GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Carboxydothermus pertinax Ug1

Best path

RR42_RS28305, ltaE, ald-dh-CoA, grdA, grdE, grdB, grdD, grdC, ackA

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 (45 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
RR42_RS28305 L-threonine:H+ symporter cpu_RS11915
ltaE L-threonine aldolase cpu_RS07735 cpu_RS03665
ald-dh-CoA acetaldehyde dehydrogenase, acylating cpu_RS07675
grdA glycine reductase component A1 cpu_RS08870
grdE glycine reductase component B, precursor to alpha/beta subunits cpu_RS08860
grdB glycine reductase component B, gamma subunit cpu_RS08875
grdD glycine reductase component C, alpha subunit cpu_RS08890
grdC glycine reductase component C, beta subunit cpu_RS08885
ackA acetate kinase cpu_RS11360
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
acs acetyl-CoA synthetase, AMP-forming cpu_RS02115 cpu_RS00155
adh acetaldehyde dehydrogenase (not acylating)
aldA lactaldehyde dehydrogenase
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB)
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) cpu_RS01335
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC)
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) cpu_RS01325 cpu_RS01320
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) cpu_RS01320 cpu_RS01325
D-LDH D-lactate dehydrogenase cpu_RS02910 cpu_RS03150
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component cpu_RS02925 cpu_RS06900
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components cpu_RS02930 cpu_RS06900
epi methylmalonyl-CoA epimerase cpu_RS07790
gcvH glycine cleavage system, H component (lipoyl protein) cpu_RS09605
gcvP glycine cleavage system, P component (glycine decarboxylase) cpu_RS09610 cpu_RS09615
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) cpu_RS09600
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) cpu_RS02910
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE)
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I
gloB hydroxyacylglutathione hydrolase (glyoxalase II) cpu_RS01285
hpcD 3-hydroxypropionyl-CoA dehydratase cpu_RS10405 cpu_RS10860
iolA malonate semialdehyde dehydrogenase (CoA-acylating)
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase)
L-LDH L-lactate dehydrogenase cpu_RS00250
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit cpu_RS06450
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit cpu_RS06455
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component cpu_RS02910
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit cpu_RS02930
lldF L-lactate dehydrogenase, LldF subunit cpu_RS02930 cpu_RS06900
lldG L-lactate dehydrogenase, LldG subunit cpu_RS02925
lpd dihydrolipoyl dehydrogenase cpu_RS02370
lutA L-lactate dehydrogenase, LutA subunit cpu_RS02930 cpu_RS02915
lutB L-lactate dehydrogenase, LutB subunit cpu_RS02930 cpu_RS06900
lutC L-lactate dehydrogenase, LutC subunit cpu_RS02925 cpu_RS06900
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit cpu_RS04735 cpu_RS07780
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit cpu_RS04730 cpu_RS07785
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components cpu_RS04735 cpu_RS07780
pccA propionyl-CoA carboxylase, alpha subunit cpu_RS04525 cpu_RS07800
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit cpu_RS04525 cpu_RS07800
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit cpu_RS07795 cpu_RS01750
pco propanyl-CoA oxidase cpu_RS01705 cpu_RS10430
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase cpu_RS11365
serP1 L-threonine uptake transporter SerP1 cpu_RS11915
snatA L-threonine transporter snatA
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase cpu_RS06700 cpu_RS11930
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase cpu_RS07830 cpu_RS07370
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 24 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 (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