GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Desulfovibrio vulgaris Miyazaki F

Best path

braC, braD, braE, braF, braG, ltaE, ald-dh-CoA, 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 (36 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) DvMF_2607 DvMF_2750
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) DvMF_2608 DvMF_2751
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) DvMF_2609 DvMF_2752
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) DvMF_2610 DvMF_1163
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) DvMF_2611 DvMF_2754
ltaE L-threonine aldolase DvMF_0572 DvMF_3097
ald-dh-CoA acetaldehyde dehydrogenase, acylating DvMF_2322
gcvP glycine cleavage system, P component (glycine decarboxylase) DvMF_0224 DvMF_0223
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) DvMF_0341
gcvH glycine cleavage system, H component (lipoyl protein) DvMF_0225
lpd dihydrolipoyl dehydrogenase DvMF_0222 DvMF_0898
Alternative steps:
ackA acetate kinase DvMF_2756 DvMF_1865
acn (2R,3S)-2-methylcitrate dehydratase DvMF_3021
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
acs acetyl-CoA synthetase, AMP-forming DvMF_1775 DvMF_2783
adh acetaldehyde dehydrogenase (not acylating) DvMF_2322 DvMF_2633
aldA lactaldehyde dehydrogenase DvMF_2146
D-LDH D-lactate dehydrogenase DvMF_2196 DvMF_1567
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component DvMF_1867 DvMF_0395
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components DvMF_1868 DvMF_0396
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) DvMF_1862 DvMF_1567
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) DvMF_1862 DvMF_1567
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I
gloB hydroxyacylglutathione hydrolase (glyoxalase II) DvMF_2853
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) DvMF_2146
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) DvMF_1008
L-LDH L-lactate dehydrogenase
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 DvMF_1567 DvMF_1862
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit DvMF_0397 DvMF_1868
lldF L-lactate dehydrogenase, LldF subunit DvMF_0396 DvMF_1868
lldG L-lactate dehydrogenase, LldG subunit DvMF_1867
lutA L-lactate dehydrogenase, LutA subunit DvMF_0397 DvMF_1868
lutB L-lactate dehydrogenase, LutB subunit DvMF_0396 DvMF_1868
lutC L-lactate dehydrogenase, LutC subunit DvMF_0395
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 DvMF_0417 DvMF_0817
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit DvMF_0417 DvMF_0817
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase DvMF_0766
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase DvMF_1864 DvMF_2625
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 DvMF_0321 DvMF_0990
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, the preprint 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