GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Methanobacterium lacus AL-21

Best path

tdcC, tdh, tynA, yvgN, aldA, lctO, acs

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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
tdcC L-threonine:H+ symporter TdcC
tdh L-threonine 3-dehydrogenase METBO_RS02090
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent)
aldA lactaldehyde dehydrogenase METBO_RS02115
lctO L-lactate oxidase or 2-monooxygenase METBO_RS10435
acs acetyl-CoA synthetase, AMP-forming METBO_RS09375 METBO_RS08510
Alternative steps:
ackA acetate kinase
acn (2R,3S)-2-methylcitrate dehydratase
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
adh acetaldehyde dehydrogenase (not acylating) METBO_RS02115
ald-dh-CoA acetaldehyde dehydrogenase, acylating
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)
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) METBO_RS06565 METBO_RS03540
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) METBO_RS07335 METBO_RS09270
D-LDH D-lactate dehydrogenase METBO_RS02145
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase
gcvH glycine cleavage system, H component (lipoyl protein)
gcvP glycine cleavage system, P component (glycine decarboxylase)
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase)
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD)
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE)
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I
gloB hydroxyacylglutathione hydrolase (glyoxalase II)
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) METBO_RS02115
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase)
L-LDH L-lactate dehydrogenase METBO_RS02955
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
lldE L-lactate dehydrogenase, LldE subunit
lldF L-lactate dehydrogenase, LldF subunit
lldG L-lactate dehydrogenase, LldG subunit
lpd dihydrolipoyl dehydrogenase METBO_RS10135
ltaE L-threonine aldolase METBO_RS00815 METBO_RS06225
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
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 METBO_RS03885
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit METBO_RS03885
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit METBO_RS02015
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase METBO_RS09215
prpC 2-methylcitrate synthase
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase METBO_RS03430
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
tdcE 2-ketobutyrate formate-lyase

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 Apr 09 2024. 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