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

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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:

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