GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Dechloromonas agitata is5

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 (46 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) K420_RS0102845
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) K420_RS0102840 K420_RS0101405
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) K420_RS0102835 K420_RS0101410
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) K420_RS0101415 K420_RS0102830
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) K420_RS0102825 K420_RS21120
ltaE L-threonine aldolase K420_RS0107485
adh acetaldehyde dehydrogenase (not acylating) K420_RS0109685 K420_RS0106575
ackA acetate kinase K420_RS0108110 K420_RS0110665
pta phosphate acetyltransferase K420_RS0110665 K420_RS0109505
gcvP glycine cleavage system, P component (glycine decarboxylase) K420_RS0111720
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) K420_RS0111730
gcvH glycine cleavage system, H component (lipoyl protein) K420_RS0111725 K420_RS18895
lpd dihydrolipoyl dehydrogenase K420_RS0102235 K420_RS0110935
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase K420_RS0110820
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
acs acetyl-CoA synthetase, AMP-forming K420_RS0111395 K420_RS0114245
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase K420_RS0109685 K420_RS0106575
D-LDH D-lactate dehydrogenase K420_RS0113835 K420_RS0102855
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component K420_RS0113825
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components K420_RS0101255 K420_RS0113830
epi methylmalonyl-CoA epimerase K420_RS0102715
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) K420_RS0102855 K420_RS0114475
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) K420_RS0102855
glcF D-lactate dehydrogenase, FeS subunit GlcF K420_RS0101260
gloA glyoxylase I K420_RS0108165
gloB hydroxyacylglutathione hydrolase (glyoxalase II) K420_RS0111225 K420_RS0109340
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 K420_RS0103335 K420_RS0101330
iolA malonate semialdehyde dehydrogenase (CoA-acylating) K420_RS0106575 K420_RS0109685
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) K420_RS0110760
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 K420_RS0116340
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component K420_RS0102855 K420_RS0114475
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit K420_RS0101260 K420_RS0113820
lldF L-lactate dehydrogenase, LldF subunit K420_RS0113830 K420_RS0101255
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit K420_RS0113820 K420_RS0101260
lutB L-lactate dehydrogenase, LutB subunit K420_RS0113830 K420_RS0101255
lutC L-lactate dehydrogenase, LutC subunit K420_RS0113825 K420_RS0101240
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit K420_RS0105510 K420_RS0102965
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit K420_RS0105510
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components K420_RS0105510 K420_RS0102965
pccA propionyl-CoA carboxylase, alpha subunit K420_RS0105525 K420_RS0103940
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit K420_RS0105525 K420_RS0105835
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit K420_RS0105520 K420_RS0103930
pco propanyl-CoA oxidase K420_RS0101730 K420_RS0103895
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase K420_RS0116920
prpC 2-methylcitrate synthase K420_RS0110920
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
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 K420_RS0104965
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase K420_RS0107755
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