GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Nocardiopsis lucentensis DSM 44048

Best path

braC, braD, braE, braF, braG, ltaE, adh, acs*, 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 (44 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) D471_RS0102655
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) D471_RS0102635 D471_RS0127515
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) D471_RS0102645 D471_RS0129920
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) D471_RS0102650 D471_RS0129925
ltaE L-threonine aldolase D471_RS0115815 D471_RS0132245
adh acetaldehyde dehydrogenase (not acylating) D471_RS0107105 D471_RS0122805
acs* acetyl-CoA synthetase, AMP-forming D471_RS37085 with D471_RS37080 D471_RS0117385
gcvP glycine cleavage system, P component (glycine decarboxylase) D471_RS0103885
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) D471_RS0117405 D471_RS0118885
gcvH glycine cleavage system, H component (lipoyl protein) D471_RS0117410
lpd dihydrolipoyl dehydrogenase D471_RS0129630 D471_RS0118870
Alternative steps:
ackA acetate kinase D471_RS0105170
acn (2R,3S)-2-methylcitrate dehydratase D471_RS0108975
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) D471_RS0108975
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase D471_RS0107105 D471_RS0122805
D-LDH D-lactate dehydrogenase D471_RS0111085 D471_RS0108145
dddA 3-hydroxypropionate dehydrogenase D471_RS0125450
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components D471_RS0124155
epi methylmalonyl-CoA epimerase D471_RS0120385
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) D471_RS0111085 D471_RS0116345
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) D471_RS0111095 D471_RS0120670
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I
gloB hydroxyacylglutathione hydrolase (glyoxalase II) D471_RS0118420 D471_RS0101740
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 D471_RS0108630 D471_RS0126255
iolA malonate semialdehyde dehydrogenase (CoA-acylating) D471_RS0122980 D471_RS0100055
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) D471_RS0111675
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 D471_RS0108645
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component D471_RS0111085
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit D471_RS0124160
lldF L-lactate dehydrogenase, LldF subunit D471_RS0124155
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit D471_RS0124160
lutB L-lactate dehydrogenase, LutB subunit D471_RS0124155
lutC L-lactate dehydrogenase, LutC subunit D471_RS0124150
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit D471_RS0121620 D471_RS0120350 with D471_RS0120355
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit D471_RS0107455 D471_RS0121620
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components D471_RS0121620
pccA propionyl-CoA carboxylase, alpha subunit D471_RS0101775 D471_RS0107025
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit D471_RS0101775 D471_RS0107025
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit D471_RS0101765 D471_RS0107030
pco propanyl-CoA oxidase D471_RS0107370 D471_RS0120145
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase D471_RS0123095
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase
RR42_RS28305 L-threonine:H+ symporter D471_RS0105135
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase D471_RS0112340 D471_RS0112815
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase D471_RS0114585 D471_RS0118875
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) D471_RS0103085 D471_RS0115115

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