Current and Filled Pathway Holes of <i>Dielma fastidiosa</i> type strain: JC13

Current and Filled Pathway Holes of Dielma fastidiosa type strain: JC13

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 Dielma fastidiosa type strain: JC13:

Current Pathway Holes: A list of reactions within metabolic pathways of Dielma fastidiosa type strain: JC13 for which no corresponding enzyme has been found.

Filled Pathway Holes: A list of former pathway holes within metabolic pathways of Dielma fastidiosa type strain: JC13 which have been filled with the assistance of the Pathway Hole Filler.


Current Pathway Holes

This table lists reactions within metabolic pathways of Dielma fastidiosa type strain: JC13 for which no corresponding enzyme has been identified in the genome. The presence of those enzymes is suggested by the presence of the pathway.

81 pathway holes (23.0%) are present in the 352 total reactions of 115 pathways

Reaction EC# Pathway(s) needing this reaction
L-arginine + H2O → urea + L-ornithine 3.5.3.1 urea cycle
L-arginino-succinate → L-arginine + fumarate 4.3.2.1 urea cycle
L-aspartate + L-citrulline + ATP → L-arginino-succinate + AMP + diphosphate + H+ 6.3.4.5 urea cycle
L-ornithine + carbamoyl phosphate → L-citrulline + phosphate + H+ 2.1.3.3 urea cycle
a debranched α-limit dextrin + n H2O → n D-glucopyranose 3.2.1.3 glycogen degradation II
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
glutathione → L-cysteinylglycine + 5-oxo-L-proline 4.3.2.7 5-oxo-L-proline metabolism
5-oxo-L-proline + ATP + 2 H2O → L-glutamate + ADP + phosphate + H+ 3.5.2.9 5-oxo-L-proline metabolism
glycerol + NAD+ → dihydroxyacetone + NADH + H+ 1.1.1.6 glycerol degradation V
preQ1 + 2 NADP+ ← preQ0 + 2 NADPH + 3 H+ 1.7.1.13 queuosine biosynthesis I (de novo)
3-keto-L-gulonate 6-phosphate + H+ → L-xylulose 5-phosphate + CO2 4.1.1.85 L-ascorbate degradation I (bacterial, anaerobic)
L-threonine → (2Z)-2-aminobut-2-enoate + H2O + H+ [none] L-threonine degradation I
2-oxobutanoate + coenzyme A → propanoyl-CoA + formate 2.3.1.- L-threonine degradation I
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
(7,8-dihydropterin-6-yl)methyl diphosphate + 4-aminobenzoate → 7,8-dihydropteroate + diphosphate 2.5.1.15 tetrahydrofolate biosynthesis
thiamine phosphate + H2O → thiamine + phosphate 3.1.3.100 thiamine diphosphate biosynthesis III (Staphylococcus)
2'-deoxycytidine + a nucleoside triphosphate → dCMP + a nucleoside diphosphate + H+ 2.7.1.74 pyrimidine deoxyribonucleosides salvage
prenol + ATP → prenyl phosphate + ADP + H+ [none] prenylated FMNH2 biosynthesis
prenyl diphosphate + H2O → prenyl phosphate + phosphate + H+ [none] prenylated FMNH2 biosynthesis
ethanolamine → ammonium + acetaldehyde 4.3.1.7 ethanolamine utilization
pppGpp + H2O → ppGpp + phosphate + H+ 3.6.1.40 ppGpp metabolism
meso-diaminopimelate + H+ → L-lysine + CO2 4.1.1.20 L-lysine biosynthesis II
L-2-acetamido-6-oxoheptanedioate + L-glutamate → N-acetyl-L,L-2,6-diaminopimelate + 2-oxoglutarate [none] L-lysine biosynthesis II
thiamine phosphate + ATP → ADP + thiamine diphosphate 2.7.4.16 thiamine diphosphate biosynthesis I (E. coli), thiamine diphosphate biosynthesis II (Bacillus)
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
molybdopterin synthase sulfur carrier subunit + ATP + H+ → carboxy-adenylated [molybdopterin-synthase sulfur-carrier protein subunit] + diphosphate 2.7.7.80 molybdopterin biosynthesis
cyclic pyranopterin phosphate + 2 thiocarboxylated [molybdopterin-synthase sulfur-carrier protein subunit] + H2O → 2 molybdopterin synthase sulfur carrier subunit + molybdopterin + 4 H+ 2.8.1.12 molybdopterin biosynthesis
(polyphosphate)(n) + H2O → (polyphosphate)(n-1) + phosphate 3.6.1.11 polyphosphate metabolism
GDP + ATP → GTP + ADP 2.7.4.6 guanosine ribonucleotides de novo biosynthesis, ppGpp metabolism
CDP + ATP → CTP + ADP 2.7.4.6 CMP phosphorylation
L-serine + a tetrahydrofolate ↔ glycine + a 5,10-methylenetetrahydrofolate + H2O 2.1.2.1 folate transformations III (E. coli), folate polyglutamylation
L-homocysteine + a 5-methyltetrahydrofolate → L-methionine + a tetrahydrofolate 2.1.1.13 folate transformations III (E. coli)
a 5-methyltetrahydrofolate + NAD+ ↔ a 5,10-methylenetetrahydrofolate + NADH + H+ 1.5.1.20 folate transformations III (E. coli)
