]-L-cysteine → an [L-cysteine desulfurase]-L-cysteine + a [TusA sulfur-carrier protein]-S-sulfanyl-L-cysteine |
2.8.1.- |
tRNA-uridine 2-thiolation and selenation (bacteria) |
|
a 5-(aminomethyl)-2-thiouridine34 in tRNA + S-adenosyl-L-methionine → S-adenosyl-L-homocysteine + a 5-[(methylamino)methyl]-2-thiouridine34 in tRNA + H+ |
2.1.1.61 |
tRNA-uridine 2-thiolation and selenation (bacteria) |
|
a 5-carboxymethylaminomethyl-2-thiouridine34 in tRNA + FAD + H2O + 2 H+ → a 5-(aminomethyl)-2-thiouridine34 in tRNA + glyoxylate + FADH2 |
[none] |
tRNA-uridine 2-thiolation and selenation (bacteria) |
|
polycistronic tRNA precursor + H2O → tRNA precursor with a 5' extension and a short 3' extension + a partially processed polycistronic tRNA precursor |
3.1.26.12 |
tRNA processing |
|
tRNA precursor with a 5' extension and a short 3' extension → tRNA precursor with a 5' extension + a ribonucleoside 5'-monophosphate |
3.1.13.5 |
tRNA processing |
|
tRNA precursor with a short 3' extension → uncharged tRNA + n a nucleoside 5'-monophosphate |
3.1.13.5 |
tRNA processing |
|
polycistronic tRNA precursor + H2O → tRNA precursor with a 5' extension and a long 3' trailer + a partially processed polycistronic tRNA precursor |
3.1.26.12 |
tRNA processing |
|
xanthine + NAD+ + H2O ↔ urate + NADH + H+ |
1.17.1.4 |
inosine 5'-phosphate degradation |
|
sn-glycerol 3-phosphate + NAD(P)+ ← glycerone phosphate + NAD(P)H + H+ |
1.1.1.94 |
CDP-diacylglycerol biosynthesis II,
CDP-diacylglycerol biosynthesis I |
|
acrylamide ← acrylonitrile + H2O |
4.2.1.84 |
acrylonitrile degradation I |
|
7,8-dihydroneopterin 3'-triphosphate + H2O → 7,8-dihydroneopterin 3'-phosphate + diphosphate + H+ |
3.6.1.67 |
6-hydroxymethyl-dihydropterin diphosphate biosynthesis I |
|
7,8-dihydroneopterin 3'-phosphate + H2O → D-erythro-7,8-dihydroneopterin + phosphate |
3.6.1.- |
6-hydroxymethyl-dihydropterin diphosphate biosynthesis I |
|
(indol-3-yl)acetamide ← (indol-3-yl)acetonitrile + H2O |
4.2.1.84 |
indole-3-acetate biosynthesis IV (bacteria) |
|
4-amino-4-deoxychorismate → 4-aminobenzoate + pyruvate + H+ |
4.1.3.38 |
4-aminobenzoate biosynthesis I |
25 pathway holes have been filled by the pathway hole filler, in 202 pathways.
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