GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Echinicola vietnamensis KMM 6221, DSM 17526

Best path

tdcC, 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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
tdcC L-threonine:H+ symporter TdcC
ltaE L-threonine aldolase Echvi_4604 Echvi_1188
adh acetaldehyde dehydrogenase (not acylating) Echvi_0535 Echvi_1497
acs acetyl-CoA synthetase, AMP-forming Echvi_1268
gcvP glycine cleavage system, P component (glycine decarboxylase) Echvi_0744
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) Echvi_0091
gcvH glycine cleavage system, H component (lipoyl protein) Echvi_4084
lpd dihydrolipoyl dehydrogenase Echvi_4609 Echvi_0770
Alternative steps:
ackA acetate kinase
acn (2R,3S)-2-methylcitrate dehydratase Echvi_4039
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Echvi_4039
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase Echvi_1572 Echvi_0481
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) Echvi_1333 Echvi_1022
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) Echvi_1333 Echvi_2909
D-LDH D-lactate dehydrogenase Echvi_3936 Echvi_3161
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components Echvi_1568
epi methylmalonyl-CoA epimerase Echvi_0089
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 Echvi_0089
gloB hydroxyacylglutathione hydrolase (glyoxalase II) Echvi_2827 Echvi_2293
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 Echvi_4069 Echvi_0069
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Echvi_0481
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) Echvi_0145 Echvi_0093
L-LDH L-lactate dehydrogenase Echvi_2076
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 Echvi_1569
lldF L-lactate dehydrogenase, LldF subunit Echvi_1568
lldG L-lactate dehydrogenase, LldG subunit Echvi_1567
lutA L-lactate dehydrogenase, LutA subunit Echvi_1569
lutB L-lactate dehydrogenase, LutB subunit Echvi_1568
lutC L-lactate dehydrogenase, LutC subunit
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit Echvi_4683 Echvi_2441
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit Echvi_4683
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components Echvi_2441 Echvi_4683
pccA propionyl-CoA carboxylase, alpha subunit Echvi_3962 Echvi_0191
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Echvi_3962 Echvi_0191
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit Echvi_0275
pccB propionyl-CoA carboxylase, beta subunit Echvi_0160 Echvi_0113
pco propanyl-CoA oxidase Echvi_0738 Echvi_2990
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase Echvi_3057
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase Echvi_4081
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase Echvi_3354 Echvi_1189
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase Echvi_0146 Echvi_0924
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) Echvi_4178 Echvi_3562

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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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, the preprint on GapMind for carbon sources, 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