Current and Filled Pathway Holes of <i>Saccharomyces cerevisiae</i> S288c

Current and Filled Pathway Holes of Saccharomyces cerevisiae S288c

A pathway hole is a pathway reaction for which no corresponding enzyme has been identified in the genome. We consider only contiguous pathways (pathways containing connected sets of reactions, as opposed to pathways containing unconnected sets of reactions) when enumerating pathway holes.

This report includes two tables regarding pathway holes in Saccharomyces cerevisiae S288c:

Current Pathway Holes: A list of reactions within metabolic pathways of Saccharomyces cerevisiae S288c for which no corresponding enzyme has been found.

Filled Pathway Holes: A list of former pathway holes within metabolic pathways of Saccharomyces cerevisiae S288c which have been filled with the assistance of the Pathway Hole Filler.


Current Pathway Holes

This table lists reactions within metabolic pathways of Saccharomyces cerevisiae S288c for which no corresponding enzyme has been identified in the genome. The presence of those enzymes is suggested by the presence of the pathway.

94 pathway holes (10.8%) are present in the 872 total reactions of 290 pathways

Reaction EC# Pathway(s) needing this reaction
an L-cysteine-S-conjugate + acetyl-CoA → a mercapturate + coenzyme A + H+ 2.3.1.80 glutathione-mediated detoxification I
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
methylarsenite-[arsenite methyltransferase] + 2 H2O → methylarsonous acid + [arsenite methyltransferase] [none] arsenic detoxification (yeast)
dimethylarsenite-[arsenite methyltransferase] + H2O → dimethylarsinous acid + [arsenite methyltransferase] [none] arsenic detoxification (yeast)
methylarsenite-[arsenite methyltransferase] + reduced thioredoxin + S-adenosyl-L-methionine → S-adenosyl-L-homocysteine + dimethylarsenite-[arsenite methyltransferase] + oxidized thioredoxin + H+ [none] arsenic detoxification (yeast)
arsenite-[arsenite methyltransferase] + reduced thioredoxin + S-adenosyl-L-methionine → S-adenosyl-L-homocysteine + methylarsenite-[arsenite methyltransferase] + oxidized thioredoxin + H+ [none] arsenic detoxification (yeast)
arsenic triglutathione + [arsenite methyltransferase] → arsenite-[arsenite methyltransferase] + 3 glutathione [none] arsenic detoxification (yeast)
dCDP + H2O → dCMP + phosphate + H+ 3.6.1.6 pyrimidine deoxyribonucleotides biosynthesis from CTP
30-oxolanosterol + reduced [NADPH-hemoprotein reductase] + dioxygen → 4,4-dimethyl-5-α-cholesta-8,14,24-trien-3-β-ol + oxidized [NADPH-hemoprotein reductase] + formate + H2O + H+ [none] zymosterol biosynthesis
30-hydroxylanosterol + reduced [NADPH-hemoprotein reductase] + dioxygen → 30-oxolanosterol + oxidized [NADPH-hemoprotein reductase] + 2 H2O [none] zymosterol biosynthesis
lanosterol + reduced [NADPH-hemoprotein reductase] + dioxygen → 30-hydroxylanosterol + oxidized [NADPH-hemoprotein reductase] + H2O [none] zymosterol biosynthesis
an [HMP-P synthase]-L-lysine + pyridoxal 5'-phosphate → an [HMP-P synthase]-(PLP-imine)-L-lysine + H2O + H+ [none] 4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis II
