GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Marinobacter adhaerens HP15

Best path

braC, braD, braE, braF, braG, tdcB, tdcE, prpC, acnD, prpF, acn, prpB

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 (49 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) HP15_3055
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) HP15_3056 HP15_2706
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) HP15_3057 HP15_2705
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) HP15_3058 HP15_2704
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) HP15_3059 HP15_2703
tdcB L-threonine dehydratase HP15_3213
tdcE 2-ketobutyrate formate-lyase
prpC 2-methylcitrate synthase HP15_1931 HP15_1516
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) HP15_1930 HP15_3433
prpF methylaconitate isomerase HP15_1929
acn (2R,3S)-2-methylcitrate dehydratase HP15_1930 HP15_2203
prpB 2-methylisocitrate lyase HP15_1932
Alternative steps:
ackA acetate kinase HP15_1245 HP15_1499
acs acetyl-CoA synthetase, AMP-forming HP15_811 HP15_2053
adh acetaldehyde dehydrogenase (not acylating) HP15_3144 HP15_3039
ald-dh-CoA acetaldehyde dehydrogenase, acylating HP15_4035 HP15_1114
aldA lactaldehyde dehydrogenase HP15_943 HP15_3144
D-LDH D-lactate dehydrogenase HP15_4091 HP15_2553
dddA 3-hydroxypropionate dehydrogenase HP15_2656 HP15_2800
DVU3032 L-lactate dehydrogenase, LutC-like component HP15_2888 HP15_4090
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components HP15_4089 HP15_2887
epi methylmalonyl-CoA epimerase
gcvH glycine cleavage system, H component (lipoyl protein) HP15_459
gcvP glycine cleavage system, P component (glycine decarboxylase)
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase)
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) HP15_3024
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) HP15_3023
glcF D-lactate dehydrogenase, FeS subunit GlcF HP15_3022
gloA glyoxylase I HP15_2890 HP15_1154
gloB hydroxyacylglutathione hydrolase (glyoxalase II) HP15_1805 HP15_1191
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 HP15_12 HP15_2692
iolA malonate semialdehyde dehydrogenase (CoA-acylating) HP15_2655 HP15_906
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) HP15_2485
L-LDH L-lactate dehydrogenase HP15_2710
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit HP15_1755
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit HP15_2886 HP15_4088
lldF L-lactate dehydrogenase, LldF subunit HP15_2887 HP15_4089
lldG L-lactate dehydrogenase, LldG subunit HP15_2888
lpd dihydrolipoyl dehydrogenase HP15_1523 HP15_65
ltaE L-threonine aldolase HP15_2715 HP15_2794
lutA L-lactate dehydrogenase, LutA subunit HP15_4088 HP15_2886
lutB L-lactate dehydrogenase, LutB subunit HP15_4089 HP15_2887
lutC L-lactate dehydrogenase, LutC subunit HP15_4090 HP15_2888
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit HP15_1792
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
pccA propionyl-CoA carboxylase, alpha subunit HP15_1002 HP15_4179
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit HP15_3934 HP15_3222
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit HP15_3935
pccB propionyl-CoA carboxylase, beta subunit HP15_1004 HP15_2538
pco propanyl-CoA oxidase HP15_3936 HP15_2
phtA L-threonine uptake permease PhtA
prpD 2-methylcitrate dehydratase HP15_1928
pta phosphate acetyltransferase HP15_1498
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA
sstT L-threonine:Na+ symporter SstT
tdcC L-threonine:H+ symporter TdcC
tdh L-threonine 3-dehydrogenase HP15_3135 HP15_2019
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) HP15_833 HP15_2827

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, 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