GapMind for catabolism of small carbon sources


L-threonine catabolism in Pseudomonas putida KT2440

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 (47 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) PP_1141 PP_4867
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) PP_1140 PP_4866
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) PP_1139 PP_4865
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) PP_1138 PP_4864
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) PP_1137 PP_4863
ltaE L-threonine aldolase PP_0321 PP_0671
adh acetaldehyde dehydrogenase (not acylating) PP_2680 PP_0545
ackA acetate kinase PP_1457
pta phosphate acetyltransferase PP_0774
gcvP glycine cleavage system, P component (glycine decarboxylase) PP_0988 PP_5192
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) PP_0986 PP_5194
gcvH glycine cleavage system, H component (lipoyl protein) PP_5193 PP_0989
lpd dihydrolipoyl dehydrogenase PP_4187 PP_4404
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase PP_2336 PP_2339
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) PP_2336 PP_2112
acs acetyl-CoA synthetase, AMP-forming PP_4487 PP_4702
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase PP_3463 PP_2487
D-LDH D-lactate dehydrogenase PP_4737 PP_1649
dddA 3-hydroxypropionate dehydrogenase PP_0056 PP_1949
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) PP_3745
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) PP_3746
glcF D-lactate dehydrogenase, FeS subunit GlcF PP_3747
gloA glyoxylase I PP_3766 PP_0893
gloB hydroxyacylglutathione hydrolase (glyoxalase II) PP_4144 PP_1617
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 PP_2217 PP_3284
iolA malonate semialdehyde dehydrogenase (CoA-acylating) PP_0597 PP_4667
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) PP_0363
L-LDH L-lactate dehydrogenase PP_4736 PP_0654
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit PP_4201
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component PP_3745 PP_5154
lctO L-lactate oxidase or 2-monooxygenase PP_4736
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
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 PP_4067 PP_0558
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit PP_5347 PP_0558
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit PP_4065
pco propanyl-CoA oxidase PP_0158 PP_2216
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase PP_4116 PP_2334
prpC 2-methylcitrate synthase PP_2335 PP_4194
prpD 2-methylcitrate dehydratase PP_2338
prpF methylaconitate isomerase PP_2337 PP_2055
RR42_RS28305 L-threonine:H+ symporter PP_1059 PP_4840
serP1 L-threonine uptake transporter SerP1 PP_4840 PP_5031
snatA L-threonine transporter snatA PP_4825
sstT L-threonine:Na+ symporter SstT PP_2443
tdcB L-threonine dehydratase PP_5149 PP_3446
tdcC L-threonine:H+ symporter TdcC PP_3589
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase PP_2682 PP_2803
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) PP_2368 PP_3671

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 (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