Current and Filled Pathway Holes of <i>Lactobacillus acidophilus</i> NCFM (LACI272621)
Current and Filled Pathway Holes of Lactobacillus acidophilus NCFM (LACI272621)
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 Lactobacillus acidophilus NCFM (LACI272621):
Current Pathway Holes : A list of reactions within metabolic pathways of Lactobacillus acidophilus NCFM (LACI272621) for which no
corresponding enzyme has been found.
Filled Pathway Holes : A list of former pathway holes within metabolic pathways of Lactobacillus acidophilus NCFM (LACI272621) which have
been filled with the assistance of the Pathway Hole Filler.
Current Pathway Holes This table lists reactions within metabolic pathways of
Lactobacillus acidophilus NCFM (LACI272621)
for which no corresponding enzyme has been identified in the genome.
The presence of those enzymes is suggested by the presence of the
pathway.
49 pathway holes (17.5%) are present in the 280 total reactions of 100 pathways
Reaction
EC#
Pathway(s) needing this reaction
N -acetyl-β-D-glucosamine-1,6-anhydro-N -acetyl-β-D-muramate + H2 O → 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 + H2 O → N -acetyl-D-muramate 6-phosphate + ADP + H+
2.7.1.170
anhydromuropeptides recycling I
(7,8-dihydropterin-6-yl)methyl diphosphate + 4-aminobenzoate → 7,8-dihydropteroate + diphosphate
2.5.1.15
tetrahydrofolate biosynthesis
CDP + ATP → CTP + ADP
2.7.4.6
CMP phosphorylation
protocatechuate + oxygen → 3-carboxy-cis ,cis -muconate + 2 H+
1.13.11.3
protocatechuate degradation II (ortho-cleavage pathway)
xanthosine + phosphate → xanthine + α-D-ribose-1-phosphate
2.4.2.1
xanthine and xanthosine salvage
polycistronic tRNA precursor + H2 O → 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 + H2 O → tRNA precursor with a 5' extension and a long 3' trailer + a partially processed polycistronic tRNA precursor
3.1.26.12
tRNA processing
di-trans,octa-cis -undecaprenyl diphosphate + H2 O → di-trans,octa-cis -undecaprenyl phosphate + phosphate + H+
3.6.1.27
di-trans,poly-cis-undecaprenyl phosphate biosynthesis
oxidized thioredoxin + reduced two electron carrier ← reduced thioredoxin + oxidized electron carrier
[none]
thioredoxin pathway
2-amino-2-deoxy-D-gluconate 6-phosphate → 2-dehydro-3-deoxy-D-gluconate 6-phosphate + ammonium
4.3.1.29
D-glucosaminate degradation
2'-deoxycytidine + a nucleoside triphosphate → dCMP + a nucleoside diphosphate + H+
2.7.1.74
pyrimidine deoxyribonucleosides salvage
2'-deoxycytidine + H+ + H2 O → 2'-deoxyuridine + ammonium
3.5.4.5
pyrimidine deoxyribonucleosides salvage
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)
D-gluconate 6-phosphate + NAD(P)+ → D-ribulose 5-phosphate + CO2 + NAD(P)H
1.1.1.351
heterolactic fermentation
dCDP + H2 O → dCMP + phosphate + H+
3.6.1.6
pyrimidine deoxyribonucleotides biosynthesis from CTP
dCDP + ATP → dCTP + ADP
2.7.4.6
pyrimidine deoxyribonucleotides de novo biosynthesis I ,
pyrimidine deoxyribonucleotides biosynthesis from CTP ,
pyrimidine deoxyribonucleotide phosphorylation
a [protein]-disulfide + reduced glutaredoxin → a [protein]-dithiol + oxidized glutaredoxin
1.8.4.-
glutathione-glutaredoxin redox reactions
GDP + ATP → GTP + ADP
2.7.4.6
ppGpp biosynthesis ,
guanosine ribonucleotides de novo biosynthesis
pppGpp + H2 O → ppGpp + phosphate + H+
3.6.1.40
ppGpp biosynthesis
L-fuculose 1-phosphate → (S )-lactaldehyde + glycerone phosphate
4.1.2.17
fucose degradation
guanosine + phosphate → guanine + α-D-ribose-1-phosphate
