GapMind for catabolism of small carbon sources


L-threonine catabolism in Acidovorax sp. GW101-3H11

Best path

snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd

Also see fitness data for the top candidates


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 (45 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
snatA L-threonine transporter snatA Ac3H11_2153 Ac3H11_817
ltaE L-threonine aldolase Ac3H11_4475 Ac3H11_2921
adh acetaldehyde dehydrogenase (not acylating) Ac3H11_4393 Ac3H11_4184
acs acetyl-CoA synthetase, AMP-forming Ac3H11_951 Ac3H11_191
gcvP glycine cleavage system, P component (glycine decarboxylase) Ac3H11_167 Ac3H11_1553
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) Ac3H11_165
gcvH glycine cleavage system, H component (lipoyl protein) Ac3H11_166
lpd dihydrolipoyl dehydrogenase Ac3H11_4091 Ac3H11_2465
Alternative steps:
ackA acetate kinase Ac3H11_4666
acn (2R,3S)-2-methylcitrate dehydratase Ac3H11_1140 Ac3H11_2323
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Ac3H11_2323 Ac3H11_1140
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase Ac3H11_1496 Ac3H11_4393
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) Ac3H11_2396 Ac3H11_4169
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) Ac3H11_1695 Ac3H11_3210
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) Ac3H11_1694 Ac3H11_4628
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) Ac3H11_1693 Ac3H11_4983
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) Ac3H11_1692 Ac3H11_1936
D-LDH D-lactate dehydrogenase Ac3H11_4909 Ac3H11_2934
dddA 3-hydroxypropionate dehydrogenase Ac3H11_3320 Ac3H11_4659
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase Ac3H11_2274
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) Ac3H11_4483 Ac3H11_4909
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) Ac3H11_3400
glcF D-lactate dehydrogenase, FeS subunit GlcF Ac3H11_3398
gloA glyoxylase I Ac3H11_2251 Ac3H11_506
gloB hydroxyacylglutathione hydrolase (glyoxalase II) Ac3H11_478 Ac3H11_3348
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 Ac3H11_2775 Ac3H11_4006
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Ac3H11_4340 Ac3H11_2357
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) Ac3H11_3830
L-LDH L-lactate dehydrogenase Ac3H11_1623 Ac3H11_1767
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit Ac3H11_2705 Ac3H11_3189
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component Ac3H11_4483 Ac3H11_4909
lctO L-lactate oxidase or 2-monooxygenase Ac3H11_2838 Ac3H11_1623
lldE L-lactate dehydrogenase, LldE subunit
lldF L-lactate dehydrogenase, LldF subunit
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit
lutB L-lactate dehydrogenase, LutB subunit
lutC L-lactate dehydrogenase, LutC subunit
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit Ac3H11_2278
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit Ac3H11_2278
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components Ac3H11_2278
pccA propionyl-CoA carboxylase, alpha subunit Ac3H11_2275 Ac3H11_3016
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Ac3H11_2275 Ac3H11_4028
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit Ac3H11_2276 Ac3H11_3010
pco propanyl-CoA oxidase Ac3H11_3533
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase Ac3H11_2831 Ac3H11_2326
prpC 2-methylcitrate synthase Ac3H11_2322 Ac3H11_3161
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase Ac3H11_2325 Ac3H11_4370
pta phosphate acetyltransferase Ac3H11_1079 Ac3H11_4331
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase Ac3H11_2042 Ac3H11_4836
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase Ac3H11_2497 Ac3H11_3163
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent)

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.



Related tools

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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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