Current and Filled Pathway Holes of <i>Escherichia coli</i> O157:H7 str. EDL933

Current and Filled Pathway Holes of Escherichia coli O157:H7 str. EDL933

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 Escherichia coli O157:H7 str. EDL933:

Current Pathway Holes: A list of reactions within metabolic pathways of Escherichia coli O157:H7 str. EDL933 for which no corresponding enzyme has been found.

Filled Pathway Holes: A list of former pathway holes within metabolic pathways of Escherichia coli O157:H7 str. EDL933 which have been filled with the assistance of the Pathway Hole Filler.


Current Pathway Holes

This table lists reactions within metabolic pathways of Escherichia coli O157:H7 str. EDL933 for which no corresponding enzyme has been identified in the genome. The presence of those enzymes is suggested by the presence of the pathway.

29 pathway holes (4.0%) are present in the 726 total reactions of 242 pathways

Reaction EC# Pathway(s) needing this reaction
acetyl-holo [citrate lyase acyl-carrier protein] + H2O → 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
acetaldehyde + NAD+ + H2O → acetate + NADH + 2 H+ 1.2.1.3 ethanol degradation II
a phosphatidylserine + H+ → a phosphatidylethanolamine + CO2 4.1.1.65 phosphatidylserine and phosphatidylethanolamine biosynthesis I
7,8-dihydroneopterin 3'-phosphate + H2O → D-erythro-7,8-dihydroneopterin + phosphate 3.6.1.- 6-hydroxymethyl-dihydropterin diphosphate biosynthesis I
S-adenosyl-L-methionine + H+ → CO2 + S-adenosyl 3-(methylsulfanyl)propylamine 4.1.1.50 spermidine biosynthesis I
an α-limit dextrin → a debranched α-limit dextrin 2.4.1.25/3.2.1.33 glycogen degradation II
a debranched α-limit dextrin + n H2O → n D-glucopyranose 3.2.1.3 glycogen degradation II
a debranched α-limit dextrin + n phosphate → n α-D-glucopyranose 1-phosphate 2.4.1.1 glycogen degradation II
isochorismate + H2O → pyruvate + (2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate 3.3.2.1 2,3-dihydroxybenzoate biosynthesis
stearoyl-[acp] + H2O → stearate + acyl-carrier protein + H+ 3.1.2.14 stearate biosynthesis II (bacteria and plants)
L-cysteine + a [molybdopterin synthase sulfurtransferase]-L-cysteine → L-alanine + a [molybdopterin synthase sulfurtransferase]-S-sulfanyl-L-cysteine 2.8.1.7 molybdopterin biosynthesis
oxidized thioredoxin + reduced two electron carrier ← reduced thioredoxin + oxidized electron carrier [none] thioredoxin pathway
(S)-citramalate ← mesaconate + H2O 4.2.1.34 L-glutamate degradation VI (to pyruvate)
(S)-citramalate → pyruvate + acetate 4.1.3.22 L-glutamate degradation VI (to pyruvate)
adenosylcob(III)alamin-[corrinoid adenosyltranferase] → [corrinoid adenosyltransferase] + adenosylcobalamin [none] adenosylcobalamin salvage from cobalamin
[corrinoid adenosyltransferase] + cob(II)alamin → cob(II)alamin-[corrinoid adenosyltranferase] [none] adenosylcobalamin salvage from cobalamin
ATP + nicotinate adenine dinucleotide + L-glutamine + H2O → L-glutamate + AMP + NAD+ + diphosphate + H+ 6.3.5.1 NAD de novo biosynthesis I (from aspartate), NAD salvage pathway I (PNC VI cycle)
β-nicotinamide D-ribonucleotide + H2O → D-ribofuranose 5-phosphate + nicotinamide + H+ 3.2.2.6/3.2.2.14 NAD salvage pathway I (PNC VI cycle)
NAD+ + H2O → β-nicotinamide D-ribonucleotide + AMP + 2 H+ 3.6.1.22 NAD salvage pathway I (PNC VI cycle)
dihydroxyacetone + ATP → glycerone phosphate + ADP + H+ 2.7.1.29 glycerol degradation II
glutarate + 2-oxoglutarate + dioxygen → (S)-2-hydroxyglutarate + succinate + CO2 1.14.11.64 L-lysine degradation I
2 acetyl-CoA ↔ acetoacetyl-CoA + coenzyme A 2.3.1.9/2.3.1.16 acetoacetate degradation (to acetyl CoA)
L-ornithine + 2-oxoglutarate ↔ L-glutamate + L-glutamate-5-semialdehyde 2.6.1.13 L-proline biosynthesis III (from L-ornithine)
a 2,3,4-saturated fatty acid + coenzyme A + ATP → a 2,3,4-saturated fatty acyl CoA + AMP + diphosphate 6.2.1.- fatty acid beta-oxidation I (generic)
L-arginine + H2O → urea + L-ornithine 3.5.3.1 putrescine biosynthesis III
7,8-dihydromonapterin triphosphate + 3 H2O → 7,8-dihydromonapterin + 3 phosphate + 2 H+ [none] tetrahydromonapterin biosynthesis
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)

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.

