GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Escherichia coli BW25113

Best path

tdcC, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd

Also see fitness data for the top candidates

Rules

Overview: L-threonine degradation in GapMind is based on MetaCyc pathway I via 2-ketobutyrate formate-lyase (link), pathway II via glycine (link), pathway III via methylglyoxal (link), and pathway IV via threonine aldolase (link). Pathway V is not thought to occur in prokaryotes and is not included.

70 steps (56 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
tdcC L-threonine:H+ symporter TdcC b3116 b2796
ltaE L-threonine aldolase b0870 b2551
adh acetaldehyde dehydrogenase (not acylating) b1746 b1241
ackA acetate kinase b3115 b2296
pta phosphate acetyltransferase b2297 b2458
gcvP glycine cleavage system, P component (glycine decarboxylase) b2903
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) b2905
gcvH glycine cleavage system, H component (lipoyl protein) b2904
lpd dihydrolipoyl dehydrogenase b0116 b3962
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase b0118 b1276
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) b1276
acs acetyl-CoA synthetase, AMP-forming b4069 b0335
ald-dh-CoA acetaldehyde dehydrogenase, acylating b1241 b2455
aldA lactaldehyde dehydrogenase b1415 b1300
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) b3458 b3460
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) b3457
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) b3456
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) b3455 b3201
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) b3454 b3201
D-LDH D-lactate dehydrogenase b1380 b2979
dddA 3-hydroxypropionate dehydrogenase b0311
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components b0307
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) b2979
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) b4468
glcF D-lactate dehydrogenase, FeS subunit GlcF b4467
gloA glyoxylase I b1651
gloB hydroxyacylglutathione hydrolase (glyoxalase II) b2154 b0212
grdA glycine reductase component A1
grdB glycine reductase component B, gamma subunit
grdC glycine reductase component C, beta subunit
grdD glycine reductase component C, alpha subunit
grdE glycine reductase component B, precursor to alpha/beta subunits
hpcD 3-hydroxypropionyl-CoA dehydratase b1393 b2341
iolA malonate semialdehyde dehydrogenase (CoA-acylating) b2661 b0312
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) b3617 b0776
L-LDH L-lactate dehydrogenase b3605 b0801
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component b2979
lctO L-lactate oxidase or 2-monooxygenase b3605
lldE L-lactate dehydrogenase, LldE subunit b0306
lldF L-lactate dehydrogenase, LldF subunit b0307
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit b0306
lutB L-lactate dehydrogenase, LutB subunit b0307
lutC L-lactate dehydrogenase, LutC subunit b0308
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit b2917
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit b2917 b4019
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components b2917
pccA propionyl-CoA carboxylase, alpha subunit b3256
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit b3256
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase b0331 b4015
prpC 2-methylcitrate synthase b0333 b0720
prpD 2-methylcitrate dehydratase b0334
prpF methylaconitate isomerase b0769
RR42_RS28305 L-threonine:H+ symporter b3795 b4208
serP1 L-threonine uptake transporter SerP1 b4208 b0112
snatA L-threonine transporter snatA b1242 b3434
sstT L-threonine:Na+ symporter SstT b3089
tdcB L-threonine dehydratase b3772 b3117
tdcE 2-ketobutyrate formate-lyase b3114 b0903
tdh L-threonine 3-dehydrogenase b3589 b3616
tynA aminoacetone oxidase b1386
yvgN methylglyoxal reductase (NADPH-dependent) b3012 b0207

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory