GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Bacteroides thetaiotaomicron VPI-5482

Best path

snatA, tdh, kbl, gcvP, gcvT, gcvH, lpd

Also see fitness data for the top candidates

Rules

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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
snatA L-threonine transporter snatA BT2270 BT1108
tdh L-threonine 3-dehydrogenase BT1370 BT3767
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) BT1371 BT0870
gcvP glycine cleavage system, P component (glycine decarboxylase) BT1147
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) BT4584
gcvH glycine cleavage system, H component (lipoyl protein) BT2519
lpd dihydrolipoyl dehydrogenase BT3186 BT0309
Alternative steps:
ackA acetate kinase BT3693 BT0704
acn (2R,3S)-2-methylcitrate dehydratase
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BT2072
acs acetyl-CoA synthetase, AMP-forming BT3755 BT2782
adh acetaldehyde dehydrogenase (not acylating) BT4512
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase
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) BT3837 BT1291
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BT3837 BT0925
D-LDH D-lactate dehydrogenase BT1575 BT1207
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component BT4457
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components BT4456
epi methylmalonyl-CoA epimerase BT1685
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
gloB hydroxyacylglutathione hydrolase (glyoxalase II) BT1146
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 BT4702
iolA malonate semialdehyde dehydrogenase (CoA-acylating)
L-LDH L-lactate dehydrogenase BT3911
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit BT1804
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit BT1805
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit BT4455
lldF L-lactate dehydrogenase, LldF subunit BT4456
lldG L-lactate dehydrogenase, LldG subunit BT4457
ltaE L-threonine aldolase BT1815 BT0738
lutA L-lactate dehydrogenase, LutA subunit BT4455
lutB L-lactate dehydrogenase, LutB subunit BT4456
lutC L-lactate dehydrogenase, LutC subunit
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit BT2090
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BT2090 BT0340
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components BT2090 BT2091
pccA propionyl-CoA carboxylase, alpha subunit BT1915 BT1449
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BT1915 BT1449
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit BT1450 BT1686
pco propanyl-CoA oxidase BT1886
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase BT_2070
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase BT3692 BT1969
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase BT4738
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) BT1383

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 Apr 09 2024. 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