03:08:02 on Thursday, 5/15/2025 (GMT-8)

29 pathway holes have been filled by the pathway hole filler, in 242 pathways.

Hole-filler Hole EC# P(has-function) All functions of hole-filler Pathway(s) requiring this reaction
araB 2.7.1.16 1.000 ribulokinase L-arabinose degradation I
bioC 2.1.1.197 1.000 malonyl-acyl carrier protein methyltransferase 8-amino-7-oxononanoate biosynthesis I
caiB 2.8.3.21 1.000 γ-butyrobetainyl-CoA:carnitine CoA transferase L-carnitine degradation I
caiD 4.2.1.149 1.000 crotonobetainyl-CoA hydratase L-carnitine degradation I
deoD 2.4.2.1 1.000 purine nucleoside phosphorylase purine deoxyribonucleosides degradation I
deoD 2.4.2.1 1.000 purine nucleoside phosphorylase purine deoxyribonucleosides degradation I
deoD 2.4.2.1 1.000 purine nucleoside phosphorylase purine deoxyribonucleosides degradation I
fabA 5.3.3.14 1.000 β-hydroxyacyl-acyl carrier protein dehydratase/isomerase (5Z)-dodecenoate biosynthesis I
fabB 2.3.1.41/2.3.1.179 0.978 3-oxoacyl-[acyl carrier protein] synthase 1 palmitate biosynthesis (type II fatty acid synthase)
fabF 2.3.1.41/2.3.1.179 1.000 3-oxoacyl-[acyl carrier protein] synthase 2 8-amino-7-oxononanoate biosynthesis I
fabH 2.3.1.38 1.000 3-oxoacyl-[acyl carrier protein] synthase 3 superpathway of fatty acid biosynthesis initiation (E. coli)
fabI 1.3.1.9 0.998 enoyl-[acyl-carrier-protein] reductase palmitate biosynthesis (type II fatty acid synthase)
fabZ 4.2.1.59 0.956 3-hydroxy-acyl-[acyl-carrier-protein] dehydratase 8-amino-7-oxononanoate biosynthesis I
fabZ 4.2.1.59 0.956 3-hydroxy-acyl-[acyl-carrier-protein] dehydratase 8-amino-7-oxononanoate biosynthesis I
fucK 2.7.1.51 1.000 L-fuculokinase D-arabinose degradation I
ilvE 2.6.1.42 1.000 branched-chain-amino-acid aminotransferase L-isoleucine biosynthesis I (from threonine)
prpB 4.1.3.30 0.999 2-methylisocitrate lyase 2-methylcitrate cycle I
purE 5.4.99.18 1.000 N5-carboxyaminoimidazole ribonucleotide mutase inosine-5'-phosphate biosynthesis I
queA 2.4.99.17 1.000 tRNA preQ134 S-adenosylmethionine ribosyltransferase-isomerase queuosine biosynthesis I (de novo)
thiF 2.7.7.73 1.000 sulfur carrier protein ThiS adenylyltransferase thiazole component of thiamine diphosphate biosynthesis I
wecD 2.3.1.210 1.000 WecD dTDP-N-acetylthomosamine biosynthesis
wecE 2.6.1.59 1.000 dTDP-4-dehydro-6-deoxy-D-glucose transaminase dTDP-N-acetylthomosamine biosynthesis
glxR 1.1.1.60 1.000 tartronate semialdehyde reductase 2 glycolate and glyoxylate degradation I
menH 4.2.99.20 1.000 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase 2-carboxy-1,4-naphthoquinol biosynthesis
scpB 4.1.1.- 1.000 methylmalonyl-CoA decarboxylase conversion of succinate to propanoate
ribE 2.5.1.78 1.000 6,7-dimethyl-8-ribityllumazine synthase flavin biosynthesis I (bacteria and plants)
wecF 2.4.1.325 1.000 TDP-N-acetylfucosamine:lipid II N-acetylfucosaminyltransferase enterobacterial common antigen biosynthesis

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