a dolichol + NAD(P)+ ↔ a dolichal + NAD(P)H + H+ 1.1.1.- dolichol and dolichyl phosphate biosynthesis
a di-trans, poly-cis-polyprenol + NAD(P)+ ↔ a di-trans, poly-cis-polyprenal + NAD(P)H + H+ 1.1.1.- dolichol and dolichyl phosphate biosynthesis
a di-trans, poly-cis-polyisoprenyl diphosphate + H2O → a di-trans, poly-cis-polyprenol + diphosphate 3.1.4.- dolichol and dolichyl phosphate biosynthesis
L-phenylalanine + 5,6,7,8-tetrahydrobiopterin + dioxygen → L-tyrosine + a 4a-hydroxytetrahydrobiopterin 1.14.16.1
5-aminopentanoate + 2-oxoglutarate ↔ L-glutamate + glutarate semialdehyde 2.6.1.48
glutarate semialdehyde + NAD+ + H2O → glutarate + NADH + 2 H+ 1.2.1.20
5-acetamidovalerate + H2O → 5-aminopentanoate + acetate 3.5.1.-
2-keto-6-acetamidocaproate + NAD+ + H2O → 5-acetamidovalerate + CO2 + NADH + H+ 1.3.1.-
N6-acetyl-L-lysine + 2-oxoglutarate ↔ L-glutamate + 2-keto-6-acetamidocaproate 2.6.1.-
L-lysine + acetyl-CoA → N6-acetyl-L-lysine + coenzyme A + H+ 2.3.1.306
ammonium + 3 NAD(P)+ + 2 H2O ← nitrite + 3 NAD(P)H + 5 H+ 1.7.1.4 alkylnitronates degradation
prenol + ATP → prenyl phosphate + ADP + H+ 2.7.1.32 prenylated FMNH2 biosynthesis
prenyl diphosphate + H2O → prenyl phosphate + phosphate + H+ 3.6.1.76 prenylated FMNH2 biosynthesis
GDP-α-D-mannose + α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-3-O-(Ser/Thr)-[protein] → α-D-Man-(1→3)-α-D-Man-(1→3)-[α-D-Man-6P-]-α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-3-O-(Ser/Thr)-[protein] + GMP + H+ 2.4.1.- protein O-mannosylation I (yeast)
acetyl-CoA + acyl-carrier protein → coenzyme A + acetyl-[acp] 2.3.1.38 fatty acid biosynthesis initiation (mitochondria)
acetaldehyde + coenzyme A + NAD+ → acetyl-CoA + NADH + H+ 1.2.1.10 L-threonine degradation IV
thiamine triphosphate + H2O → thiamine diphosphate + phosphate + H+ 3.6.1.28 thiamin triphosphate metabolism
ATP + thiamine diphosphate → thiamine triphosphate + ADP 2.7.4.15 thiamin triphosphate metabolism
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)
D-arabinofuranose + NADP+ → D-arabinono-1,4-lactone + NADPH + H+ 1.1.1.427 dehydro-D-arabinono-1,4-lactone biosynthesis
ADP-α-D-glucose + D-glucopyranose 6-phosphate → α,α-trehalose 6-phosphate + ADP + H+ 2.4.1.347 trehalose biosynthesis II
9-cis, 11-trans-octadecadienoyl-CoA + 2 coenzyme A + 2 NAD+ + 2 dioxygen + 2 H2O → 5-cis, 7-trans-tetradecadienoyl-CoA + 2 acetyl-CoA + 2 hydrogen peroxide + 2 NADH + 2 H+ [none] 9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent)
10-cis-heptadecenoyl-CoA + 2 coenzyme A + 2 NAD+ + 2 H2O + 2 dioxygen → 6-cis-tridecenoyl-CoA + 2 acetyl-CoA + 2 hydrogen peroxide + 2 NADH + 2 H+ [none] 10-cis-heptadecenoyl-CoA degradation
dodecanoyl-[acp domain within a fatty acid synthase] + coenzyme A → lauroyl-CoA + holo-[acyl carrier protein] domain within a fatty acid synthase 2.3.1.- palmitate biosynthesis (cytoplasm)
palmitoyl-[acp domain within a fatty acid synthase] + H2O → palmitate + holo-[acyl carrier protein] domain within a fatty acid synthase + H+ 3.1.2.14 palmitate biosynthesis (cytoplasm)
