GapMind for catabolism of small carbon sources


L-threonine catabolism in Shewanella loihica PV-4

Best path

sstT, 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 (44 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
sstT L-threonine:Na+ symporter SstT Shew_1458
ltaE L-threonine aldolase Shew_1155 Shew_1185
adh acetaldehyde dehydrogenase (not acylating) Shew_3574 Shew_1910
ackA acetate kinase Shew_2393
pta phosphate acetyltransferase Shew_2394
gcvP glycine cleavage system, P component (glycine decarboxylase) Shew_3062
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) Shew_3064
gcvH glycine cleavage system, H component (lipoyl protein) Shew_3063
lpd dihydrolipoyl dehydrogenase Shew_3429 Shew_3660
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase Shew_1822 Shew_3424
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Shew_1822
acs acetyl-CoA synthetase, AMP-forming Shew_1533 Shew_2568
ald-dh-CoA acetaldehyde dehydrogenase, acylating Shew_1910
aldA lactaldehyde dehydrogenase Shew_0967 Shew_3574
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) Shew_2609
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) Shew_2608
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) Shew_2611 Shew_3310
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) Shew_2606 Shew_3310
D-LDH D-lactate dehydrogenase Shew_3136 Shew_0787
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components Shew_3005
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD)
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE)
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I Shew_2073
gloB hydroxyacylglutathione hydrolase (glyoxalase II) Shew_2114 Shew_2269
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 Shew_2425 Shew_1670
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Shew_0965 Shew_1668
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) Shew_3709 Shew_1720
L-LDH L-lactate dehydrogenase
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit Shew_2677
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit Shew_3004
lldF L-lactate dehydrogenase, LldF subunit Shew_3005
lldG L-lactate dehydrogenase, LldG subunit Shew_3006
lutA L-lactate dehydrogenase, LutA subunit Shew_3004
lutB L-lactate dehydrogenase, LutB subunit Shew_3005
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 Shew_2573 Shew_3365
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Shew_2573 Shew_3365
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit Shew_1220
pccB propionyl-CoA carboxylase, beta subunit Shew_2571 Shew_2867
pco propanyl-CoA oxidase Shew_0900
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase Shew_1276 Shew_1820
prpC 2-methylcitrate synthase Shew_1821 Shew_1650
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase Shew_1823
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA Shew_1911
tdcB L-threonine dehydratase Shew_0293
tdcC L-threonine:H+ symporter TdcC Shew_0739
tdcE 2-ketobutyrate formate-lyase Shew_2390
tdh L-threonine 3-dehydrogenase Shew_3710 Shew_1166
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