GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Maridesulfovibrio zosterae DSM 11974

Best path

sstT, tdh, kbl, 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 (40 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
sstT L-threonine:Na+ symporter SstT H589_RS0103050
tdh L-threonine 3-dehydrogenase H589_RS0108180 H589_RS0101400
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) H589_RS0108175 H589_RS0110460
gcvP glycine cleavage system, P component (glycine decarboxylase) H589_RS0105190 H589_RS0105195
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) H589_RS0114420
gcvH glycine cleavage system, H component (lipoyl protein) H589_RS0105185
lpd dihydrolipoyl dehydrogenase H589_RS0105200 H589_RS0113295
Alternative steps:
ackA acetate kinase H589_RS0112470 H589_RS0114375
acn (2R,3S)-2-methylcitrate dehydratase
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
acs acetyl-CoA synthetase, AMP-forming H589_RS0105060 H589_RS0103275
adh acetaldehyde dehydrogenase (not acylating) H589_RS0102680 H589_RS0118155
ald-dh-CoA* acetaldehyde dehydrogenase, acylating H589_RS19990 with H589_RS0116280 H589_RS0116325
aldA lactaldehyde dehydrogenase H589_RS0109990 H589_RS0118155
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) H589_RS0112340 H589_RS0101635
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) H589_RS0112345 H589_RS0101630
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) H589_RS0112350 H589_RS0101625
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) H589_RS0112355 H589_RS0101640
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) H589_RS0101620 H589_RS0112360
D-LDH D-lactate dehydrogenase H589_RS0110950 H589_RS0105840
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component H589_RS0112475
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components H589_RS0112480 H589_RS0112460
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) H589_RS0112455 H589_RS0101760
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) H589_RS0112455 H589_RS0101760
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I H589_RS20095
gloB hydroxyacylglutathione hydrolase (glyoxalase II) H589_RS0106235 H589_RS0105210
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) H589_RS0107295
L-LDH L-lactate dehydrogenase
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 H589_RS0101760 H589_RS0112455
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit
lldF L-lactate dehydrogenase, LldF subunit H589_RS0112480
lldG L-lactate dehydrogenase, LldG subunit H589_RS0112475
ltaE L-threonine aldolase H589_RS0104430 H589_RS0117145
lutA L-lactate dehydrogenase, LutA subunit H589_RS0112480 H589_RS0112460
lutB L-lactate dehydrogenase, LutB subunit H589_RS0112480
lutC L-lactate dehydrogenase, LutC subunit H589_RS0112475
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 H589_RS0114155 H589_RS0104280
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit H589_RS0104280 H589_RS0114155
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase H589_RS0100550
phtA L-threonine uptake permease PhtA H589_RS0105255
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase H589_RS0106360
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase H589_RS0112465 H589_RS0117515
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA H589_RS0101745
tdcB L-threonine dehydratase
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) H589_RS0105505

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.

Links

Downloads

Related tools

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