GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Thiothrix lacustris DSM 21227

Best path

braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd

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 (43 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) Q394_RS0102910
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) Q394_RS0102915 Q394_RS0106645
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) Q394_RS0102920
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) Q394_RS0102925 Q394_RS0106655
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) Q394_RS0102930 Q394_RS0106660
ltaE L-threonine aldolase Q394_RS0103425
adh acetaldehyde dehydrogenase (not acylating) Q394_RS0104930 Q394_RS0117580
ackA acetate kinase Q394_RS0101900 Q394_RS0113170
pta phosphate acetyltransferase Q394_RS0101895 Q394_RS0107505
gcvP glycine cleavage system, P component (glycine decarboxylase) Q394_RS0116020
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) Q394_RS0116030
gcvH glycine cleavage system, H component (lipoyl protein) Q394_RS0116025
lpd dihydrolipoyl dehydrogenase Q394_RS0108515 Q394_RS0106590
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase Q394_RS0100860 Q394_RS0102890
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Q394_RS0100860
acs acetyl-CoA synthetase, AMP-forming Q394_RS0112815 Q394_RS0100870
ald-dh-CoA acetaldehyde dehydrogenase, acylating Q394_RS0111965
aldA lactaldehyde dehydrogenase Q394_RS0104930 Q394_RS0111975
D-LDH D-lactate dehydrogenase Q394_RS0104480
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component Q394_RS0108645
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components Q394_RS0108640
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) Q394_RS0104480
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) Q394_RS0104475
glcF D-lactate dehydrogenase, FeS subunit GlcF Q394_RS0104470
gloA glyoxylase I Q394_RS0116425
gloB hydroxyacylglutathione hydrolase (glyoxalase II) Q394_RS0112625 Q394_RS0108675
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) Q394_RS0104930 Q394_RS0117580
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) Q394_RS0110655
L-LDH L-lactate dehydrogenase Q394_RS0115755
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 Q394_RS0104480
lctO L-lactate oxidase or 2-monooxygenase Q394_RS0115755
lldE L-lactate dehydrogenase, LldE subunit Q394_RS0108635
lldF L-lactate dehydrogenase, LldF subunit Q394_RS0108640
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit Q394_RS0108635
lutB L-lactate dehydrogenase, LutB subunit Q394_RS0108640
lutC L-lactate dehydrogenase, LutC subunit Q394_RS0108645
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 Q394_RS0109800 Q394_RS0109245
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Q394_RS0109800 Q394_RS0109245
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase Q394_RS0115650 Q394_RS0100850
prpC 2-methylcitrate synthase Q394_RS0100855 Q394_RS0102885
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase Q394_RS0100865
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 Q394_RS0105245
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase Q394_RS0100600
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 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