GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Desulfoscipio geothermicus DSM 3669

Best path

tdcC, 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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
tdcC L-threonine:H+ symporter TdcC
tdcB L-threonine dehydratase BM299_RS07595
tdcE 2-ketobutyrate formate-lyase
pccA propionyl-CoA carboxylase, alpha subunit BM299_RS06260
pccB propionyl-CoA carboxylase, beta subunit BM299_RS10410 BM299_RS09155
epi methylmalonyl-CoA epimerase BM299_RS09150
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit BM299_RS09140 BM299_RS05960
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BM299_RS05955 BM299_RS09145
Alternative steps:
ackA acetate kinase
acn (2R,3S)-2-methylcitrate dehydratase
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BM299_RS00665
acs acetyl-CoA synthetase, AMP-forming BM299_RS11405 BM299_RS14480
adh acetaldehyde dehydrogenase (not acylating) BM299_RS16640
ald-dh-CoA acetaldehyde dehydrogenase, acylating BM299_RS16640 BM299_RS10310
aldA lactaldehyde dehydrogenase
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) BM299_RS15860 BM299_RS05470
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BM299_RS15855 BM299_RS11075
D-LDH D-lactate dehydrogenase BM299_RS10985 BM299_RS04225
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component BM299_RS04200
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components BM299_RS04205
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) BM299_RS10985 BM299_RS04225
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) BM299_RS10985 BM299_RS04225
glcF D-lactate dehydrogenase, FeS subunit GlcF BM299_RS10990
gloA glyoxylase I
gloB hydroxyacylglutathione hydrolase (glyoxalase II) BM299_RS06670 BM299_RS06675
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 BM299_RS07795 BM299_RS00820
iolA malonate semialdehyde dehydrogenase (CoA-acylating)
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) BM299_RS00615
L-LDH L-lactate dehydrogenase BM299_RS09160 BM299_RS11870
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit BM299_RS04215 BM299_RS06050
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit BM299_RS04220 BM299_RS10480
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component BM299_RS04225 BM299_RS10985
lctO L-lactate oxidase or 2-monooxygenase BM299_RS04190
lldE L-lactate dehydrogenase, LldE subunit
lldF L-lactate dehydrogenase, LldF subunit BM299_RS04205
lldG L-lactate dehydrogenase, LldG subunit
lpd dihydrolipoyl dehydrogenase
ltaE L-threonine aldolase BM299_RS15005 BM299_RS02615
lutA L-lactate dehydrogenase, LutA subunit BM299_RS04205
lutB L-lactate dehydrogenase, LutB subunit BM299_RS04205
lutC L-lactate dehydrogenase, LutC subunit BM299_RS04200
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components BM299_RS05960 BM299_RS09140
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BM299_RS06260
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase BM299_RS17105 BM299_RS11335
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA
sstT L-threonine:Na+ symporter SstT
tdh L-threonine 3-dehydrogenase BM299_RS08815 BM299_RS08795
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) BM299_RS17245

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