GapMind for catabolism of small carbon sources


L-threonine catabolism in Ruegeria conchae TW15

Best path

snatA, 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 (43 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
snatA L-threonine transporter snatA G7G_RS0106075 G7G_RS0105385
ltaE L-threonine aldolase G7G_RS0112510 G7G_RS0111845
adh acetaldehyde dehydrogenase (not acylating) G7G_RS0104060 G7G_RS0111065
ackA acetate kinase G7G_RS0109955
pta phosphate acetyltransferase G7G_RS0111665 G7G_RS0104460
gcvP glycine cleavage system, P component (glycine decarboxylase) G7G_RS0110380
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) G7G_RS0110370 G7G_RS0115830
gcvH glycine cleavage system, H component (lipoyl protein) G7G_RS0110375
lpd dihydrolipoyl dehydrogenase G7G_RS0114415 G7G_RS0122165
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase G7G_RS0113975 G7G_RS0120980
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) G7G_RS0113975
acs acetyl-CoA synthetase, AMP-forming G7G_RS0105955 G7G_RS0104455
ald-dh-CoA acetaldehyde dehydrogenase, acylating G7G_RS0121370 G7G_RS0107180
aldA lactaldehyde dehydrogenase G7G_RS0116915 G7G_RS0121155
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) G7G_RS0107425
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) G7G_RS0101020 G7G_RS0107445
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) G7G_RS0107430 G7G_RS0115350
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) G7G_RS0115355 G7G_RS0107435
D-LDH D-lactate dehydrogenase G7G_RS0120340 G7G_RS0112035
dddA 3-hydroxypropionate dehydrogenase G7G_RS0101190 G7G_RS0113310
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase G7G_RS0112770
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) G7G_RS0104345 G7G_RS0120340
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) G7G_RS0104350
glcF D-lactate dehydrogenase, FeS subunit GlcF G7G_RS0104355
gloA glyoxylase I G7G_RS0108420 G7G_RS0105000
gloB hydroxyacylglutathione hydrolase (glyoxalase II) G7G_RS0112455 G7G_RS0110900
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 G7G_RS0116465 G7G_RS0122460
iolA malonate semialdehyde dehydrogenase (CoA-acylating) G7G_RS0106675 G7G_RS0111640
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) G7G_RS0116435 G7G_RS0119350
L-LDH L-lactate dehydrogenase G7G_RS0102695 G7G_RS0117895
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 G7G_RS0112035
lctO L-lactate oxidase or 2-monooxygenase G7G_RS0102695 G7G_RS0113560
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 G7G_RS0113370 G7G_RS0117980
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit G7G_RS0113370 G7G_RS0117980
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components G7G_RS0113370 G7G_RS0117980
pccA propionyl-CoA carboxylase, alpha subunit G7G_RS0113355 G7G_RS0117665
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit G7G_RS0113355 G7G_RS0120085
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit G7G_RS0120080
pccB propionyl-CoA carboxylase, beta subunit G7G_RS0113330 G7G_RS0117675
pco propanyl-CoA oxidase G7G_RS0107335 G7G_RS0117695
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase G7G_RS0107985
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase G7G_RS0118570 G7G_RS0112915
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase G7G_RS0116430 G7G_RS0120925
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 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