GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Cupriavidus basilensis 4G11

Best path

RR42_RS28305, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd

Also see fitness data for the top candidates

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 (55 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
RR42_RS28305 L-threonine:H+ symporter RR42_RS28305 RR42_RS05070
ltaE L-threonine aldolase RR42_RS15115 RR42_RS15485
adh acetaldehyde dehydrogenase (not acylating) RR42_RS34255 RR42_RS25005
ackA acetate kinase RR42_RS03800 RR42_RS22745
pta phosphate acetyltransferase RR42_RS33690 RR42_RS03805
gcvP glycine cleavage system, P component (glycine decarboxylase) RR42_RS20070
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) RR42_RS20060
gcvH glycine cleavage system, H component (lipoyl protein) RR42_RS20065
lpd dihydrolipoyl dehydrogenase RR42_RS07380 RR42_RS26115
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase RR42_RS11270 RR42_RS23515
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) RR42_RS11270 RR42_RS14490
acs acetyl-CoA synthetase, AMP-forming RR42_RS13880 RR42_RS10650
ald-dh-CoA acetaldehyde dehydrogenase, acylating RR42_RS27895 RR42_RS32630
aldA lactaldehyde dehydrogenase RR42_RS25010 RR42_RS27780
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) RR42_RS14425 RR42_RS20120
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) RR42_RS14420 RR42_RS16975
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) RR42_RS14415 RR42_RS16970
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) RR42_RS29450 RR42_RS14410
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) RR42_RS14405 RR42_RS16960
D-LDH D-lactate dehydrogenase RR42_RS17285 RR42_RS06435
dddA 3-hydroxypropionate dehydrogenase RR42_RS20290 RR42_RS29710
DVU3032 L-lactate dehydrogenase, LutC-like component RR42_RS14200
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components RR42_RS07435 RR42_RS21285
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) RR42_RS17300 RR42_RS29885
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) RR42_RS17310 RR42_RS29880
glcF D-lactate dehydrogenase, FeS subunit GlcF RR42_RS17315 RR42_RS29875
gloA glyoxylase I RR42_RS02800 RR42_RS34275
gloB hydroxyacylglutathione hydrolase (glyoxalase II) RR42_RS13570 RR42_RS19750
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 RR42_RS23710 RR42_RS18250
iolA malonate semialdehyde dehydrogenase (CoA-acylating) RR42_RS01580 RR42_RS34225
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) RR42_RS28295 RR42_RS22865
L-LDH L-lactate dehydrogenase RR42_RS03780 RR42_RS29130
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit RR42_RS04575
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component RR42_RS17285 RR42_RS26635
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit RR42_RS07430 RR42_RS21295
lldF L-lactate dehydrogenase, LldF subunit RR42_RS21285 RR42_RS07435
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit RR42_RS21295 RR42_RS07430
lutB L-lactate dehydrogenase, LutB subunit RR42_RS21285 RR42_RS07435
lutC L-lactate dehydrogenase, LutC subunit RR42_RS21290 RR42_RS14200
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit RR42_RS01600
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components RR42_RS01600
pccA propionyl-CoA carboxylase, alpha subunit RR42_RS26895 RR42_RS32735
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit RR42_RS17700 RR42_RS29420
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit RR42_RS26895
pccB propionyl-CoA carboxylase, beta subunit RR42_RS26905 RR42_RS29410
pco propanyl-CoA oxidase RR42_RS08770 RR42_RS15400
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase RR42_RS12200 RR42_RS11260
prpC 2-methylcitrate synthase RR42_RS11265 RR42_RS14475
prpD 2-methylcitrate dehydratase RR42_RS14485
prpF methylaconitate isomerase RR42_RS11275 RR42_RS23050
serP1 L-threonine uptake transporter SerP1 RR42_RS28305 RR42_RS33495
snatA L-threonine transporter snatA RR42_RS18900
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase RR42_RS02315 RR42_RS33880
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase RR42_RS28300 RR42_RS22860
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) RR42_RS35195 RR42_RS17795

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 Sep 17 2021. 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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