GapMind for catabolism of small carbon sources


L-threonine catabolism in Chromobacterium vaccinii MWU205

Best path

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


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 (49 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
tdcC L-threonine:H+ symporter TdcC VL52_RS12080
ltaE L-threonine aldolase VL52_RS15620 VL52_RS11385
adh acetaldehyde dehydrogenase (not acylating) VL52_RS21455 VL52_RS06935
ackA acetate kinase VL52_RS15345 VL52_RS02270
pta phosphate acetyltransferase VL52_RS15350 VL52_RS02265
gcvP glycine cleavage system, P component (glycine decarboxylase) VL52_RS02865
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) VL52_RS02855
gcvH glycine cleavage system, H component (lipoyl protein) VL52_RS02860
lpd dihydrolipoyl dehydrogenase VL52_RS06780 VL52_RS01105
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase VL52_RS06920 VL52_RS16820
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) VL52_RS06920 VL52_RS13705
acs acetyl-CoA synthetase, AMP-forming VL52_RS11020 VL52_RS20355
ald-dh-CoA acetaldehyde dehydrogenase, acylating VL52_RS13795
aldA lactaldehyde dehydrogenase VL52_RS07105 VL52_RS21455
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) VL52_RS09675 VL52_RS22490
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) VL52_RS15500
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) VL52_RS15495
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) VL52_RS15490 VL52_RS03360
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) VL52_RS15485 VL52_RS03360
D-LDH D-lactate dehydrogenase VL52_RS18670 VL52_RS20375
dddA 3-hydroxypropionate dehydrogenase VL52_RS11315
DVU3032 L-lactate dehydrogenase, LutC-like component VL52_RS18660
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components VL52_RS18665
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) VL52_RS20375 VL52_RS18670
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE)
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I VL52_RS13355 VL52_RS04985
gloB hydroxyacylglutathione hydrolase (glyoxalase II) VL52_RS05620 VL52_RS12240
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 VL52_RS18865 VL52_RS21030
iolA malonate semialdehyde dehydrogenase (CoA-acylating) VL52_RS11940 VL52_RS21020
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) VL52_RS13405 VL52_RS00340
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
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component VL52_RS20375
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit VL52_RS18655
lldF L-lactate dehydrogenase, LldF subunit VL52_RS18665
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit VL52_RS18655
lutB L-lactate dehydrogenase, LutB subunit VL52_RS18665
lutC L-lactate dehydrogenase, LutC subunit VL52_RS18660
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 VL52_RS19945 VL52_RS01580
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit VL52_RS01580 VL52_RS19945
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit VL52_RS19955
pco propanyl-CoA oxidase VL52_RS20895 VL52_RS19965
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase VL52_RS13445 VL52_RS06905
prpC 2-methylcitrate synthase VL52_RS06910 VL52_RS01125
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase VL52_RS06925 VL52_RS07045
RR42_RS28305 L-threonine:H+ symporter VL52_RS13800 VL52_RS00285
serP1 L-threonine uptake transporter SerP1 VL52_RS00290 VL52_RS00285
snatA L-threonine transporter snatA VL52_RS11865 VL52_RS00260
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase VL52_RS15040 VL52_RS10860
tdcE 2-ketobutyrate formate-lyase VL52_RS12070
tdh L-threonine 3-dehydrogenase VL52_RS13400 VL52_RS10400
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) VL52_RS19845 VL52_RS14040

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 24 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:

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