GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Desulfovibrio vulgaris Hildenborough

Best path

braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, 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 (35 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) DVU0547 DVU0712
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) DVU0548 DVU0713
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) DVU0549 DVU0714
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) DVU0550 DVU2741
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) DVU0551 DVU0716
ltaE L-threonine aldolase DVU1878 DVU1203
adh acetaldehyde dehydrogenase (not acylating) DVU3319 DVU3294
ackA acetate kinase DVU0723 DVU3030
pta phosphate acetyltransferase DVU3029 DVU0627
gcvP glycine cleavage system, P component (glycine decarboxylase) DVU1425 DVU1424
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) DVU1684
gcvH glycine cleavage system, H component (lipoyl protein) DVU1426
lpd dihydrolipoyl dehydrogenase DVU1423 DVU1037
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
acs acetyl-CoA synthetase, AMP-forming DVU2969 DVU0748
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase DVU3319 DVU3294
D-LDH D-lactate dehydrogenase DVU0253 DVU0390
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component DVU3032 DVU1781
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components DVU3033 DVU1782
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) DVU3027 DVU0827
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) DVU3027 DVU0827
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I
gloB hydroxyacylglutathione hydrolase (glyoxalase II) DVU2765
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
iolA malonate semialdehyde dehydrogenase (CoA-acylating) DVU3319
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) DVU2564
L-LDH L-lactate dehydrogenase DVU0600
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 DVU0390 DVU3027
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit DVU1783 DVU3033
lldF L-lactate dehydrogenase, LldF subunit DVU1782 DVU3033
lldG L-lactate dehydrogenase, LldG subunit DVU3032
lutA L-lactate dehydrogenase, LutA subunit DVU1783 DVU3033
lutB L-lactate dehydrogenase, LutB subunit DVU1782 DVU3033
lutC L-lactate dehydrogenase, LutC subunit DVU1781 DVU3032
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 DVU1834 DVU2226
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit DVU1834 DVU2226
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase DVU2064
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase DVU2405 DVU2545
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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