GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Sphingomonas koreensis DSMZ 15582

Best path

snatA, tdh, kbl, 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 (40 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
snatA L-threonine transporter snatA Ga0059261_1304
tdh L-threonine 3-dehydrogenase Ga0059261_2605 Ga0059261_0846
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) Ga0059261_2606 Ga0059261_2444
gcvP glycine cleavage system, P component (glycine decarboxylase) Ga0059261_3258 Ga0059261_3259
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) Ga0059261_3256
gcvH glycine cleavage system, H component (lipoyl protein) Ga0059261_3257
lpd dihydrolipoyl dehydrogenase Ga0059261_3715 Ga0059261_1343
Alternative steps:
ackA acetate kinase Ga0059261_3309 Ga0059261_2551
acn (2R,3S)-2-methylcitrate dehydratase Ga0059261_3296
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Ga0059261_3296
acs acetyl-CoA synthetase, AMP-forming Ga0059261_1313 Ga0059261_0337
adh acetaldehyde dehydrogenase (not acylating) Ga0059261_4132 Ga0059261_1495
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase Ga0059261_1680 Ga0059261_3374
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) Ga0059261_2542 Ga0059261_4235
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) Ga0059261_2542 Ga0059261_0624
D-LDH D-lactate dehydrogenase Ga0059261_0219 Ga0059261_1572
dddA 3-hydroxypropionate dehydrogenase Ga0059261_2257 Ga0059261_2901
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase Ga0059261_3985
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) Ga0059261_2631
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) Ga0059261_2632
glcF D-lactate dehydrogenase, FeS subunit GlcF Ga0059261_2633
gloA glyoxylase I
gloB hydroxyacylglutathione hydrolase (glyoxalase II) Ga0059261_2759 Ga0059261_2228
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 Ga0059261_3685 Ga0059261_2668
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Ga0059261_3677 Ga0059261_3374
L-LDH L-lactate dehydrogenase Ga0059261_2629 Ga0059261_1338
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit Ga0059261_2280 Ga0059261_2885
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component Ga0059261_2631 Ga0059261_1691
lctO L-lactate oxidase or 2-monooxygenase Ga0059261_2629
lldE L-lactate dehydrogenase, LldE subunit
lldF L-lactate dehydrogenase, LldF subunit
lldG L-lactate dehydrogenase, LldG subunit
ltaE L-threonine aldolase Ga0059261_2028 Ga0059261_1986
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 Ga0059261_3988
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit Ga0059261_3988
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components Ga0059261_3988
pccA propionyl-CoA carboxylase, alpha subunit Ga0059261_3993 Ga0059261_4056
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Ga0059261_3993 Ga0059261_0292
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit Ga0059261_3982 Ga0059261_4055
pco propanyl-CoA oxidase Ga0059261_2164
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase Ga0059261_0941
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase Ga0059261_0523
pta phosphate acetyltransferase Ga0059261_2552
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase Ga0059261_3694 Ga0059261_3754
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
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 (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