Current and Filled Pathway Holes of <i>Peptostreptococcaceae bacterium oral taxon 113</i> W5053
Current and Filled Pathway Holes of Peptostreptococcaceae bacterium oral taxon 113 W5053
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 Peptostreptococcaceae bacterium oral taxon 113 W5053:
Current Pathway Holes : A list of reactions within metabolic pathways of Peptostreptococcaceae bacterium oral taxon 113 W5053 for which no
corresponding enzyme has been found.
Filled Pathway Holes : A list of former pathway holes within metabolic pathways of Peptostreptococcaceae bacterium oral taxon 113 W5053 which have
been filled with the assistance of the Pathway Hole Filler.
Current Pathway Holes This table lists reactions within metabolic pathways of
Peptostreptococcaceae bacterium oral taxon 113 W5053
for which no corresponding enzyme has been identified in the genome.
The presence of those enzymes is suggested by the presence of the
pathway.
55 pathway holes (25.9%) are present in the 212 total reactions of 75 pathways
Reaction
EC#
Pathway(s) needing this reaction
thiamine phosphate + H2 O → thiamine + phosphate
3.1.3.100
thiamine diphosphate biosynthesis III (Staphylococcus)
L-aspartate + 2-oxoglutarate ↔ oxaloacetate + L-glutamate
2.6.1.1
L-glutamate degradation II
2'-deoxyadenosine + H+ + H2 O → ammonium + 2'-deoxyinosine
3.5.4.4
purine deoxyribonucleosides degradation I
N -acetyl-L-glutamate + ATP → N -acetylglutamyl-phosphate + ADP
2.7.2.8
L-arginine biosynthesis II (acetyl cycle)
N -acetyl-L-glutamate 5-semialdehyde + NADP+ + phosphate ← N -acetylglutamyl-phosphate + NADPH + H+
1.2.1.38
L-arginine biosynthesis II (acetyl cycle)
N -acetyl-L-ornithine + 2-oxoglutarate ← L-glutamate + N -acetyl-L-glutamate 5-semialdehyde
2.6.1.11
L-arginine biosynthesis II (acetyl cycle)
L-ornithine + carbamoyl phosphate → L-citrulline + phosphate + H+
2.1.3.3
L-arginine biosynthesis II (acetyl cycle)
L-arginino-succinate → L-arginine + fumarate
4.3.2.1
L-arginine biosynthesis II (acetyl cycle)
L-aspartate + L-citrulline + ATP → L-arginino-succinate + AMP + diphosphate + H+
6.3.4.5
L-arginine biosynthesis II (acetyl cycle)
pppGpp + H2 O → ppGpp + phosphate + H+
3.6.1.40
ppGpp biosynthesis
(cis )-gondoyl-[acp] + NAD+ ← (2E,11Z)-icosa-2,11-dienoyl-[acp] + NADH + H+
1.3.1.9
gondoate biosynthesis (anaerobic)
(3R,11Z)-3-hydroxy-icos-11-enoyl-[acp] → (2E,11Z)-icosa-2,11-dienoyl-[acp] + H2 O
4.2.1.59
gondoate biosynthesis (anaerobic)
oleoyl-[acp] + malonyl-[acp] + H+ → (11Z)-3-oxo-icos-11-enoyl-[acp] + acyl-carrier protein + CO2
2.3.1.41/2.3.1.179
gondoate biosynthesis (anaerobic)
7-carboxy-7-deazaguanine + ammonium + ATP → preQ0 + ADP + phosphate + H+ + H2 O
6.3.4.20
preQ0 biosynthesis
6-carboxy-5,6,7,8-tetrahydropterin + H+ → 7-carboxy-7-deazaguanine + ammonium
4.3.99.3
preQ0 biosynthesis
CDP + ATP → CTP + ADP
2.7.4.6
CMP phosphorylation
α-D-ribose-1-phosphate → D-ribose 5-phosphate
5.4.2.7
purine ribonucleosides degradation
adenosine + H2 O + H+ → inosine + ammonium
3.5.4.4
purine ribonucleosides degradation
5-amino-6-(5-phospho-D-ribitylamino)uracil + H2 O → 5-amino-6-(D-ribitylamino)uracil + phosphate
3.1.3.104
flavin biosynthesis I (bacteria and plants)
xanthine + NAD+ + H2 O → urate + NADH + H+
1.17.1.4
inosine 5'-phosphate degradation
(L-threonylcarbamoyl)adenylate + an adenine37 in tRNA → an N 6 -L-threonylcarbamoyladenine37 in tRNA + AMP
2.3.1.234
N6-L-threonylcarbamoyladenosine37-modified tRNA biosynthesis
(3R )-3-hydroxyoctadecanoyl-[acp] → (2E )-octadec-2-enoyl-[acp] + H2 O
2.3.1.86/4.2.1.59
stearate biosynthesis II (bacteria and plants)
palmitoyl-[acp] + malonyl-CoA + H+ → 3-oxooctadecanoyl-[acp] + CO2 + coenzyme A
2.3.1.41
stearate biosynthesis II (bacteria and plants)
2,3,4-saturated fatty acyl-[acp] + malonyl-[acp] + H+ → 3-oxoacyl-[acyl-carrier protein] + CO2 + acyl-carrier protein
2.3.1.41/2.3.1.85/2.3.1.86/2.3.1.179
fatty acid elongation -- saturated
(3R )-3-hydroxyacyl-[acyl-carrier protein] → trans -2-enoyl-[acyl-carrier protein] + H2 O
2.3.1.85/2.3.1.86/4.2.1.59
fatty acid elongation -- saturated
oxidized thioredoxin + reduced two electron carrier ← reduced thioredoxin + oxidized electron carrier
[none]
thioredoxin pathway