palmitoyl-[acp domain within a fatty acid synthase] + NADP+ ← (2E)-hexadec-2-enoyl-[acp domain within a fatty acid synthase] + NADPH + H+ 2.3.1.85/2.3.1.86 palmitate biosynthesis (cytoplasm)
(3R)-3-hydroxyhexadecanoyl-[acp domain within a fatty acid synthase] + NADP+ ← 3-oxohexadecanoyl-[acp domain within a fatty acid synthase] + NADPH + H+ 2.3.1.85/2.3.1.86 palmitate biosynthesis (cytoplasm)
myristoyl-[acp domain within a fatty acid synthase] + malonyl-CoA + H+ → 3-oxohexadecanoyl-[acp domain within a fatty acid synthase] + CO2 + coenzyme A 2.3.1.85/2.3.1.86 palmitate biosynthesis (cytoplasm)
myristoyl-[acp domain within a fatty acid synthase] + NADP+ ← (2E)-tetradec-2-enoyl-[acp domain within a fatty acid synthase] + NADPH + H+ 2.3.1.85/2.3.1.86 palmitate biosynthesis (cytoplasm)
(3R)-3-hydroxytetradecanoyl-[acp domain within a fatty acid synthase] + NADP+ ← 3-oxotetradecanoyl-[acp domain within a fatty acid synthase] + NADPH + H+ 2.3.1.85/2.3.1.86 palmitate biosynthesis (cytoplasm)
dodecanoyl-[acp domain within a fatty acid synthase] + malonyl-CoA + H+ → 3-oxotetradecanoyl-[acp domain within a fatty acid synthase] + CO2 + coenzyme A 2.3.1.85/2.3.1.86 palmitate biosynthesis (cytoplasm)
dodecanoyl-[acp domain within a fatty acid synthase] + H2O → holo-[acyl carrier protein] domain within a fatty acid synthase + laurate + H+ 3.1.2.21 palmitate biosynthesis (cytoplasm)
dodecanoyl-[acp domain within a fatty acid synthase] + NADP+ ← (2E)-dodec-2-enoyl-[acp domain within a fatty acid synthase] + NADPH + H+ 2.3.1.85/2.3.1.86 palmitate biosynthesis (cytoplasm)
(3R)-3-hydroxydodecanoyl-[acp domain within a fatty acid synthase] + NADP+ ← 3-oxododecanoyl-[acp domain within a fatty acid synthase] + NADPH + H+ 2.3.1.85/2.3.1.86 palmitate biosynthesis (cytoplasm)
decanoyl-[acp domain within a fatty acid synthase] + malonyl-CoA + H+ → 3-oxododecanoyl-[acp domain within a fatty acid synthase] + CO2 + coenzyme A 2.3.1.85/2.3.1.86 palmitate biosynthesis (cytoplasm)
decanoyl-[acp domain within a fatty acid synthase] + NADP+ ← (2E)-dec-2-enoyl-[acp domain within a fatty acid synthase] + NADPH + H+ 2.3.1.85/2.3.1.86 palmitate biosynthesis (cytoplasm)
(3R)-3-hydroxydecanoyl-[acp domain within a fatty acid synthase] + NADP+ ← 3-oxodecanoyl-[acp domain within a fatty acid synthase] + NADPH + H+ 2.3.1.85/2.3.1.86 palmitate biosynthesis (cytoplasm)
octanoyl-[acp domain within a fatty acid synthase] + malonyl-CoA + H+ → 3-oxodecanoyl-[acp domain within a fatty acid synthase] + CO2 + coenzyme A 2.3.1.85/2.3.1.86 palmitate biosynthesis (cytoplasm)
octanoyl-[acp domain within a fatty acid synthase] + NADP+ ← (2E)-oct-2-enoyl-[acp domain within a fatty acid synthase] + NADPH + H+ 2.3.1.85/2.3.1.86 palmitate biosynthesis (cytoplasm)
(3R)-3-hydroxyoctanoyl-[acp domain within a fatty acid synthase] + NADP+ ← 3-oxooctanoyl-[acp domain within a fatty acid synthase] + NADPH + H+ 2.3.1.85/2.3.1.86 palmitate biosynthesis (cytoplasm)
hexanoyl-[acp domain within a fatty acid synthase] + malonyl-CoA + H+ → 3-oxooctanoyl-[acp domain within a fatty acid synthase] + CO2 + coenzyme A 2.3.1.85/2.3.1.86 palmitate biosynthesis (cytoplasm)
