GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Frankia alni ACN14a

Best path

tdcC, ltaE, adh, acs, 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 (44 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
tdcC L-threonine:H+ symporter TdcC
ltaE L-threonine aldolase FRAAL_RS01725 FRAAL_RS25875
adh acetaldehyde dehydrogenase (not acylating) FRAAL_RS14730 FRAAL_RS22990
acs acetyl-CoA synthetase, AMP-forming FRAAL_RS25625 FRAAL_RS01710
gcvP glycine cleavage system, P component (glycine decarboxylase) FRAAL_RS28075
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) FRAAL_RS22450
gcvH glycine cleavage system, H component (lipoyl protein) FRAAL_RS09910
lpd dihydrolipoyl dehydrogenase FRAAL_RS15765 FRAAL_RS22460
Alternative steps:
ackA acetate kinase FRAAL_RS25005
acn (2R,3S)-2-methylcitrate dehydratase FRAAL_RS08975
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) FRAAL_RS08975
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase FRAAL_RS14890 FRAAL_RS12640
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) FRAAL_RS03125
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) FRAAL_RS03130
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) FRAAL_RS03135 FRAAL_RS16765
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) FRAAL_RS03140 FRAAL_RS03430
D-LDH D-lactate dehydrogenase FRAAL_RS16885 FRAAL_RS23870
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components FRAAL_RS14605
epi methylmalonyl-CoA epimerase FRAAL_RS18690
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) FRAAL_RS23870 FRAAL_RS16885
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) FRAAL_RS23870 FRAAL_RS16885
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I
gloB hydroxyacylglutathione hydrolase (glyoxalase II) FRAAL_RS09795 FRAAL_RS08525
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 FRAAL_RS13585 FRAAL_RS25610
iolA malonate semialdehyde dehydrogenase (CoA-acylating) FRAAL_RS06170 FRAAL_RS13635
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) FRAAL_RS26140 FRAAL_RS26025
L-LDH L-lactate dehydrogenase FRAAL_RS15640 FRAAL_RS16695
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit FRAAL_RS25590
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component FRAAL_RS16885 FRAAL_RS23870
lctO L-lactate oxidase or 2-monooxygenase FRAAL_RS16695 FRAAL_RS15640
lldE L-lactate dehydrogenase, LldE subunit FRAAL_RS14610
lldF L-lactate dehydrogenase, LldF subunit FRAAL_RS14605
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit FRAAL_RS14610
lutB L-lactate dehydrogenase, LutB subunit FRAAL_RS14605
lutC L-lactate dehydrogenase, LutC subunit
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit FRAAL_RS21590 FRAAL_RS25780
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit FRAAL_RS21590 FRAAL_RS25780
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components FRAAL_RS21590 FRAAL_RS25555
pccA propionyl-CoA carboxylase, alpha subunit FRAAL_RS05280 FRAAL_RS13800
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit FRAAL_RS05280 FRAAL_RS13800
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit FRAAL_RS05285 FRAAL_RS24695
pco propanyl-CoA oxidase
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase FRAAL_RS10320 FRAAL_RS21895
prpC 2-methylcitrate synthase FRAAL_RS10400 FRAAL_RS00530
prpD 2-methylcitrate dehydratase FRAAL_RS21900
prpF methylaconitate isomerase
pta phosphate acetyltransferase
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase FRAAL_RS05015 FRAAL_RS16990
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase FRAAL_RS09800 FRAAL_RS21075
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) FRAAL_RS08100 FRAAL_RS13185

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