GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Hyphomicrobium sulfonivorans WDL6

Best path

braC, braD, braE, braF, braG, tdcB, tdcE, pccA, pccB, epi, mcm-large, mcm-small

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 (45 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) APY04_RS10585
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) APY04_RS10560
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) APY04_RS10565
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) APY04_RS10570 APY04_RS08115
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) APY04_RS10575 APY04_RS08095
tdcB L-threonine dehydratase APY04_RS13150 APY04_RS06705
tdcE 2-ketobutyrate formate-lyase
pccA propionyl-CoA carboxylase, alpha subunit APY04_RS01365 APY04_RS04340
pccB propionyl-CoA carboxylase, beta subunit APY04_RS01350
epi methylmalonyl-CoA epimerase APY04_RS05325
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit APY04_RS02350 APY04_RS09520
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit APY04_RS02350 APY04_RS09520
Alternative steps:
ackA acetate kinase
acn (2R,3S)-2-methylcitrate dehydratase APY04_RS03620
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) APY04_RS03620
acs acetyl-CoA synthetase, AMP-forming APY04_RS03055 APY04_RS09270
adh acetaldehyde dehydrogenase (not acylating) APY04_RS13805 APY04_RS06730
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase APY04_RS06730 APY04_RS13805
D-LDH D-lactate dehydrogenase APY04_RS15255 APY04_RS06870
dddA 3-hydroxypropionate dehydrogenase APY04_RS08265
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components APY04_RS06885
gcvH glycine cleavage system, H component (lipoyl protein)
gcvP glycine cleavage system, P component (glycine decarboxylase)
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) APY04_RS13045
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) APY04_RS06680 APY04_RS06870
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) APY04_RS06865 APY04_RS06685
glcF D-lactate dehydrogenase, FeS subunit GlcF APY04_RS06690 APY04_RS06860
gloA glyoxylase I
gloB hydroxyacylglutathione hydrolase (glyoxalase II) APY04_RS06535 APY04_RS16800
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 APY04_RS10815 APY04_RS07375
iolA malonate semialdehyde dehydrogenase (CoA-acylating) APY04_RS10965 APY04_RS06730
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) APY04_RS04940 APY04_RS00035
L-LDH L-lactate dehydrogenase APY04_RS03475 APY04_RS14310
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit APY04_RS03325 APY04_RS00410
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component APY04_RS06680 APY04_RS06870
lctO L-lactate oxidase or 2-monooxygenase APY04_RS14310
lldE L-lactate dehydrogenase, LldE subunit APY04_RS06880
lldF L-lactate dehydrogenase, LldF subunit APY04_RS06885
lldG L-lactate dehydrogenase, LldG subunit
lpd dihydrolipoyl dehydrogenase APY04_RS12540 APY04_RS06755
ltaE L-threonine aldolase APY04_RS00040
lutA L-lactate dehydrogenase, LutA subunit APY04_RS06880
lutB L-lactate dehydrogenase, LutB subunit APY04_RS06885
lutC L-lactate dehydrogenase, LutC subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components APY04_RS02350 APY04_RS09520
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit APY04_RS01365 APY04_RS04340
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase APY04_RS15350
prpC 2-methylcitrate synthase APY04_RS13425 APY04_RS08420
prpD 2-methylcitrate dehydratase APY04_RS15370
prpF methylaconitate isomerase
pta phosphate acetyltransferase
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA APY04_RS16210
sstT L-threonine:Na+ symporter SstT
tdcC L-threonine:H+ symporter TdcC
tdh L-threonine 3-dehydrogenase APY04_RS04935 APY04_RS15335
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) APY04_RS01300

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