GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Dinoroseobacter shibae DFL-12

Best path

snatA, ltaE, adh, ackA, pta, 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 (44 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
snatA L-threonine transporter snatA Dshi_1348
ltaE L-threonine aldolase Dshi_2144 Dshi_0821
adh acetaldehyde dehydrogenase (not acylating) Dshi_3017 Dshi_1095
ackA acetate kinase Dshi_0632 Dshi_5006
pta phosphate acetyltransferase Dshi_1825 Dshi_0633
gcvP glycine cleavage system, P component (glycine decarboxylase) Dshi_2680
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) Dshi_2682 Dshi_2115
gcvH glycine cleavage system, H component (lipoyl protein) Dshi_2681
lpd dihydrolipoyl dehydrogenase Dshi_1966 Dshi_2886
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase Dshi_1851 Dshi_2060
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Dshi_1851
acs acetyl-CoA synthetase, AMP-forming Dshi_3553 Dshi_1399
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase Dshi_2436 Dshi_1095
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) Dshi_1977
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) Dshi_1518 Dshi_1979
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) Dshi_1978
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) Dshi_1521 Dshi_1981
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) Dshi_1520 Dshi_1980
D-LDH D-lactate dehydrogenase Dshi_1361 Dshi_2076
dddA 3-hydroxypropionate dehydrogenase Dshi_0804 Dshi_1428
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase Dshi_2630
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) Dshi_2896 Dshi_1361
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) Dshi_2895 Dshi_2076
glcF D-lactate dehydrogenase, FeS subunit GlcF Dshi_2894
gloA glyoxylase I Dshi_2070 Dshi_0767
gloB hydroxyacylglutathione hydrolase (glyoxalase II) Dshi_2691 Dshi_0474
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 Dshi_3370 Dshi_1048
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Dshi_1747 Dshi_0577
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) Dshi_3546 Dshi_3190
L-LDH L-lactate dehydrogenase Dshi_0948 Dshi_2876
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit Dshi_0216
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component Dshi_2896 Dshi_2076
lctO L-lactate oxidase or 2-monooxygenase Dshi_0948 Dshi_2484
lldE L-lactate dehydrogenase, LldE subunit
lldF L-lactate dehydrogenase, LldF subunit
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit
lutB L-lactate dehydrogenase, LutB subunit
lutC L-lactate dehydrogenase, LutC subunit
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit Dshi_0726 Dshi_2855
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit Dshi_0726 Dshi_2855
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components Dshi_0726 Dshi_2855
pccA propionyl-CoA carboxylase, alpha subunit Dshi_0723 Dshi_1301
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Dshi_0723 Dshi_1395
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit Dshi_0718 Dshi_1300
pco propanyl-CoA oxidase Dshi_2357 Dshi_1297
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase Dshi_0689 Dshi_1092
prpC 2-methylcitrate synthase Dshi_1806
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase Dshi_3473 Dshi_0888
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase Dshi_4159 Dshi_2036
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