GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Synechococcus elongatus PCC 7942

Best path

braC, braD, braE, braF, braG, 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 (30 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) Synpcc7942_1861
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) Synpcc7942_2177 Synpcc7942_2495
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) Synpcc7942_1894
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) Synpcc7942_1893 Synpcc7942_2493
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) Synpcc7942_0815 Synpcc7942_2492
ltaE L-threonine aldolase Synpcc7942_0282
adh acetaldehyde dehydrogenase (not acylating) Synpcc7942_0489
acs acetyl-CoA synthetase, AMP-forming Synpcc7942_1352
gcvP glycine cleavage system, P component (glycine decarboxylase) Synpcc7942_2047
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) Synpcc7942_2308
gcvH glycine cleavage system, H component (lipoyl protein) Synpcc7942_2046
lpd dihydrolipoyl dehydrogenase Synpcc7942_1198 Synpcc7942_0842
Alternative steps:
ackA acetate kinase Synpcc7942_2079 Synpcc7942_0588
acn (2R,3S)-2-methylcitrate dehydratase Synpcc7942_0903
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase Synpcc7942_0489
D-LDH D-lactate dehydrogenase Synpcc7942_1347 Synpcc7942_0276
dddA 3-hydroxypropionate dehydrogenase
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) Synpcc7942_0276
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) Synpcc7942_1718
glcF D-lactate dehydrogenase, FeS subunit GlcF Synpcc7942_1717
gloA glyoxylase I Synpcc7942_0638
gloB hydroxyacylglutathione hydrolase (glyoxalase II) Synpcc7942_0458 Synpcc7942_1403
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 Synpcc7942_0597
iolA malonate semialdehyde dehydrogenase (CoA-acylating)
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) Synpcc7942_0027
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 Synpcc7942_0276
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit
lldF L-lactate dehydrogenase, LldF subunit
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit Synpcc7942_1717
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 Synpcc7942_1379
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Synpcc7942_1379
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase Synpcc7942_0612
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA Synpcc7942_2083 Synpcc7942_1365
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase Synpcc7942_0459
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