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.ck
lipoprotein posttranslational modification
a queuosine in tRNA + oxidized electron carrier + H2 O ← an epoxyqueuosine34 in tRNA + reduced two electron carrier
1.17.99.6
queuosine biosynthesis
preQ1 + 2 NADP+ ← preQ0 + 2 NADPH + 3 H+
1.7.1.13
queuosine biosynthesis
S -methyl-5'-thioinosine + phosphate → hypoxanthine + S -(methyl-5-thio-α-D-ribose 1-phosphate
2.4.2.44
S-methyl-5'-thioadenosine degradation III
2 ATP + L-glutamine + hydrogencarbonate + H2 O → L-glutamate + carbamoyl phosphate + 2 ADP + phosphate + 2 H+
6.3.5.5
L-arginine biosynthesis II (acetyl cycle) ,
UMP biosynthesis III
N 1 -(5-phospho-β-D-ribosyl)glycinamide + formate + ATP → N 2 -formyl-N 1 -(5-phospho-β-D-ribosyl)glycinamide + ADP + phosphate + H+
2.1.2.-
5-aminoimidazole ribonucleotide biosynthesis II
[chaperone-ADP]-[disordered-form scaffold protein] complex + ATP → [Fe-S cluster biosynthesis chaperone]-ATP + [disordered-form [Fe-S] cluster scaffold protein] + ADP
3.6.4.-
[2Fe-2S] iron-sulfur cluster biosynthesis
[chaperone-ATP]-[co-chaperone]-[scaffold protein-(2Fe-2S)] complex + apo -iron-sulfur protein → [chaperone-ADP]-[disordered-form scaffold protein] complex + [Fe-S cluster biosynthesis co-chaperone] + holo -[2Fe-2S] cluster protein + phosphate
[none]
[2Fe-2S] iron-sulfur cluster biosynthesis
[co-chaperone]-[scaffold protein-(2Fe-2S)] complex + [Fe-S cluster biosynthesis chaperone]-ATP → [chaperone-ATP]-[co-chaperone]-[scaffold protein-(2Fe-2S)] complex
[none]
[2Fe-2S] iron-sulfur cluster biosynthesis
[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
[S -sulfanyl-L-cysteine desulfurase]2 + [disordered-form [Fe-S] cluster scaffold protein] → S -sulfanyl-[cysteine desulfurase]-[disordered-form scaffold protein] complex
[none]
[2Fe-2S] iron-sulfur cluster biosynthesis
UDP + ATP → UTP + ADP
2.7.4.6
UTP and CTP de novo biosynthesis
a 2,3,4-saturated (3R )-3-hydroxyacyl-CoA ↔ a 2,3,4-saturated (3S )-3-hydroxyacyl-CoA
5.1.2.3
fatty acid beta-oxidation I
glycine + γ-L-glutamyl-L-cysteine + ATP → ADP + glutathione + phosphate + H+
6.3.2.3
glutathione biosynthesis
L-aspartate + oxygen → 2-iminosuccinate + hydrogen peroxide + H+
1.4.3.16
NAD biosynthesis I (from aspartate)
2-iminosuccinate + glycerone phosphate → quinolinate + phosphate + 2 H2 O
2.5.1.72
NAD biosynthesis I (from aspartate)
β-nicotinate D-ribonucleotide + CO2 + diphosphate ← 5-phospho-α-D-ribose 1-diphosphate + quinolinate + 2 H+
2.4.2.19
NAD biosynthesis I (from aspartate)
acetaldehyde + coenzyme A + NAD+ → acetyl-CoA + NADH + H+
1.2.1.10
2'-deoxy-alpha-D-ribose 1-phosphate degradation
2-deoxy-α-D-ribose 1-phosphate → 2-deoxy-D-ribose 5-phosphate
5.4.2.7
2'-deoxy-alpha-D-ribose 1-phosphate degradation
GDP + ATP → GTP + ADP
2.7.4.6
guanosine ribonucleotides de novo biosynthesis ,
ppGpp biosynthesis
thiamine phosphate + ATP → ADP + thiamine diphosphate
2.7.4.16
thiamine diphosphate biosynthesis I (E. coli) ,
thiamine diphosphate biosynthesis II (Bacillus)
adenylo-succinate → fumarate + AMP
4.3.2.2
adenosine ribonucleotides de novo biosynthesis
L-aspartate + IMP + GTP → adenylo-succinate + GDP + phosphate + 2 H+
6.3.4.4
adenosine ribonucleotides de novo biosynthesis
β-D-fructofuranose 6-phosphate + L-glutamine ↔ D-glucosamine 6-phosphate + L-glutamate
2.6.1.16
UDP-N-acetyl-D-glucosamine biosynthesis I
acetyl-CoA + a [carboxyl-carrier protein dimer]-N 6 -carboxybiotinyl-L-lysine → malonyl-CoA + a [biotin carboxyl-carrier-protein dimer]-N 6 -biotinyl-L-lysine
2.1.3.15
fatty acid biosynthesis initiation I
acyl-carrier protein + malonyl-CoA → coenzyme A + malonyl-[acp]
2.3.1.39/2.3.1.85/2.3.1.86
fatty acid biosynthesis initiation I
guanosine + H2 O → D-ribofuranose + guanine
3.2.2.1
guanine and guanosine salvage II
acyl-[acyl-carrier protein] + phosphate → an acyl phosphate + acyl-carrier protein
2.3.1.-
CDP-diacylglycerol biosynthesis III
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.
03:03:54 on Saturday, 6/07/2025 (GMT-8)
24 pathway holes have been filled by the pathway hole filler, in 75 pathways.
Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Sat Jun 7, 2025, BIOCYC17.
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