GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Pseudomonas fluorescens FW300-N2E3

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 (53 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) AO353_17125 AO353_13340
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) AO353_17120 AO353_13345
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) AO353_17115 AO353_13350
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) AO353_17110 AO353_13530
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) AO353_17105 AO353_13360
ltaE L-threonine aldolase AO353_07670 AO353_14020
adh acetaldehyde dehydrogenase (not acylating) AO353_22390 AO353_06560
ackA acetate kinase AO353_04410
pta phosphate acetyltransferase AO353_05065
gcvP glycine cleavage system, P component (glycine decarboxylase) AO353_03500 AO353_08720
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) AO353_03510 AO353_08735
gcvH glycine cleavage system, H component (lipoyl protein) AO353_08730 AO353_03495
lpd dihydrolipoyl dehydrogenase AO353_26650 AO353_01825
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase AO353_00890 AO353_21605
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) AO353_00890 AO353_00565
acs acetyl-CoA synthetase, AMP-forming AO353_03060 AO353_14365
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase AO353_19510 AO353_06560
D-LDH D-lactate dehydrogenase AO353_05720 AO353_02740
dddA 3-hydroxypropionate dehydrogenase AO353_26740 AO353_07810
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components AO353_05710
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) AO353_21310
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) AO353_21305 AO353_21310
glcF D-lactate dehydrogenase, FeS subunit GlcF AO353_21300
gloA glyoxylase I AO353_26955
gloB hydroxyacylglutathione hydrolase (glyoxalase II) AO353_23490 AO353_16585
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 AO353_25675 AO353_24830
iolA malonate semialdehyde dehydrogenase (CoA-acylating) AO353_21350 AO353_06080
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) AO353_07520
L-LDH L-lactate dehydrogenase AO353_23830
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit AO353_01230
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component AO353_21310 AO353_08505
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit AO353_05705
lldF L-lactate dehydrogenase, LldF subunit AO353_05710
lldG L-lactate dehydrogenase, LldG subunit AO353_05715
lutA L-lactate dehydrogenase, LutA subunit AO353_05705
lutB L-lactate dehydrogenase, LutB subunit AO353_05710
lutC L-lactate dehydrogenase, LutC subunit AO353_05715
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 AO353_20335 AO353_19305
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit AO353_10030 AO353_13675
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit AO353_20345 AO353_19320
pco propanyl-CoA oxidase AO353_11100
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase AO353_00900 AO353_27735
prpC 2-methylcitrate synthase AO353_00895 AO353_01860
prpD 2-methylcitrate dehydratase AO353_00880
prpF methylaconitate isomerase AO353_00885 AO353_26715
RR42_RS28305 L-threonine:H+ symporter AO353_16120 AO353_12275
serP1 L-threonine uptake transporter SerP1 AO353_25190 AO353_05965
snatA L-threonine transporter snatA AO353_13635
sstT L-threonine:Na+ symporter SstT AO353_20105
tdcB L-threonine dehydratase AO353_08485 AO353_29000
tdcC L-threonine:H+ symporter TdcC AO353_21595 AO353_15495
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase AO353_17425 AO353_22415
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) AO353_19655 AO353_28090

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