GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Pseudomonas simiae WCS417

Best path

braC, braD, braE, braF, braG, 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 (43 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) PS417_06615 PS417_02655
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) PS417_06610 PS417_02660
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) PS417_06605 PS417_02665
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) PS417_06600 PS417_17675
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) PS417_06595 PS417_02675
ltaE L-threonine aldolase PS417_26205 PS417_21665
adh acetaldehyde dehydrogenase (not acylating) PS417_17430 PS417_24810
ackA acetate kinase PS417_22945
pta phosphate acetyltransferase PS417_03730
gcvP glycine cleavage system, P component (glycine decarboxylase) PS417_22360
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) PS417_22370 PS417_27255
gcvH glycine cleavage system, H component (lipoyl protein) PS417_27250 PS417_22355
lpd dihydrolipoyl dehydrogenase PS417_17560 PS417_08905
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase PS417_21070 PS417_14990
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) PS417_21070 PS417_07515
acs acetyl-CoA synthetase, AMP-forming PS417_21750 PS417_23925
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase PS417_17430 PS417_24810
D-LDH D-lactate dehydrogenase PS417_24110 PS417_16375
dddA 3-hydroxypropionate dehydrogenase PS417_10560 PS417_26345
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)
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE)
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I PS417_14035
gloB hydroxyacylglutathione hydrolase (glyoxalase II) PS417_12220 PS417_06335
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 PS417_13845 PS417_10680
iolA malonate semialdehyde dehydrogenase (CoA-acylating) PS417_10925 PS417_03250
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) PS417_26000 PS417_06915
L-LDH L-lactate dehydrogenase PS417_19130 PS417_15625
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit PS417_21295
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component
lctO L-lactate oxidase or 2-monooxygenase PS417_15625 PS417_19130
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 PS417_19595 PS417_17030
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit PS417_28215 PS417_02965
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit PS417_17020 PS417_19580
pco propanyl-CoA oxidase PS417_00580 PS417_13850
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase PS417_21080 PS417_16570
prpC 2-methylcitrate synthase PS417_21075 PS417_08870
prpD 2-methylcitrate dehydratase PS417_21060
prpF methylaconitate isomerase PS417_21065 PS417_07225
RR42_RS28305 L-threonine:H+ symporter PS417_05405 PS417_01755
serP1 L-threonine uptake transporter SerP1 PS417_14545 PS417_23700
snatA L-threonine transporter snatA PS417_02925
sstT L-threonine:Na+ symporter SstT PS417_10435
tdcB L-threonine dehydratase PS417_27010 PS417_12665
tdcC L-threonine:H+ symporter TdcC PS417_14995 PS417_05070
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase PS417_06905 PS417_25740
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) PS417_10670 PS417_15340

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