GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Dechlorosoma suillum PS

Best path

phtA, ltaE, adh, acs, 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 (50 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
phtA L-threonine uptake permease PhtA Dsui_3451
ltaE L-threonine aldolase Dsui_1265 Dsui_2254
adh acetaldehyde dehydrogenase (not acylating) Dsui_1464 Dsui_0437
acs acetyl-CoA synthetase, AMP-forming Dsui_2003 Dsui_2187
gcvP glycine cleavage system, P component (glycine decarboxylase) Dsui_2737
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) Dsui_2735
gcvH glycine cleavage system, H component (lipoyl protein) Dsui_2736
lpd dihydrolipoyl dehydrogenase Dsui_1576 Dsui_2219
Alternative steps:
ackA acetate kinase Dsui_1003 Dsui_3033
acn (2R,3S)-2-methylcitrate dehydratase Dsui_2205 Dsui_2347
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Dsui_2347
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase Dsui_1464 Dsui_0437
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) Dsui_0630
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) Dsui_0629 Dsui_2060
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) Dsui_0628 Dsui_2059
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) Dsui_0627 Dsui_2058
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) Dsui_2057 Dsui_0626
D-LDH D-lactate dehydrogenase Dsui_0378 Dsui_2542
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components Dsui_1583 Dsui_0126
epi methylmalonyl-CoA epimerase Dsui_0512
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) Dsui_3415 Dsui_0378
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) Dsui_3414
glcF D-lactate dehydrogenase, FeS subunit GlcF Dsui_3413
gloA glyoxylase I Dsui_1204
gloB hydroxyacylglutathione hydrolase (glyoxalase II) Dsui_2484 Dsui_3107
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 Dsui_1378 Dsui_0521
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Dsui_0437 Dsui_0105
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) Dsui_2881
L-LDH L-lactate dehydrogenase Dsui_1668
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit Dsui_3150 Dsui_0576
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit Dsui_3149 Dsui_0575
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component Dsui_0378 Dsui_3415
lctO L-lactate oxidase or 2-monooxygenase Dsui_1668
lldE L-lactate dehydrogenase, LldE subunit Dsui_1582
lldF L-lactate dehydrogenase, LldF subunit Dsui_0126 Dsui_1583
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit Dsui_1582
lutB L-lactate dehydrogenase, LutB subunit Dsui_1583 Dsui_0126
lutC L-lactate dehydrogenase, LutC subunit Dsui_0123 Dsui_1584
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit Dsui_0519 Dsui_1105
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit Dsui_0519
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components Dsui_0519 Dsui_1105
pccA propionyl-CoA carboxylase, alpha subunit Dsui_0516 Dsui_0982
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Dsui_0516 Dsui_0389
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit Dsui_0517 Dsui_0980
pco propanyl-CoA oxidase Dsui_1637 Dsui_3369
prpB 2-methylisocitrate lyase Dsui_0011
prpC 2-methylcitrate synthase Dsui_2216
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase Dsui_3032 Dsui_0130
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 Dsui_0728
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase Dsui_2228
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