hexanoyl-[acp domain within a fatty acid synthase] + NADP+ ← (2E)-hex-2-enoyl-[acp domain within a fatty acid synthase] + NADPH + H+ 2.3.1.85/2.3.1.86 palmitate biosynthesis (cytoplasm)
(3R)-3-hydroxyhexanoyl-[acp domain within a fatty acid synthase] + NADP+ ← 3-oxohexanoyl-[acp domain within a fatty acid synthase] + NADPH + H+ 2.3.1.85/2.3.1.86 palmitate biosynthesis (cytoplasm)
butanoyl-[acp domain within a fatty acid synthase] + malonyl-CoA + H+ → 3-oxohexanoyl-[acp domain within a fatty acid synthase] + CO2 + coenzyme A 2.3.1.85/2.3.1.86 palmitate biosynthesis (cytoplasm)
butanoyl-[acp domain within a fatty acid synthase] + NADP+ ← (2E)-but-2-enoyl-[acp domain within a fatty acid synthase] + NADPH + H+ 2.3.1.85/2.3.1.86 palmitate biosynthesis (cytoplasm)
(3R)-3-hydroxybutanoyl-[acp domain within a fatty acid synthase] + NADP+ ← acetoacetyl-[acp domain within a fatty acid synthase] + NADPH + H+ 2.3.1.85/2.3.1.86 palmitate biosynthesis (cytoplasm)
D-myo-inositol (1,3,4,5)-tetrakisphosphate + H2O → D-myo-inositol (1,4,5)-trisphosphate + phosphate 3.1.3.62 D-myo-inositol (1,3,4)-trisphosphate biosynthesis
5-amino-6-(5-phospho-D-ribitylamino)uracil + H2O → 5-amino-6-(D-ribitylamino)uracil + phosphate 3.1.3.104 flavin biosynthesis III (fungi)
(2E,5Z)-tetradec-2,5-enoyl-CoA + coenzyme A + dioxygen + H2O → (3Z)-dodec-3-enoyl-CoA + hydrogen peroxide + acetyl-CoA [none] oleate beta-oxidation (isomerase-dependent)
oleoyl-CoA + 2 coenzyme A + 2 NAD+ + 2 dioxygen + 2 H2O → (5Z)-tetradecenoyl-CoA + 2 hydrogen peroxide + 2 acetyl-CoA + 2 NADH + 2 H+ [none] oleate beta-oxidation (isomerase-dependent)
GDP-α-D-mannose + Man9GlcNAc2-[protein] (isomer 9A1,2,3,4B1,3) → Man10GlcNAc2-[protein] (isomer 10A1,2,3,4B1,3,4) + GDP + H+ 2.4.1.- protein N-glycosylation processing of proteins targeted for retention in cellular organelles (cis-Golgi, yeast)
[protein] with an N-terminal 5-oxo-L-proline + H2O → 5-oxo-L-proline + peptide 3.4.19.3 5-oxo-L-proline metabolism
formyl-CoA + H2O → formate + coenzyme A + H+ 3.1.2.10 oxalate degradation VI
L-serine + H+ → ethanolamine + CO2 4.1.1.- phosphatidylethanolamine biosynthesis II
oxidized thioredoxin + reduced two electron carrier ← reduced thioredoxin + oxidized electron carrier [none] thioredoxin system
2-phospho-D-glycerate ↔ 3-phospho-D-glycerate 5.4.2.12 gluconeogenesis, glycolysis
(E)-4-coumaroyl-CoA + (R)-3-(4-hydroxyphenyl)lactate ↔ 4-coumarate + (R)-3-(4-hydroxyphenyl)lactoyl-CoA 2.8.3.17 4-hydroxybenzoate biosynthesis I (eukaryotes)
4-coumarate + H2O → 4-hydroxybenzaldehyde + acetate 4.1.2.66 4-hydroxybenzoate biosynthesis I (eukaryotes)
(R)-3-(4-hydroxyphenyl)lactate + NAD+ ← 3-(4-hydroxyphenyl)pyruvate + NADH + H+ 1.1.1.110 4-hydroxybenzoate biosynthesis I (eukaryotes)
a 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + ATP → 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate + ADP + H+ 2.7.1.153 3-phosphoinositide biosynthesis
a 1-phosphatidyl-1D-myo-inositol 4-phosphate + ATP → a 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphate + ADP + H+ 2.7.1.154 3-phosphoinositide biosynthesis
