GapMind for catabolism of small carbon sources

 

Definition of L-threonine catabolism

As rules and steps, or see full text

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.

Steps

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)

braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE)

tdcC: L-threonine:H+ symporter TdcC

sstT: L-threonine:Na+ symporter SstT

serP1: L-threonine uptake transporter SerP1

phtA: L-threonine uptake permease PhtA

snatA: L-threonine transporter snatA

RR42_RS28305: L-threonine:H+ symporter

pccA: propionyl-CoA carboxylase, alpha subunit

pccB: propionyl-CoA carboxylase, beta subunit

pccA1: propionyl-CoA carboxylase, biotin carboxyl carrier subunit

pccA2: propionyl-CoA carboxylase, biotin carboxylase subunit

mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components

mcm-large: methylmalonyl-CoA mutase, large (catalytic) subunit

mcm-small: methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit

prpC: 2-methylcitrate synthase

prpD: 2-methylcitrate dehydratase

acn: (2R,3S)-2-methylcitrate dehydratase

prpB: 2-methylisocitrate lyase

acnD: 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)

prpF: methylaconitate isomerase

epi: methylmalonyl-CoA epimerase

pco: propanyl-CoA oxidase

hpcD: 3-hydroxypropionyl-CoA dehydratase

dddA: 3-hydroxypropionate dehydrogenase

iolA: malonate semialdehyde dehydrogenase (CoA-acylating)

ald-dh-CoA: acetaldehyde dehydrogenase, acylating

adh: acetaldehyde dehydrogenase (not acylating)

acs: acetyl-CoA synthetase, AMP-forming

ackA: acetate kinase

pta: phosphate acetyltransferase

grdA: glycine reductase component A1

grdE: glycine reductase component B, precursor to alpha/beta subunits

grdB: glycine reductase component B, gamma subunit

grdD: glycine reductase component C, alpha subunit

grdC: glycine reductase component C, beta subunit

gcvP: glycine cleavage system, P component (glycine decarboxylase)

gcvT: glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase)

gcvH: glycine cleavage system, H component (lipoyl protein)

lpd: dihydrolipoyl dehydrogenase

gloA: glyoxylase I

gloB: hydroxyacylglutathione hydrolase (glyoxalase II)

D-LDH: D-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

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

yvgN: methylglyoxal reductase (NADPH-dependent)

aldA: lactaldehyde dehydrogenase

L-LDH: L-lactate dehydrogenase

lldE: L-lactate dehydrogenase, LldE subunit

lldF: L-lactate dehydrogenase, LldF subunit

lldG: L-lactate dehydrogenase, LldG subunit

lutA: L-lactate dehydrogenase, LutA subunit

lutB: L-lactate dehydrogenase, LutB subunit

lutC: L-lactate dehydrogenase, LutC subunit

DVU3033: L-lactate dehydrogenase, fused LutA/LutB components

DVU3032: L-lactate dehydrogenase, LutC-like component

lctO: L-lactate oxidase or 2-monooxygenase

tdcB: L-threonine dehydratase

tdcE: 2-ketobutyrate formate-lyase

tdh: L-threonine 3-dehydrogenase

kbl: glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase)

tynA: aminoacetone oxidase

ltaE: L-threonine aldolase

Links

Downloads

Related tools

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