GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Shewanella oneidensis MR-1

Best path

sstT, 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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
sstT L-threonine:Na+ symporter SstT SO3122
ltaE L-threonine aldolase SO3338 SO3471
adh acetaldehyde dehydrogenase (not acylating) SO4480 SO2136
ackA acetate kinase SO2915 SO3613
pta phosphate acetyltransferase SO2916
gcvP glycine cleavage system, P component (glycine decarboxylase) SO0781
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) SO0779
gcvH glycine cleavage system, H component (lipoyl protein) SO0780
lpd dihydrolipoyl dehydrogenase SO0426 SO4702
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase SO0343 SO0432
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) SO0343
acs acetyl-CoA synthetase, AMP-forming SO2743 SO3664
ald-dh-CoA acetaldehyde dehydrogenase, acylating SO2136
aldA lactaldehyde dehydrogenase SO3496 SO4480
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) SO3960 SO1865
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) SO3960 SO1042
D-LDH D-lactate dehydrogenase SO1521 SO0968
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components SO1519
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 SO2044 SO1734
gloB hydroxyacylglutathione hydrolase (glyoxalase II) SO2563 SO3054
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 SO1680 SO3088
iolA malonate semialdehyde dehydrogenase (CoA-acylating) SO1678 SO3496
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) SO4674 SO2739
L-LDH L-lactate dehydrogenase
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
lldE L-lactate dehydrogenase, LldE subunit SO1520
lldF L-lactate dehydrogenase, LldF subunit SO1519
lldG L-lactate dehydrogenase, LldG subunit SO1518
lutA L-lactate dehydrogenase, LutA subunit SO1520
lutB L-lactate dehydrogenase, LutB subunit SO1519
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 SO1894 SO0840
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit SO1894 SO0840
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit SO1896
pco propanyl-CoA oxidase
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase SO0345 SO1484
prpC 2-methylcitrate synthase SO0344 SO1926
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase SO0342
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA SO2137
tdcB L-threonine dehydratase SO4344
tdcC L-threonine:H+ symporter TdcC SO0919
tdcE 2-ketobutyrate formate-lyase SO2912
tdh L-threonine 3-dehydrogenase SO4673 SO1490
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent)

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