GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Pedobacter sp. GW460-11-11-14-LB5

Best path

tdcC, 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 (42 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
tdcC L-threonine:H+ symporter TdcC
ltaE L-threonine aldolase CA265_RS02210 CA265_RS19165
adh acetaldehyde dehydrogenase (not acylating) CA265_RS19780 CA265_RS21385
ackA acetate kinase CA265_RS10080
pta phosphate acetyltransferase CA265_RS10075 CA265_RS19000
gcvP glycine cleavage system, P component (glycine decarboxylase) CA265_RS25185
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) CA265_RS23960
gcvH glycine cleavage system, H component (lipoyl protein) CA265_RS18980
lpd dihydrolipoyl dehydrogenase CA265_RS05155 CA265_RS24150
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase CA265_RS16400 CA265_RS16405
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
acs acetyl-CoA synthetase, AMP-forming CA265_RS16340
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase CA265_RS02630 CA265_RS14635
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB)
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD)
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) CA265_RS25230 CA265_RS15245
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) CA265_RS25230 CA265_RS04345
D-LDH D-lactate dehydrogenase CA265_RS10420 CA265_RS09620
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component CA265_RS21010
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components CA265_RS18400
epi methylmalonyl-CoA epimerase CA265_RS10815
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) CA265_RS09620
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE)
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I CA265_RS22395
gloB hydroxyacylglutathione hydrolase (glyoxalase II) CA265_RS19735 CA265_RS25095
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 CA265_RS20005 CA265_RS09125
iolA malonate semialdehyde dehydrogenase (CoA-acylating) CA265_RS14635
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) CA265_RS15280 CA265_RS13580
L-LDH L-lactate dehydrogenase CA265_RS08335 CA265_RS03080
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit CA265_RS08865
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component CA265_RS09620
lctO L-lactate oxidase or 2-monooxygenase CA265_RS08335
lldE L-lactate dehydrogenase, LldE subunit CA265_RS07800
lldF L-lactate dehydrogenase, LldF subunit CA265_RS18400
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit CA265_RS07800
lutB L-lactate dehydrogenase, LutB subunit CA265_RS18400
lutC L-lactate dehydrogenase, LutC subunit
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit CA265_RS25460 CA265_RS14780
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit CA265_RS20010
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components CA265_RS14780 CA265_RS25460
pccA propionyl-CoA carboxylase, alpha subunit CA265_RS02215 CA265_RS18365
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit CA265_RS02215 CA265_RS18365
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit CA265_RS16635 CA265_RS10640
pco propanyl-CoA oxidase CA265_RS14465 CA265_RS09630
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase CA265_RS08845
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 CA265_RS15860
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase CA265_RS15335 CA265_RS12005
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) CA265_RS00430

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, 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