Current and Filled Pathway Holes of <i>Escherichia coli</i> K-12 substr. MG1655

Current and Filled Pathway Holes of Escherichia coli K-12 substr. MG1655

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 K-12 substr. MG1655:

Current Pathway Holes: A list of reactions within metabolic pathways of Escherichia coli K-12 substr. MG1655 for which no corresponding enzyme has been found.

Filled Pathway Holes: A list of former pathway holes within metabolic pathways of Escherichia coli K-12 substr. MG1655 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 K-12 substr. MG1655 for which no corresponding enzyme has been identified in the genome. The presence of those enzymes is suggested by the presence of the pathway.

41 pathway holes (3.9%) are present in the 1053 total reactions of 346 pathways

Reaction EC# Pathway(s) needing this reaction
malonyl-[acp] methyl ester + malonyl-[acp] + H+ → 3-oxoglutaryl-[acp] methyl ester + CO2 + an acyl-carrier protein 2.3.1.41/2.3.1.179 8-amino-7-oxononanoate biosynthesis I
D-xylono-1,4-lactone + H2O → D-xylonate + H+ 3.1.1.68 D-xylose degradation III
D-xylopyranose + NADP+ → D-xylono-1,4-lactone + NADPH + H+ 1.1.1.424 D-xylose degradation III
2,5-dioxopentanoate + NADP+ + H2O → 2-oxoglutarate + NADPH + 2 H+ 1.2.1.26 D-xylose degradation III
2-dehydro-3-deoxy-D-pentonate → 2,5-dioxopentanoate + H2O 4.2.1.141 D-xylose degradation III
a phosphatidylhomoserine + H+ → a phosphatidylpropanolamine + CO2 4.1.1.- phosphatidylhomoserine and phosphatidylpropanolamine biosynthesis
D-arabinitol + NAD+ ↔ D-xylulose + NADH + H+ 1.1.1.11 D-arabinitol degradation I
4,5-secobiotin + S-adenosyl-L-methionine → 5'-deoxyadenosine + L-methionine + biotin + H+ [none] biotin biosynthesis from 8-amino-7-oxononanoate I
D-ribulose + ATP → ADP + D-ribulose 5-phosphate + H+ 2.7.1.16/2.7.1.47
ribitol + NAD+ → D-ribulose + NADH + H+ 1.1.1.56
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
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)
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
7,8-dihydromonapterin triphosphate + 3 H2O → 7,8-dihydromonapterin + 3 phosphate + 2 H+ [none] tetrahydromonapterin biosynthesis
xylitol + NAD+ → D-xylulose + NADH + H+ 1.1.1.9 xylitol degradation I
[HypCDE]-Fe(CO)(CN)2 + HycE → {[NiFe]-hydrogenase large subunit}-Fe(CO)(CN)2 + HypCDE trimer [none] NiFe(CO)(CN)2 cofactor biosynthesis
2-dehydro-3-deoxy-L-galactonate + NAD+ → 3-deoxy-D-glycero-2,5-hexodiulosonate + NADH + H+ 1.1.1.389 3,6-anhydro-alpha-L-galactopyranose degradation
3,6-anhydro-L-galactofuranose + NAD(P)+ + H2O → 3,6-anhydro-L-galactonate + NAD(P)H + 2 H+ [none] 3,6-anhydro-alpha-L-galactopyranose degradation
[oxidized DsbA protein][periplasm] + a [protein]-dithiol[periplasm] → [reduced DsbA protein][periplasm] + a [protein]-disulfide[periplasm] 1.8.4.15
[reduced DsbA protein][periplasm] + [oxidized DsbB protein][inner membrane] → [oxidized DsbA protein][periplasm] + [reduced DsbB protein][inner membrane] [none]
[reduced DsbB protein] + a quinone → [oxidized DsbB protein] + a quinol [none]
[IscU-Fe2+] + [IscS]2 → [IscS]2[IscU-Fe2+]2 [none] [2Fe-2S] iron-sulfur cluster biosynthesis (bacterial IscS system)
[IscU iron-sulfur cluster scaffold protein dimer carrying a [2Fe-2S]+2 cluster] → [IscU iron-sulfur cluster scaffold protein carrying a [2Fe-2S]+2 cluster] + [IscU iron-sulfur cluster scaffold protein] [none] [2Fe-2S] iron-sulfur cluster biosynthesis (bacterial IscS system)
[IscS]2[IscU-[1Fe-1S] cluster]2 + 2 [IscU-Fe2+] → [IscS]2[IscU-Fe2+]2 + 2 [IscU iron-sulfur cluster scaffold protein carrying a [1Fe-1S]0 cluster] [none] [2Fe-2S] iron-sulfur cluster biosynthesis (bacterial IscS system)
[IscS-S]2[IscU-Fe]2 → [IscS]2[IscU-S-Fe]2 [none] [2Fe-2S] iron-sulfur cluster biosynthesis (bacterial IscS system)
6-sulfo-α-D-quinovose ↔ 6-sulfo-β-D-quinovose 5.1.3.43 sulfoquinovose degradation I
dodecanoyl-[acp] + H2O → an acyl-carrier protein + dodecanoate + H+ 3.1.2.21 palmitate biosynthesis II (type II fatty acid synthase)
palmitoyl-[acp] + H2O → palmitate + an acyl-carrier protein + H+ 3.1.2.14 palmitate biosynthesis II (type II fatty acid synthase)
ATP + hydrogen carbonate + propanoyl-CoA ↔ ADP + (S)-methylmalonyl-CoA + phosphate + H+ 6.4.1.3 propanoyl CoA degradation I
(R)-methylmalonyl-CoA ↔ (S)-methylmalonyl-CoA 5.1.99.1 propanoyl CoA degradation I
ATP + nicotinate adenine dinucleotide + L-glutamine + H2O → AMP + L-glutamate + NAD+ + diphosphate + H+ 6.3.5.1 NAD de novo biosynthesis I, NAD salvage pathway I (PNC VI cycle), NAD salvage pathway II (PNC IV cycle)
NAD+ + H2O → β-nicotinamide D-ribonucleotide + AMP + 2 H+ 3.6.1.22 NAD salvage pathway I (PNC VI cycle), NAD salvage pathway II (PNC IV cycle)
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)
demethylated methyl acceptor + S-adenosyl-L-methionine → S-adenosyl-L-homocysteine + methylated methyl acceptor + H+ 2.1.1.- autoinducer AI-2 biosynthesis I
7,8-dihydroneopterin 3'-phosphate + H2O → D-erythro-7,8-dihydroneopterin + phosphate 3.6.1.- 6-hydroxymethyl-dihydropterin diphosphate biosynthesis I
glycolate + NAD+ → glyoxylate + NADH + H+ 1.1.1.26 D-xylose degradation IV
glycolaldehyde + oxidized electron carrier → glycolate + reduced two electron carrier + H+ 1.2.99.- D-xylose degradation IV
D-xylono-1,5-lactone + H2O → D-xylonate + H+ 3.1.1.110 D-xylose degradation IV
D-xylopyranose + NAD(P)+ → D-xylono-1,5-lactone + NAD(P)H + H+ 1.1.1.359 D-xylose degradation IV

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.

22:32:47 on Wednesday, 5/20/2026 (GMT-8)

Hole-filler Hole EC# P(has-function) All functions of hole-filler Pathway(s) requiring this reaction
No filled pathway holes have been identified for Escherichia coli K-12 substr. MG1655.

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Please cite the following article in publications resulting from the use of EcoCyc: Frontiers in Microbiology 2021
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