GapMind for catabolism of small carbon sources


L-threonine catabolism in Dyella japonica UNC79MFTsu3.2

Best path

RR42_RS28305, 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 (43 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
RR42_RS28305 L-threonine:H+ symporter N515DRAFT_2630 N515DRAFT_3653
ltaE L-threonine aldolase N515DRAFT_4398 N515DRAFT_1841
adh acetaldehyde dehydrogenase (not acylating) N515DRAFT_0465 N515DRAFT_3729
acs acetyl-CoA synthetase, AMP-forming N515DRAFT_3075 N515DRAFT_0016
gcvP glycine cleavage system, P component (glycine decarboxylase) N515DRAFT_0055
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) N515DRAFT_4331
gcvH glycine cleavage system, H component (lipoyl protein) N515DRAFT_4332
lpd dihydrolipoyl dehydrogenase N515DRAFT_2155 N515DRAFT_2778
Alternative steps:
ackA acetate kinase N515DRAFT_2456
acn (2R,3S)-2-methylcitrate dehydratase N515DRAFT_0029 N515DRAFT_1420
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) N515DRAFT_0029 N515DRAFT_1419
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase N515DRAFT_0379 N515DRAFT_3729
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB)
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD)
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC)
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) N515DRAFT_3950 N515DRAFT_1687
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) N515DRAFT_3950 N515DRAFT_1248
D-LDH D-lactate dehydrogenase N515DRAFT_3582 N515DRAFT_1999
dddA 3-hydroxypropionate dehydrogenase N515DRAFT_4337
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) N515DRAFT_1999 N515DRAFT_3582
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) N515DRAFT_1999
glcF D-lactate dehydrogenase, FeS subunit GlcF N515DRAFT_2104
gloA glyoxylase I N515DRAFT_3310
gloB hydroxyacylglutathione hydrolase (glyoxalase II) N515DRAFT_0434 N515DRAFT_3712
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 N515DRAFT_1164 N515DRAFT_0416
iolA malonate semialdehyde dehydrogenase (CoA-acylating) N515DRAFT_3729 N515DRAFT_2488
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) N515DRAFT_0037 N515DRAFT_0547
L-LDH L-lactate dehydrogenase N515DRAFT_1250
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit N515DRAFT_4319
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component N515DRAFT_1999 N515DRAFT_3582
lctO L-lactate oxidase or 2-monooxygenase N515DRAFT_1250
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 N515DRAFT_0973
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit N515DRAFT_0973
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components N515DRAFT_0973
pccA propionyl-CoA carboxylase, alpha subunit N515DRAFT_0927 N515DRAFT_3374
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit N515DRAFT_3374 N515DRAFT_0927
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit N515DRAFT_0936
pco propanyl-CoA oxidase N515DRAFT_0484 N515DRAFT_0492
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase N515DRAFT_4123 N515DRAFT_0020
prpC 2-methylcitrate synthase N515DRAFT_0021 N515DRAFT_2064
prpD 2-methylcitrate dehydratase N515DRAFT_0031
prpF methylaconitate isomerase N515DRAFT_0030
pta phosphate acetyltransferase N515DRAFT_2182
serP1 L-threonine uptake transporter SerP1 N515DRAFT_2630 N515DRAFT_3653
snatA L-threonine transporter snatA
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase N515DRAFT_0565 N515DRAFT_3206
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase N515DRAFT_0039 N515DRAFT_2489
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.



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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