2.4.2.1/2.4.2.15
guanine and guanosine salvage
L-aspartate + L-citrulline + ATP → L-arginino-succinate + AMP + diphosphate + H+
6.3.4.5
urea cycle
succinyl-CoA + oxalate ↔ succinate + oxalyl-CoA
2.8.3.2
oxalate degradation II
3-phospho-L-serine + 2-oxoglutarate ← L-glutamate + 3-phospho-hydroxypyruvate
2.6.1.52
L-serine biosynthesis
(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)
a 5-methyltetrahydrofolate + 2 oxidized ferredoxin [iron-sulfur] cluster ← a 5,10-methylenetetrahydrofolate + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
1.5.7.1
folate transformations I
a tetrahydrofolate + trimethyl sulfonium ← dimethyl sulfide + a 5-methyltetrahydrofolate + H+
2.1.1.19
folate transformations I
L-alanyl-D-glutamate → L-alanyl-L-glutamate
5.1.1.20
muropeptide degradation
L-alanyl-γ-D-glutamyl-meso -diaminopimelate + H2 O → L-alanyl-D-glutamate + meso -diaminopimelate
[none]
muropeptide degradation
UDP + ATP → UTP + ADP
2.7.4.6
UTP and CTP de novo biosynthesis
pyruvate + L-valine → L-alanine + 3-methyl-2-oxobutanoate
2.6.1.66
L-alanine biosynthesis I
a 5-methyltetrahydrofolate + NAD+ ← a 5,10-methylenetetrahydrofolate + NADH + H+
1.5.1.20
folate transformations I ,
N10-formyl-tetrahydrofolate biosynthesis
D-ribulose 1-phosphate → glycolaldehyde + glycerone phosphate
[none]
D-arabinose degradation I
acetyl-holo [citrate lyase acyl-carrier protein] + H2 O → holo [citrate lyase acyl-carrier protein] + acetate + H+
3.1.2.16
citrate lyase activation
holo [citrate lyase acyl-carrier protein] + S-acetyl phosphopantetheine → acetyl-holo [citrate lyase acyl-carrier protein] + 4'-phosphopantetheine
2.3.1.49
citrate lyase activation
(S )-3-hydroxy-3-methylglutaryl-CoA → acetoacetate + acetyl-CoA
4.1.3.4
mevalonate degradation
(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)
4-aminobutanoate + 2-oxoglutarate → succinate semialdehyde + L-glutamate
2.6.1.19
4-aminobutanoate degradation I
mercuriphenyl acetate + H+ → Hg2+ + benzene + acetate
4.99.1.2
phenylmercury acetate degradation
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.-
lipoprotein posttranslational modification
demethylated methyl acceptor + S -adenosyl-L-methionine ↔ S -adenosyl-L-homocysteine + methylated methyl acceptor + H+
2.1.1.-
S-adenosyl-L-methionine cycle I ,
autoinducer AI-2 biosynthesis I
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
a CDP-diacylglycerol + L-serine → CMP + a phosphatidylserine + H+
2.7.8.8
phosphatidylethanolamine biosynthesis I
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.
19:10:07 on Thursday, 6/12/2025 (GMT-8)
46 pathway holes have been filled by the pathway hole filler, in 100 pathways.
Hole-filler
Hole EC#
P(has-function)
All functions of hole-filler
Pathway(s) requiring this reaction
LBA1098
1.3.1.9
0.990
glucose-1-dehydrogenase
fatty acid elongation -- saturated
LBA1098
1.3.1.9
0.990
glucose-1-dehydrogenase
gondoate biosynthesis (anaerobic)
LBA1098
1.3.1.10/1.3.1.39/1.3.1.104/2.3.1.85/2.3.1.86
0.987
glucose-1-dehydrogenase
fatty acid elongation -- saturated
LBA1098
1.3.1.9
0.990
glucose-1-dehydrogenase
stearate biosynthesis II (bacteria and plants)
LBA1220
none
0.999
pyridine mercuric reductase
N10-formyl-tetrahydrofolate biosynthesis ,
folate transformations I
citX
2.7.7.61
0.996
apo-citrate lyase
citrate lyase activation
metA
2.3.1.30
1.000
homoserine O-succinyltransferase
L-cysteine biosynthesis I
folD
1.5.1.15
1.000
bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase
folate transformations I
pyrB
2.1.3.3
1.000
aspartate carbamoyltransferase
urea cycle
LBA1476
3.5.1.105
0.979
cellobiose phosphotransferase
chitobiose degradation
rbsD
5.1.3.29
1.000
D-ribose pyranase
fucose degradation
rbsK
2.7.1.83
0.990
ribokinase
pseudouridine degradation
nadD
2.7.7.18
1.000
nicotinate-nucleotide adenyltransferase
NAD biosynthesis I (from aspartate)
LBA0016
2.7.1.1/2.7.1.2
0.999
fructokinase
trehalose degradation I (low osmolarity) ,
sucrose degradation III (sucrose invertase) ,
heterolactic fermentation
purN
2.1.2.2
1.000
phosphoribosyl glycinamide formyltransferase
5-aminoimidazole ribonucleotide biosynthesis I
purN
3.5.1.10
0.958
phosphoribosyl glycinamide formyltransferase
folate transformations I
purK
2.1.2.-
1.000
5-(carboxyamino)imidazole ribonucleotide synthase
superpathway of 5-aminoimidazole ribonucleotide biosynthesis ,
5-aminoimidazole ribonucleotide biosynthesis II
murC
6.3.2.45
0.991
UDP-N-acetylmuramate--L-alanine ligase
anhydromuropeptides recycling I
ssdh
1.2.1.21
0.999
NAD-dependent aldehyde dehydrogenase
D-arabinose degradation I
LBA1841
3.1.3.3
0.987
phosphoglycerate mutase
L-serine biosynthesis
purB
5.5.1.2
0.991
adenylosuccinate lyase
protocatechuate degradation II (ortho-cleavage pathway)
dltA
6.2.1.3
0.916
D-alanine--poly(phosphoribitol) ligase subunit 1
stearate biosynthesis II (bacteria and plants)
dltA
6.2.1.1
0.993
D-alanine--poly(phosphoribitol) ligase subunit 1
ethanol degradation II
rnpA
2.7.7.56
0.923
ribonuclease P
tRNA processing
rnpA
2.7.7.56
0.923
ribonuclease P
tRNA processing
LBA0266
6.3.2.10
0.994
d-ala-d-ala adding enzyme
UDP-N-acetylmuramoyl-pentapeptide biosynthesis I (meso-diaminopimelate containing)
gltX
6.1.1.24
1.000
glutamyl-tRNA synthetase
glutaminyl-tRNAgln biosynthesis via transamidation
LBA0354
2.7.1.51
0.990
gluconate kinase
fucose degradation
LBA0354
none
0.990
gluconate kinase
D-arabinose degradation I
LBA0383
2.7.4.6
0.985
DNA polymerase III subunit delta
pyrimidine deoxyribonucleotide phosphorylation ,
pyrimidine deoxyribonucleotides biosynthesis from CTP ,
pyrimidine deoxyribonucleotides de novo biosynthesis I
LBA0449
3.1.13.1
1.000
ribonuclease R
tRNA processing
LBA0449
3.1.13.1
1.000
ribonuclease R
tRNA processing
LBA0651
3.1.1.31
0.999
isomerase
heterolactic fermentation ,
pentose phosphate pathway (oxidative branch) I
fabG
2.3.1.41
0.998
3-oxoacyl-ACP reductase
stearate biosynthesis II (bacteria and plants)
LBA0687
5.4.2.7
0.999
phosphoglucomutase
2'-deoxy-alpha-D-ribose 1-phosphate degradation
LBA0717
3.1.3.11
0.990
HAD superfamily hydrolase
glycolysis I (from glucose 6-phosphate)
LBA0854
4.1.2.14/4.1.2.55
0.987
4-hydroxy-tetrahydrodipicolinate synthase
D-glucosaminate degradation
LBA0865
3.2.2.1
0.996
nucleoside hydrolase
guanine and guanosine salvage II
LBA0886
2.7.1.1/2.7.1.2
0.925
sugar kinase
trehalose degradation I (low osmolarity) ,
sucrose degradation III (sucrose invertase) ,
heterolactic fermentation
fumC
4.3.2.1
0.996
fumarate hydratase
urea cycle
LBA0908
1.4.3.16
1.000
fumarate reductase flavoprotein subunit
NAD biosynthesis I (from aspartate)
LBA0913
3.1.1.24
0.990
hydrolase
protocatechuate degradation II (ortho-cleavage pathway)
relA
3.1.7.2
1.000
ppGpp synthetase
ppGpp biosynthesis
relA
3.1.7.2
1.000
ppGpp synthetase
ppGpp biosynthesis
kpyK
2.7.9.2
0.984
pyruvate kinase
glycolysis I (from glucose 6-phosphate)
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