GapMind for catabolism of small carbon sources


L-threonine catabolism in Pseudomonas stutzeri RCH2

Best path

braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, 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 (48 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) Psest_1312
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) Psest_1311 Psest_1092
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) Psest_1310
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) Psest_1309 Psest_1089
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) Psest_1308 Psest_3854
ltaE L-threonine aldolase Psest_2990 Psest_3404
adh acetaldehyde dehydrogenase (not acylating) Psest_2276 Psest_0671
ackA acetate kinase Psest_3137 Psest_3213
pta phosphate acetyltransferase Psest_3214
gcvP glycine cleavage system, P component (glycine decarboxylase) Psest_0183
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) Psest_0181
gcvH glycine cleavage system, H component (lipoyl protein) Psest_0182 Psest_4125
lpd dihydrolipoyl dehydrogenase Psest_2492 Psest_1663
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase Psest_2319 Psest_2309
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Psest_2319 Psest_2521
acs acetyl-CoA synthetase, AMP-forming Psest_2657 Psest_2220
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase Psest_0905 Psest_0375
D-LDH D-lactate dehydrogenase Psest_0951 Psest_4064
dddA 3-hydroxypropionate dehydrogenase Psest_2633
DVU3032 L-lactate dehydrogenase, LutC-like component Psest_0953
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components Psest_0953
epi methylmalonyl-CoA epimerase Psest_4071
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) Psest_3841
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) Psest_3840
glcF D-lactate dehydrogenase, FeS subunit GlcF Psest_3839
gloA glyoxylase I Psest_3120 Psest_2668
gloB hydroxyacylglutathione hydrolase (glyoxalase II) Psest_2071 Psest_2815
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 Psest_2437 Psest_3109
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Psest_2436 Psest_3781
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) Psest_0412
L-LDH L-lactate dehydrogenase
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit Psest_1706
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit Psest_0954
lldF L-lactate dehydrogenase, LldF subunit Psest_0953
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit Psest_0954
lutB L-lactate dehydrogenase, LutB subunit Psest_0953
lutC L-lactate dehydrogenase, LutC subunit Psest_0952
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
pccA propionyl-CoA carboxylase, alpha subunit Psest_1080 Psest_1019
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Psest_4085 Psest_1019
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit Psest_1083
pco propanyl-CoA oxidase Psest_3830
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase Psest_2321 Psest_2567
prpC 2-methylcitrate synthase Psest_2320 Psest_2499
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase Psest_2318
RR42_RS28305 L-threonine:H+ symporter Psest_1697
serP1 L-threonine uptake transporter SerP1 Psest_1697
snatA L-threonine transporter snatA
sstT L-threonine:Na+ symporter SstT Psest_2478
tdcB L-threonine dehydratase Psest_3866
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase Psest_0672 Psest_3782
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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