3-hydroxy-heptanoyl-CoA + coenzyme A + NAD+ + H2O + dioxygen → 3-hydroxypentanoyl-CoA + acetyl-CoA + hydrogen peroxide + NADH + H+ [none] 10-cis-heptadecenoyl-CoA degradation, 10-trans-heptadecenoyl-CoA degradation (reductase-dependent), 10-trans-heptadecenoyl-CoA degradation (MFE-dependent)
(3R)-hydroxynonanoyl-CoA + coenzyme A + NAD+ + H2O + dioxygen → 3-hydroxy-heptanoyl-CoA + acetyl-CoA + hydrogen peroxide + NADH + H+ [none] 10-cis-heptadecenoyl-CoA degradation, 10-trans-heptadecenoyl-CoA degradation (reductase-dependent), 10-trans-heptadecenoyl-CoA degradation (MFE-dependent)
(3R)-hydroxy-undecanoyl-CoA + coenzyme A + NAD+ + H2O + dioxygen → (3R)-hydroxynonanoyl-CoA + acetyl-CoA + hydrogen peroxide + NADH + H+ [none] 10-cis-heptadecenoyl-CoA degradation, 10-trans-heptadecenoyl-CoA degradation (reductase-dependent)
10-trans-heptadecenoyl-CoA + 2 coenzyme A + 2 NAD+ + 2 H2O + 2 dioxygen → 6-trans-tridecenoyl-CoA + 2 acetyl-CoA + 2 hydrogen peroxide + 2 NADH + 2 H+ [none] 10-trans-heptadecenoyl-CoA degradation (reductase-dependent)
adenosine + phosphate ↔ α-D-ribose-1-phosphate + adenine 2.4.2.1 purine ribonucleosides degradation
2-all trans-hexaprenyl-6-methoxyphenol + NADPH + dioxygen + H+ → 2-all trans-hexaprenyl-6-methoxyhydroquinone + NADP+ + H2O 1.14.13.- ubiquinol-6 biosynthesis from 4-aminobenzoate (yeast), ubiquinol-6 biosynthesis from 4-hydroxybenzoate (eukaryotic)
3-all trans-hexaprenyl-4-hydroxy-5-methoxybenzoate + H+ → 2-all trans-hexaprenyl-6-methoxyphenol + CO2 4.1.1.- ubiquinol-6 biosynthesis from 4-aminobenzoate (yeast), ubiquinol-6 biosynthesis from 4-hydroxybenzoate (eukaryotic)
an N10-formyltetrahydrofolate + H2O → a tetrahydrofolate + formate + H+ 3.5.1.10 folate transformations I
L-homocysteine + a 5-methyltetrahydrofolate → L-methionine + a tetrahydrofolate 2.1.1.13 folate transformations I
(3R)-3-hydroxyoctadecanoyl-[acp domain within a fatty acid synthase] + NADP+ ← 3-oxooctadecanoyl-[acp domain within a fatty acid synthase] + NADPH + H+ 2.3.1.86 stearate biosynthesis
stearoyl-[acp domain within a fatty acid synthase] + NADP+ ← (2E)-octadec-2-enoyl-[acp domain within a fatty acid synthase] + NADPH + H+ 2.3.1.86 stearate biosynthesis
palmitoyl-[acp domain within a fatty acid synthase] + malonyl-CoA + H+ → 3-oxooctadecanoyl-[acp domain within a fatty acid synthase] + CO2 + coenzyme A 2.3.1.86 stearate biosynthesis
stearoyl-[acp domain within a fatty acid synthase] + coenzyme A → stearoyl-CoA + [acyl carrier protein] domain within a fatty acid synthase 2.3.1.86 stearate biosynthesis
xanthosine + phosphate ↔ xanthine + α-D-ribose-1-phosphate 2.4.2.1 xanthine and xanthosine salvage, purine ribonucleosides degradation
C20 sphinganine + 2 ferrocytochrome b5 + dioxygen + 2 H+ → C20 phytosphingosine + 2 ferricytochrome b5 + H2O 1.14.18.5 sphingolipid biosynthesis (yeast)
stearoyl-CoA + L-serine + H+ → C20 3-dehydrosphinganine + CO2 + coenzyme A 2.3.1.50 sphingolipid biosynthesis (yeast)
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
formylaminopyrimidine + H2O → aminomethylpyrimidine + formate 3.5.1.- base-degraded thiamin salvage
2 a 1,2-diacyl-sn-glycerol ↔ a triacyl-sn-glycerol + a 2-acylglycerol 2.3.1.- triacylglycerol biosynthesis