L-aspartate + carbamoyl phosphate → N-carbamoyl-L-aspartate + phosphate + H+ 2.1.3.2 UMP biosynthesis III
dADP + ATP → dATP + ADP 2.7.4.6 adenosine deoxyribonucleotides de novo biosynthesis II
O-phospho-L-serine + H2O → L-serine + phosphate 3.1.3.3 L-serine biosynthesis I
UDP-N-acetyl-α-D-muramate + L-alanyl-γ-D-glutamyl-meso-diaminopimelate + ATP → UDP-N-acetyl-α-D-muramoyl-L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimelate + ADP + phosphate + H+ 6.3.2.45 anhydromuropeptides recycling I
GlcNAc-1,6-anhMurNAc-L-Ala-γ-D-Glu-DAP-D-Ala + H2O → N-acetyl-β-D-glucosamine-1,6-anhydro-N-acetyl-β-D-muramate + L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanine 3.5.1.28 anhydromuropeptides recycling I
N-acetyl-β-D-glucosamine-1,6-anhydro-N-acetyl-β-D-muramate + H2O → N-acetyl-β-D-glucosamine + 1,6-anhydro-N-acetyl-β-muramate 3.2.1.52 anhydromuropeptides recycling I
1,6-anhydro-N-acetyl-β-muramate + ATP + H2O → N-acetyl-D-muramate 6-phosphate + ADP + H+ 2.7.1.170 anhydromuropeptides recycling I
a [lipoyl-carrier protein] N6-octanoyl-L-lysine + [Fe-S] cluster scaffold protein carrying a [4Fe-4S]+2 cluster + 2 reduced ferredoxin [iron-sulfur] cluster + 2 S-adenosyl-L-methionine + 6 H+ → a [lipoyl-carrier protein]-N6-[(R)-dihydrolipoyl]-L-lysine + 2 5'-deoxyadenosine + 2 L-methionine + [Fe-S] cluster scaffold protein + 2 sulfide(2-) + 4 Fe2+ + 2 oxidized ferredoxin [iron-sulfur] cluster 2.8.1.8 lipoate biosynthesis and incorporation II
(R)-lactate + NAD+ ← pyruvate + NADH + H+ 1.1.1.28 heterolactic fermentation
D-xylulose 5-phosphate + phosphate → D-glyceraldehyde 3-phosphate + acetyl phosphate + H2O 4.1.2.9 heterolactic fermentation
D-gluconate 6-phosphate + NAD(P)+ → D-ribulose 5-phosphate + CO2 + NAD(P)H 1.1.1.351 heterolactic fermentation
D-glucopyranose 6-phosphate → 1D-myo-inositol 3-monophosphate 5.5.1.4 myo-inositol biosynthesis
a [lipoyl-carrier protein]-N6-[(R)-lipoyl]-L-lysine + H2O → a [lipoyl-carrier protein]-L-lysine + (R)-lipoate 3.5.1.- lipoate salvage II
a [glycine-cleavage complex H protein] N6-[(R)-lipoyl]-L-lysine + a [lipoyl-carrier protein]-L-lysine → a [lipoyl-carrier protein]-N6-[(R)-lipoyl]-L-lysine + [glycine cleavage system lipoyl-carrier protein]-L-lysine 2.3.1.200 lipoate salvage II
L-tyrosine + 2-oxoglutarate ↔ 3-(4-hydroxyphenyl)pyruvate + L-glutamate 2.6.1.1/2.6.1.5/2.6.1.27/2.6.1.57 L-tyrosine biosynthesis I
an acyl-CoA + a 2-lysophosphatidate → a phosphatidate + coenzyme A 2.3.1.51 CDP-diacylglycerol biosynthesis I
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)
4-phosphooxy-L-threonine + NAD+ → 3-amino-1-hydroxyacetone 1-phosphate + CO2 + NADH 1.1.1.262 pyridoxal 5'-phosphate biosynthesis I
4-phospho-D-erythronate + NAD+ → (3R)-3-hydroxy-2-oxo-4 phosphooxybutanoate + NADH + H+ 1.1.1.290 pyridoxal 5'-phosphate biosynthesis I
1-deoxy-D-xylulose 5-phosphate + 3-amino-1-hydroxyacetone 1-phosphate → pyridoxine 5'-phosphate + phosphate + H+ + 2 H2O 2.6.99.2 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
6-phospho D-glucono-1,5-lactone + H2O → D-gluconate 6-phosphate + H+ 3.1.1.31 heterolactic fermentation, pentose phosphate pathway (oxidative branch) I
[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
L-aspartate + 2-oxoglutarate ↔ oxaloacetate + L-glutamate 2.6.1.1 L-glutamate degradation II
N-acetyl-D-mannosamine + ATP → N-acetyl-D-mannosamine 6-phosphate + ADP + H+ 2.7.1.60 N-acetylneuraminate and N-acetylmannosamine degradation I
N-acetylneuraminate → N-acetyl-D-mannosamine + pyruvate 4.1.3.3 N-acetylneuraminate and N-acetylmannosamine degradation I
N,N'-diacetylchitobiose 6'-phosphate + H2O → N-monoacetylchitobiose 6'-phosphate + acetate 3.5.1.105 chitobiose degradation
xanthine + NAD+ + H2O ↔ urate + NADH + H+ 1.17.1.4 inosine 5'-phosphate degradation
XMP + H2O → xanthosine + phosphate 3.1.3.5 inosine 5'-phosphate degradation
WO2-molybdopterin cofactor + molybdopterin + H+ → bis(tungstenpterin) cofactor + H2O 2.10.1.- bis(tungstenpterin) cofactor biosynthesis
UDP + ATP → UTP + ADP 2.7.4.6 UTP and CTP de novo biosynthesis
dGDP + ATP → dGTP + ADP 2.7.4.6 guanosine deoxyribonucleotides de novo biosynthesis II
guanosine + H2O → D-ribofuranose + guanine 3.2.2.1 guanine and guanosine salvage II

