GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Trichormus variabilis ATCC 29413

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 (37 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) AVA_RS24325
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) AVA_RS15215 AVA_RS02360
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) AVA_RS18780
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) AVA_RS18775 AVA_RS02375
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) AVA_RS04995 AVA_RS02390
ltaE L-threonine aldolase AVA_RS25130 AVA_RS10490
adh acetaldehyde dehydrogenase (not acylating) AVA_RS17895 AVA_RS18330
acs acetyl-CoA synthetase, AMP-forming AVA_RS06110 AVA_RS20210
gcvP glycine cleavage system, P component (glycine decarboxylase) AVA_RS13980
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) AVA_RS13970
gcvH glycine cleavage system, H component (lipoyl protein) AVA_RS13975
lpd dihydrolipoyl dehydrogenase AVA_RS09725 AVA_RS17515
Alternative steps:
ackA acetate kinase AVA_RS02475 AVA_RS15285
acn (2R,3S)-2-methylcitrate dehydratase AVA_RS02880
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase AVA_RS07875 AVA_RS14900
D-LDH D-lactate dehydrogenase AVA_RS13470 AVA_RS19050
dddA 3-hydroxypropionate dehydrogenase AVA_RS28440
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) AVA_RS12760
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE)
glcF D-lactate dehydrogenase, FeS subunit GlcF AVA_RS23135
gloA glyoxylase I AVA_RS00700
gloB hydroxyacylglutathione hydrolase (glyoxalase II) AVA_RS01645 AVA_RS05520
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 AVA_RS00835
iolA malonate semialdehyde dehydrogenase (CoA-acylating) AVA_RS07875 AVA_RS14900
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) AVA_RS14265
L-LDH L-lactate dehydrogenase AVA_RS06445 AVA_RS07240
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 AVA_RS12760
lctO L-lactate oxidase or 2-monooxygenase AVA_RS07240
lldE L-lactate dehydrogenase, LldE subunit
lldF L-lactate dehydrogenase, LldF subunit
lldG L-lactate dehydrogenase, LldG subunit
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 AVA_RS02615
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit AVA_RS02615
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase AVA_RS08030
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase AVA_RS24140
prpC 2-methylcitrate synthase AVA_RS13735
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA AVA_RS25690
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase AVA_RS03415 AVA_RS13915
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase AVA_RS11870 AVA_RS00775
tynA aminoacetone oxidase AVA_RS17470
yvgN methylglyoxal reductase (NADPH-dependent) AVA_RS28625 AVA_RS15670

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