Filled Pathway Holes

Key:
Hole-filler The gene whose product is predicted to catalyze the missing reaction.
Hole EC# The EC number of the missing reaction (links to the reaction page).
P(has-function) The probability that the hole-filler catalyzes the missing reaction as determined by the PHFiller.
All functions of hole-filler All current annotations of the hole-filler, including the function of the missing reaction to which it has been assigned.
Pathway(s) requiring this reaction All metabolic pathways in which the pathway hole occurs in the database.

21:56:17 on Thursday, 5/22/2025 (GMT-8)

14 pathway holes have been filled by the pathway hole filler, in 290 pathways.

Hole-filler Hole EC# P(has-function) All functions of hole-filler Pathway(s) requiring this reaction
NFS1 2.8.1.- 1.000 L-cysteine desulfurase iron-sulfur cluster biosynthesis
GCD6 2.7.7.22 0.434 translation initiation factor catalytic subunit epsilon dolichyl phosphate D-mannose biosynthesis
NCS6 2.8.1.- 0.980 cytoplasmic tRNA 2-thiolation protein 1 tRNA-uridine 2-thiolation (cytoplasmic)
UBA4 2.8.1.- 0.978 adenylyltransferase and sulfurtransferase UBA4 tRNA-uridine 2-thiolation (cytoplasmic)
NNR2 4.2.1.93 0.999 NADHX dehydratase NADH repair
VIP1 2.7.1.158 0.997 inositol polyphosphate kinase 1D-myo-inositol hexakisphosphate biosynthesis I (from Ins(1,4,5)P3), inositol diphosphates biosynthesis, inositol phosphate biosynthesis
ARG82 2.7.1.151 0.984 ARGRIII inositol polyphosphate multikinase
MSS4 2.7.1.68 1.000 1-phosphatidylinositol-4-phosphate 5-kinase
AAT2 2.6.1.88 0.978 aspartate transaminase methionine salvage pathway
AAH1 3.5.4.2 0.991 adenine deaminase adenine and adenosine salvage IV

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Thu May 22, 2025, BIOCYC14A.