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.

23:16:12 on Friday, 7/18/2025 (GMT-8)

18 pathway holes have been filled by the pathway hole filler, in 115 pathways.

Hole-filler Hole EC# P(has-function) All functions of hole-filler Pathway(s) requiring this reaction
RS01765 3.5.1.47 0.907 amidohydrolase L-lysine biosynthesis II
RS02745 5.1.99.6 1.000 NAD(P)H-hydrate dehydratase NADH repair
RS05765 2.6.1.9 1.000 histidinol-phosphate aminotransferase family protein L-histidine biosynthesis
RS06915 2.8.1.- 0.999 cysteine desulfurase [2Fe-2S] iron-sulfur cluster biosynthesis
RS06915 2.8.1.- 0.999 cysteine desulfurase [2Fe-2S] iron-sulfur cluster biosynthesis
RS07735 2.7.6.5 1.000 bifunctional (p)ppGpp synthetase/guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase ppGpp metabolism
RS07735 3.1.7.2 1.000 bifunctional (p)ppGpp synthetase/guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase ppGpp metabolism
RS10095 2.7.1.83 0.996 winged helix-turn-helix transcriptional regulator pseudouridine degradation
RS11220 2.7.1.4 0.954 carbohydrate kinase sucrose degradation III (sucrose invertase), heterolactic fermentation
RS12910 1.1.1.25 0.999 hypothetical protein chorismate biosynthesis from 3-dehydroquinate
RS12910 2.7.1.71 0.964 hypothetical protein chorismate biosynthesis from 3-dehydroquinate
glmU 2.3.1.157 0.975 hypothetical protein UDP-N-acetyl-D-glucosamine biosynthesis I, anhydromuropeptides recycling I
glmU 2.7.7.23 0.975 hypothetical protein UDP-N-acetyl-D-glucosamine biosynthesis I, anhydromuropeptides recycling I
RS14035 2.7.1.1/2.7.1.2 0.909 ROK family protein glycolysis III (from glucose), glycogen degradation II, sucrose degradation III (sucrose invertase), heterolactic fermentation
RS16865 2.7.1.6 0.998 hypothetical protein D-galactose degradation I (Leloir pathway)
RS17030 2.7.7.75 0.917 MogA/MoaB family molybdenum cofactor biosynthesis protein bis(tungstenpterin) cofactor biosynthesis, molybdenum cofactor biosynthesis
RS17385 1.1.1.94 0.995 NAD(P)-dependent glycerol-3-phosphate dehydrogenase CDP-diacylglycerol biosynthesis I
RS17455 3.1.2.6 0.991 MBL fold metallo-hydrolase methylglyoxal degradation I

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