GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Polaribacter dokdonensis DSW-5

Best path

tdcC, 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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
tdcC L-threonine:H+ symporter TdcC
ltaE L-threonine aldolase I602_RS11615 I602_RS11885
adh acetaldehyde dehydrogenase (not acylating) I602_RS06450 I602_RS02060
ackA acetate kinase I602_RS09360
pta phosphate acetyltransferase I602_RS09365 I602_RS07960
gcvP glycine cleavage system, P component (glycine decarboxylase) I602_RS02100
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) I602_RS10390
gcvH glycine cleavage system, H component (lipoyl protein) I602_RS07945
lpd dihydrolipoyl dehydrogenase I602_RS12805 I602_RS04785
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase I602_RS10495 I602_RS10500
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) I602_RS10500
acs acetyl-CoA synthetase, AMP-forming I602_RS01605
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase I602_RS02060 I602_RS00985
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) I602_RS11370 I602_RS06375
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) I602_RS11370 I602_RS12395
D-LDH D-lactate dehydrogenase I602_RS05850 I602_RS02090
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase I602_RS05035
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 I602_RS05035
gloB hydroxyacylglutathione hydrolase (glyoxalase II) I602_RS04485
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 I602_RS05270
iolA malonate semialdehyde dehydrogenase (CoA-acylating) I602_RS02060
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) I602_RS03990 I602_RS09690
L-LDH L-lactate dehydrogenase I602_RS02670
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 I602_RS00950 I602_RS08695
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit I602_RS00950
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components I602_RS08695 I602_RS00950
pccA propionyl-CoA carboxylase, alpha subunit I602_RS05480
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit I602_RS05480
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit I602_RS09370
pco propanyl-CoA oxidase I602_RS04215 I602_RS01265
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase I602_RS02205
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
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 I602_RS08510
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase I602_RS06135
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.

Links

Downloads

Related tools

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