GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Dokdonella koreensis DS-123

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 I596_RS00125 I596_RS02940
adh acetaldehyde dehydrogenase (not acylating) I596_RS04570 I596_RS02880
acs acetyl-CoA synthetase, AMP-forming I596_RS00340 I596_RS03300
gcvP glycine cleavage system, P component (glycine decarboxylase) I596_RS15740 I596_RS03290
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) I596_RS03280
gcvH glycine cleavage system, H component (lipoyl protein) I596_RS03285
lpd dihydrolipoyl dehydrogenase I596_RS06610 I596_RS14685
Alternative steps:
ackA acetate kinase I596_RS06530
acn (2R,3S)-2-methylcitrate dehydratase I596_RS07590 I596_RS07575
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) I596_RS07575
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase I596_RS04140 I596_RS04570
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) I596_RS07805 I596_RS15380
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) I596_RS07805 I596_RS15380
D-LDH D-lactate dehydrogenase I596_RS07265 I596_RS02995
dddA 3-hydroxypropionate dehydrogenase I596_RS04725
DVU3032 L-lactate dehydrogenase, LutC-like component I596_RS04115
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components I596_RS04120
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) I596_RS02995 I596_RS07265
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) I596_RS02995
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I I596_RS07745
gloB hydroxyacylglutathione hydrolase (glyoxalase II) I596_RS09925 I596_RS12580
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 I596_RS12940 I596_RS04715
iolA malonate semialdehyde dehydrogenase (CoA-acylating) I596_RS04705 I596_RS02225
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) I596_RS09480 I596_RS17070
L-LDH L-lactate dehydrogenase
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit I596_RS11775
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component I596_RS02995 I596_RS07265
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit I596_RS04110
lldF L-lactate dehydrogenase, LldF subunit I596_RS04120
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit I596_RS04110
lutB L-lactate dehydrogenase, LutB subunit I596_RS04120
lutC L-lactate dehydrogenase, LutC subunit I596_RS04115
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit I596_RS05545
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit I596_RS05545
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components I596_RS05545
pccA propionyl-CoA carboxylase, alpha subunit I596_RS08895 I596_RS01860
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit I596_RS01860 I596_RS08895
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit I596_RS05360
pco propanyl-CoA oxidase I596_RS15145 I596_RS15670
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase I596_RS00395 I596_RS03320
prpC 2-methylcitrate synthase I596_RS03335 I596_RS12560
prpD 2-methylcitrate dehydratase I596_RS14135
prpF methylaconitate isomerase
pta phosphate acetyltransferase I596_RS13815
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 I596_RS17335 I596_RS16215
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase I596_RS09150 I596_RS08115
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.

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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