GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Geotalea uraniireducens Rf4

Best path

snatA, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd

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 (48 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
snatA L-threonine transporter snatA GURA_RS03275
ltaE L-threonine aldolase GURA_RS09475 GURA_RS09525
adh acetaldehyde dehydrogenase (not acylating) GURA_RS00565 GURA_RS16875
ackA acetate kinase GURA_RS17300 GURA_RS13515
pta phosphate acetyltransferase GURA_RS17295 GURA_RS10515
gcvP glycine cleavage system, P component (glycine decarboxylase) GURA_RS01730 GURA_RS01725
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) GURA_RS01740
gcvH glycine cleavage system, H component (lipoyl protein) GURA_RS09265 GURA_RS01735
lpd dihydrolipoyl dehydrogenase GURA_RS06450 GURA_RS04270
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase GURA_RS09830
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
acs acetyl-CoA synthetase, AMP-forming GURA_RS08185 GURA_RS08015
ald-dh-CoA acetaldehyde dehydrogenase, acylating GURA_RS18035
aldA lactaldehyde dehydrogenase GURA_RS08035 GURA_RS16875
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) GURA_RS10795
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) GURA_RS10790
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) GURA_RS10785 GURA_RS00575
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) GURA_RS10775 GURA_RS00570
D-LDH D-lactate dehydrogenase GURA_RS11155 GURA_RS03295
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component GURA_RS00765
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components GURA_RS00760 GURA_RS03300
epi methylmalonyl-CoA epimerase GURA_RS03330
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) GURA_RS11155 GURA_RS03295
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) GURA_RS11155
glcF D-lactate dehydrogenase, FeS subunit GlcF GURA_RS11150
gloA glyoxylase I
gloB hydroxyacylglutathione hydrolase (glyoxalase II) GURA_RS14900
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 GURA_RS15480
iolA malonate semialdehyde dehydrogenase (CoA-acylating) GURA_RS16875 GURA_RS00565
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) GURA_RS16515
L-LDH L-lactate dehydrogenase GURA_RS11125
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit GURA_RS06185 GURA_RS12285
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit GURA_RS12280 GURA_RS06190
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component GURA_RS11155 GURA_RS03295
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit
lldF L-lactate dehydrogenase, LldF subunit GURA_RS00760
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit GURA_RS00760 GURA_RS11150
lutB L-lactate dehydrogenase, LutB subunit GURA_RS00760
lutC L-lactate dehydrogenase, LutC subunit
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit GURA_RS03325 GURA_RS17755
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit GURA_RS10270 GURA_RS17760
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components GURA_RS06825 GURA_RS03325
pccA propionyl-CoA carboxylase, alpha subunit GURA_RS09260 GURA_RS14795
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit GURA_RS09260 GURA_RS14795
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit GURA_RS03310 GURA_RS17790
pco propanyl-CoA oxidase GURA_RS15315 GURA_RS16870
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase GURA_RS00355
prpC 2-methylcitrate synthase GURA_RS00360 GURA_RS08025
prpD 2-methylcitrate dehydratase GURA_RS00365
prpF methylaconitate isomerase
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase GURA_RS20520
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase GURA_RS12310 GURA_RS06110
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) GURA_RS22240

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 Apr 09 2024. 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:

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