GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Caulobacter crescentus NA1000

Best path

snatA, ltaE, adh, acs, 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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
snatA L-threonine transporter snatA CCNA_00105
ltaE L-threonine aldolase CCNA_03190 CCNA_01419
adh acetaldehyde dehydrogenase (not acylating) CCNA_03695 CCNA_03242
acs acetyl-CoA synthetase, AMP-forming CCNA_03696 CCNA_01889
gcvP glycine cleavage system, P component (glycine decarboxylase) CCNA_03462 CCNA_03463
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) CCNA_03465
gcvH glycine cleavage system, H component (lipoyl protein) CCNA_03464
lpd dihydrolipoyl dehydrogenase CCNA_00346 CCNA_01805
Alternative steps:
ackA acetate kinase
acn (2R,3S)-2-methylcitrate dehydratase CCNA_03781
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) CCNA_03781
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase CCNA_03243 CCNA_03695
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) CCNA_03714 CCNA_03235
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) CCNA_03714 CCNA_01670
D-LDH D-lactate dehydrogenase CCNA_03500 CCNA_03322
dddA 3-hydroxypropionate dehydrogenase CCNA_01337 CCNA_00994
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase CCNA_02011
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD)
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE)
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I CCNA_01375
gloB hydroxyacylglutathione hydrolase (glyoxalase II) CCNA_01241 CCNA_00553
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 CCNA_00006 CCNA_02658
iolA malonate semialdehyde dehydrogenase (CoA-acylating) CCNA_01360 CCNA_02357
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) CCNA_01417 CCNA_01220
L-LDH L-lactate dehydrogenase CCNA_01209 CCNA_03770
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
lctO L-lactate oxidase or 2-monooxygenase CCNA_01462 CCNA_01209
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 CCNA_02459 CCNA_03177
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit CCNA_03177 CCNA_02459
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components CCNA_02459 CCNA_03177
pccA propionyl-CoA carboxylase, alpha subunit CCNA_02261 CCNA_02250
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit CCNA_02261 CCNA_01961
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit CCNA_02054 CCNA_02252
pco propanyl-CoA oxidase
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase CCNA_01980 CCNA_01841
prpC 2-methylcitrate synthase CCNA_03757 CCNA_01983
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase CCNA_03663 CCNA_02704
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase CCNA_03750 CCNA_03203
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase CCNA_02929 CCNA_02479
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) CCNA_03541

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