GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Arenitalea lutea P7-3-5

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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
snatA L-threonine transporter snatA P735_RS0109455 P735_RS0104225
ltaE L-threonine aldolase P735_RS0114410 P735_RS0102665
adh acetaldehyde dehydrogenase (not acylating) P735_RS0104655 P735_RS0109795
ackA acetate kinase P735_RS0109320
pta phosphate acetyltransferase P735_RS0109325 P735_RS0108665
gcvP glycine cleavage system, P component (glycine decarboxylase) P735_RS0101525
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) P735_RS0113360
gcvH glycine cleavage system, H component (lipoyl protein) P735_RS0108680
lpd dihydrolipoyl dehydrogenase P735_RS0103120 P735_RS0106335
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase P735_RS0112220
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
acs acetyl-CoA synthetase, AMP-forming P735_RS0106600 P735_RS0106605
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase P735_RS0105425 P735_RS0105445
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) P735_RS0107145 P735_RS0102575
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) P735_RS0107145 P735_RS0104055
D-LDH D-lactate dehydrogenase P735_RS0104390 P735_RS0112340
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component P735_RS0105450
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components P735_RS0105455
epi methylmalonyl-CoA epimerase P735_RS0104990
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
gloA glyoxylase I
gloB hydroxyacylglutathione hydrolase (glyoxalase II) P735_RS0114615
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 P735_RS0112595
iolA malonate semialdehyde dehydrogenase (CoA-acylating) P735_RS0109795
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) P735_RS0104750 P735_RS0114385
L-LDH L-lactate dehydrogenase P735_RS0102070
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
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit P735_RS0105460
lldF L-lactate dehydrogenase, LldF subunit P735_RS0105455
lldG L-lactate dehydrogenase, LldG subunit P735_RS0105450
lutA L-lactate dehydrogenase, LutA subunit P735_RS0105460
lutB L-lactate dehydrogenase, LutB subunit P735_RS0105455
lutC L-lactate dehydrogenase, LutC subunit
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit P735_RS0102225 P735_RS0111025
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit P735_RS0102225 P735_RS0111025
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components P735_RS0111025 P735_RS0102225
pccA propionyl-CoA carboxylase, alpha subunit P735_RS0106540 P735_RS0104945
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit P735_RS0106540 P735_RS0104945
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit P735_RS0106545 P735_RS0107740
pco propanyl-CoA oxidase P735_RS0100785 P735_RS0101365
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase P735_RS0101850
prpD 2-methylcitrate dehydratase
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 P735_RS0109075 P735_RS0109280
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase P735_RS0105860
tdh L-threonine 3-dehydrogenase P735_RS0104255 P735_RS0107490
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 24 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 (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