GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Lactobacillus silagei IWT126

Best path

serP1, tdh, tynA, yvgN, aldA, lctO, ackA, pta

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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
serP1 L-threonine uptake transporter SerP1 CES79_RS01015 CES79_RS04050
tdh L-threonine 3-dehydrogenase CES79_RS07670 CES79_RS02635
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) CES79_RS10880 CES79_RS01880
aldA lactaldehyde dehydrogenase CES79_RS01180
lctO L-lactate oxidase or 2-monooxygenase CES79_RS00310
ackA acetate kinase CES79_RS11275 CES79_RS12115
pta phosphate acetyltransferase CES79_RS04940
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase CES79_RS02945
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) CES79_RS02945
acs acetyl-CoA synthetase, AMP-forming
adh acetaldehyde dehydrogenase (not acylating) CES79_RS07645 CES79_RS01180
ald-dh-CoA acetaldehyde dehydrogenase, acylating CES79_RS07645
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) CES79_RS10005
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) CES79_RS10015 CES79_RS10020
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) CES79_RS10020 CES79_RS09760
D-LDH D-lactate dehydrogenase CES79_RS08650 CES79_RS00010
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) CES79_RS05340
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) CES79_RS02910
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE)
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I CES79_RS11995
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) CES79_RS01180
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase)
L-LDH L-lactate dehydrogenase CES79_RS12070 CES79_RS00345
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 CES79_RS02910
lldE L-lactate dehydrogenase, LldE subunit
lldF L-lactate dehydrogenase, LldF subunit
lldG L-lactate dehydrogenase, LldG subunit
lpd dihydrolipoyl dehydrogenase CES79_RS09625 CES79_RS04335
ltaE L-threonine aldolase CES79_RS05245
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 CES79_RS05880 CES79_RS03295
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit CES79_RS05880 CES79_RS03295
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase CES79_RS05910
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase CES79_RS02950
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
RR42_RS28305 L-threonine:H+ symporter CES79_RS11280 CES79_RS01925
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

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