GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Phaeobacter inhibens BS107

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 (42 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
snatA L-threonine transporter snatA PGA1_c19770
tdh L-threonine 3-dehydrogenase PGA1_c34320 PGA1_c27200
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) PGA1_c34330 PGA1_c20350
gcvP glycine cleavage system, P component (glycine decarboxylase) PGA1_78p00310
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) PGA1_78p00290 PGA1_c33110
gcvH glycine cleavage system, H component (lipoyl protein) PGA1_c05560 PGA1_78p00300
lpd dihydrolipoyl dehydrogenase PGA1_c17390 PGA1_c23190
Alternative steps:
ackA acetate kinase PGA1_c28840
acn (2R,3S)-2-methylcitrate dehydratase PGA1_c18830
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) PGA1_c18830
acs acetyl-CoA synthetase, AMP-forming PGA1_c12950 PGA1_c11900
adh acetaldehyde dehydrogenase (not acylating) PGA1_c32800 PGA1_c29650
ald-dh-CoA acetaldehyde dehydrogenase, acylating PGA1_c19350
aldA lactaldehyde dehydrogenase PGA1_c21070 PGA1_c32800
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) PGA1_c15940 PGA1_c02590
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) PGA1_c15910 PGA1_c02610
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) PGA1_c15920 PGA1_c02620
D-LDH D-lactate dehydrogenase PGA1_c28240 PGA1_c06340
dddA 3-hydroxypropionate dehydrogenase PGA1_c30400 PGA1_c21660
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase PGA1_c24490
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) PGA1_c29720 PGA1_c28240
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) PGA1_c29710
glcF D-lactate dehydrogenase, FeS subunit GlcF PGA1_c29700
gloA glyoxylase I PGA1_c21210
gloB hydroxyacylglutathione hydrolase (glyoxalase II) PGA1_c31600 PGA1_c25140
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 PGA1_c36500 PGA1_262p01980
iolA malonate semialdehyde dehydrogenase (CoA-acylating) PGA1_c17300 PGA1_c21670
L-LDH L-lactate dehydrogenase PGA1_c04920 PGA1_c03650
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit PGA1_c01240
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component PGA1_c28240 PGA1_c29720
lctO L-lactate oxidase or 2-monooxygenase PGA1_c04920 PGA1_c07690
lldE L-lactate dehydrogenase, LldE subunit
lldF L-lactate dehydrogenase, LldF subunit
lldG L-lactate dehydrogenase, LldG subunit
ltaE L-threonine aldolase PGA1_c25010 PGA1_c11870
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 PGA1_c21510 PGA1_c03840
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit PGA1_c21510 PGA1_c03840
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components PGA1_c21510 PGA1_c03840
pccA propionyl-CoA carboxylase, alpha subunit PGA1_c21540 PGA1_c10330
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit PGA1_c21540 PGA1_c12600
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit PGA1_c21600 PGA1_c10320
pco propanyl-CoA oxidase PGA1_c15710
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase PGA1_c28860 PGA1_c16970
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase PGA1_c28850
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase PGA1_c34900 PGA1_c04590
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 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