GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Burkholderia vietnamiensis G4

Best path

braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd

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 (57 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) WP_043292326.1 WP_011882928.1
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) WP_011880725.1 WP_012467843.1
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) WP_011880724.1 WP_011885760.1
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) WP_011880723.1 WP_011885759.1
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) WP_011880722.1 WP_011885758.1
ltaE L-threonine aldolase WP_011880997.1 WP_014722503.1
adh acetaldehyde dehydrogenase (not acylating) WP_011881627.1 WP_011880891.1
acs acetyl-CoA synthetase, AMP-forming WP_011885480.1 WP_011880617.1
gcvP glycine cleavage system, P component (glycine decarboxylase) WP_011882850.1
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) WP_011882852.1 WP_011875686.1
gcvH glycine cleavage system, H component (lipoyl protein) WP_011882851.1
lpd dihydrolipoyl dehydrogenase WP_011882684.1 WP_011885424.1
Alternative steps:
ackA acetate kinase WP_011885604.1 WP_011880246.1
acn (2R,3S)-2-methylcitrate dehydratase WP_011881024.1 WP_011879819.1
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) WP_011881024.1 WP_011881710.1
ald-dh-CoA acetaldehyde dehydrogenase, acylating WP_011875732.1 WP_011882650.1
aldA lactaldehyde dehydrogenase WP_011880783.1 WP_011886229.1
D-LDH D-lactate dehydrogenase WP_011883332.1 WP_011883448.1
dddA 3-hydroxypropionate dehydrogenase WP_011882794.1 WP_011880327.1
DVU3032 L-lactate dehydrogenase, LutC-like component WP_011883915.1
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components WP_011886021.1 WP_011885418.1
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) WP_011883331.1 WP_011883332.1
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) WP_011883330.1 WP_011883332.1
glcF D-lactate dehydrogenase, FeS subunit GlcF WP_011883329.1
gloA glyoxylase I WP_011885970.1
gloB hydroxyacylglutathione hydrolase (glyoxalase II) WP_011884270.1 WP_011882935.1
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 WP_011881868.1 WP_011883164.1
iolA malonate semialdehyde dehydrogenase (CoA-acylating) WP_011884470.1 WP_011882148.1
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) WP_011881130.1 WP_011886180.1
L-LDH L-lactate dehydrogenase WP_011882697.1
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit WP_011880115.1
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit WP_011880114.1 WP_011883849.1
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component WP_011883332.1 WP_011884515.1
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit WP_011880331.1 WP_011885419.1
lldF L-lactate dehydrogenase, LldF subunit WP_006481909.1 WP_011886021.1
lldG L-lactate dehydrogenase, LldG subunit WP_006481910.1
lutA L-lactate dehydrogenase, LutA subunit WP_011886019.1 WP_011885419.1
lutB L-lactate dehydrogenase, LutB subunit WP_011886021.1 WP_011885418.1
lutC L-lactate dehydrogenase, LutC subunit WP_011886020.1 WP_011883915.1
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit WP_011880186.1
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit WP_011880186.1 WP_011886165.1
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components WP_011880186.1
pccA propionyl-CoA carboxylase, alpha subunit WP_011880843.1 WP_011883218.1
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit WP_011881198.1 WP_011883218.1
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit WP_011880845.1
pco propanyl-CoA oxidase WP_011884927.1 WP_011883419.1
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase WP_011885172.1 WP_011881026.1
prpC 2-methylcitrate synthase WP_011881025.1 WP_011881720.1
prpD 2-methylcitrate dehydratase WP_011881711.1
prpF methylaconitate isomerase WP_011881023.1 WP_011879868.1
pta phosphate acetyltransferase WP_011880255.1 WP_011882626.1
RR42_RS28305 L-threonine:H+ symporter WP_011881650.1 WP_011882166.1
serP1 L-threonine uptake transporter SerP1 WP_011881650.1 WP_011882166.1
snatA L-threonine transporter snatA WP_011883055.1 WP_011883203.1
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase WP_011886005.1 WP_011882427.1
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase WP_011881129.1 WP_011881898.1
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) WP_011880954.1 WP_011885789.1

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