GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Arcobacter nitrofigilis DSM 7299

Best path

snatA, tdcB, tdcE, prpC, acnD, prpF, acn, prpB

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 (37 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
snatA L-threonine transporter snatA ARNIT_RS09940 ARNIT_RS09155
tdcB L-threonine dehydratase ARNIT_RS02585
tdcE 2-ketobutyrate formate-lyase
prpC 2-methylcitrate synthase ARNIT_RS13715 ARNIT_RS13330
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) ARNIT_RS13720
prpF methylaconitate isomerase ARNIT_RS13725
acn (2R,3S)-2-methylcitrate dehydratase ARNIT_RS13720 ARNIT_RS06740
prpB 2-methylisocitrate lyase ARNIT_RS13710
Alternative steps:
ackA acetate kinase ARNIT_RS03780 ARNIT_RS03760
acs acetyl-CoA synthetase, AMP-forming ARNIT_RS15075
adh acetaldehyde dehydrogenase (not acylating) ARNIT_RS13950 ARNIT_RS06115
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase ARNIT_RS00055 ARNIT_RS05955
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) ARNIT_RS08960 ARNIT_RS06925
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) ARNIT_RS08955
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) ARNIT_RS08950 ARNIT_RS06935
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) ARNIT_RS08945 ARNIT_RS06940
D-LDH D-lactate dehydrogenase ARNIT_RS00600 ARNIT_RS11485
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component ARNIT_RS00630
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components ARNIT_RS00635
epi methylmalonyl-CoA epimerase
gcvH glycine cleavage system, H component (lipoyl protein)
gcvP glycine cleavage system, P component (glycine decarboxylase)
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase)
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) ARNIT_RS11485
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE)
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I ARNIT_RS00490
gloB hydroxyacylglutathione hydrolase (glyoxalase II) ARNIT_RS08080
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 ARNIT_RS06725
iolA malonate semialdehyde dehydrogenase (CoA-acylating) ARNIT_RS04410 ARNIT_RS05955
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase)
L-LDH L-lactate dehydrogenase ARNIT_RS07815 ARNIT_RS09570
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 ARNIT_RS11485
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit ARNIT_RS00640
lldF L-lactate dehydrogenase, LldF subunit ARNIT_RS00635
lldG L-lactate dehydrogenase, LldG subunit ARNIT_RS00630
lpd dihydrolipoyl dehydrogenase ARNIT_RS13025 ARNIT_RS09935
ltaE L-threonine aldolase ARNIT_RS09420 ARNIT_RS04650
lutA L-lactate dehydrogenase, LutA subunit ARNIT_RS00640
lutB L-lactate dehydrogenase, LutB subunit ARNIT_RS00635
lutC L-lactate dehydrogenase, LutC subunit
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
pccA propionyl-CoA carboxylase, alpha subunit ARNIT_RS13965 ARNIT_RS00660
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit ARNIT_RS13965 ARNIT_RS00660
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase ARNIT_RS04600
phtA L-threonine uptake permease PhtA
prpD 2-methylcitrate dehydratase
pta phosphate acetyltransferase ARNIT_RS03765
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
sstT L-threonine:Na+ symporter SstT
tdcC L-threonine:H+ symporter TdcC
tdh L-threonine 3-dehydrogenase
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) ARNIT_RS10410

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