snatA, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
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.
Or see definitions of steps
Step | Description | Best candidate | 2nd candidate |
---|---|---|---|
snatA | L-threonine transporter snatA | BXU11_RS04800 | |
ltaE | L-threonine aldolase | BXU11_RS08210 | BXU11_RS14300 |
adh | acetaldehyde dehydrogenase (not acylating) | BXU11_RS01185 | BXU11_RS12805 |
ackA | acetate kinase | BXU11_RS08385 | |
pta | phosphate acetyltransferase | BXU11_RS08380 | BXU11_RS03485 |
gcvP | glycine cleavage system, P component (glycine decarboxylase) | BXU11_RS04370 | |
gcvT | glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) | BXU11_RS12605 | |
gcvH | glycine cleavage system, H component (lipoyl protein) | BXU11_RS03500 | |
lpd | dihydrolipoyl dehydrogenase | BXU11_RS12530 | BXU11_RS08250 |
Alternative steps: | |||
acn | (2R,3S)-2-methylcitrate dehydratase | BXU11_RS10770 | |
acnD | 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) | ||
acs | acetyl-CoA synthetase, AMP-forming | BXU11_RS15515 | BXU11_RS13450 |
ald-dh-CoA | acetaldehyde dehydrogenase, acylating | ||
aldA | lactaldehyde dehydrogenase | BXU11_RS01185 | BXU11_RS04005 |
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) | BXU11_RS05265 | |
braG | L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | BXU11_RS05265 | BXU11_RS06900 |
D-LDH* | D-lactate dehydrogenase | BXU11_RS01240 with BXU11_RS01235 | BXU11_RS02295 |
dddA | 3-hydroxypropionate dehydrogenase | ||
DVU3032 | L-lactate dehydrogenase, LutC-like component | ||
DVU3033 | L-lactate dehydrogenase, fused LutA/LutB components | ||
epi | methylmalonyl-CoA epimerase | BXU11_RS02910 | |
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) | ||
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 | BXU11_RS02105 | |
iolA | malonate semialdehyde dehydrogenase (CoA-acylating) | ||
kbl | glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) | BXU11_RS00340 | BXU11_RS09195 |
L-LDH | L-lactate dehydrogenase | BXU11_RS06540 | |
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 | ||
lldF | L-lactate dehydrogenase, LldF subunit | ||
lldG | L-lactate dehydrogenase, LldG subunit | ||
lutA | L-lactate dehydrogenase, LutA subunit | ||
lutB | L-lactate dehydrogenase, LutB subunit | ||
lutC | L-lactate dehydrogenase, LutC subunit | ||
mcm-large | methylmalonyl-CoA mutase, large (catalytic) subunit | BXU11_RS09065 | |
mcm-small | methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit | BXU11_RS09065 | BXU11_RS11800 |
mcmA | methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components | BXU11_RS09065 | |
pccA | propionyl-CoA carboxylase, alpha subunit | BXU11_RS09415 | BXU11_RS02955 |
pccA1 | propionyl-CoA carboxylase, biotin carboxyl carrier subunit | BXU11_RS09415 | BXU11_RS02955 |
pccA2 | propionyl-CoA carboxylase, biotin carboxylase subunit | ||
pccB | propionyl-CoA carboxylase, beta subunit | BXU11_RS09410 | BXU11_RS08190 |
pco | propanyl-CoA oxidase | BXU11_RS00155 | BXU11_RS04315 |
phtA | L-threonine uptake permease PhtA | ||
prpB | 2-methylisocitrate lyase | BXU11_RS02765 | |
prpC | 2-methylcitrate synthase | BXU11_RS04785 | |
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 | BXU11_RS11050 | BXU11_RS12485 |
tdcC | L-threonine:H+ symporter TdcC | ||
tdcE | 2-ketobutyrate formate-lyase | BXU11_RS13740 | |
tdh | L-threonine 3-dehydrogenase | BXU11_RS01305 | |
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.
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:
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