GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Paucidesulfovibrio gracilis DSM 16080

Best path

braC, braD, braE, braF, braG, tdh, kbl, 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 (34 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) B5D49_RS00095 B5D49_RS04220
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) B5D49_RS00090 B5D49_RS04225
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) B5D49_RS04230 B5D49_RS00085
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) B5D49_RS00080 B5D49_RS00870
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) B5D49_RS04235 B5D49_RS00075
tdh L-threonine 3-dehydrogenase B5D49_RS01275 B5D49_RS02645
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) B5D49_RS01270
gcvP glycine cleavage system, P component (glycine decarboxylase) B5D49_RS04120 B5D49_RS04115
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) B5D49_RS06090
gcvH glycine cleavage system, H component (lipoyl protein) B5D49_RS04125
lpd dihydrolipoyl dehydrogenase B5D49_RS04110 B5D49_RS13200
Alternative steps:
ackA acetate kinase B5D49_RS13115
acn (2R,3S)-2-methylcitrate dehydratase
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
acs acetyl-CoA synthetase, AMP-forming B5D49_RS08710 B5D49_RS12880
adh acetaldehyde dehydrogenase (not acylating) B5D49_RS13965 B5D49_RS04205
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase B5D49_RS13965 B5D49_RS04205
D-LDH D-lactate dehydrogenase B5D49_RS07870 B5D49_RS10655
dddA 3-hydroxypropionate dehydrogenase B5D49_RS13960
DVU3032 L-lactate dehydrogenase, LutC-like component B5D49_RS13120
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components B5D49_RS13125 B5D49_RS13105
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) B5D49_RS13100 B5D49_RS10975
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE)
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I
gloB hydroxyacylglutathione hydrolase (glyoxalase II) B5D49_RS02570 B5D49_RS04435
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
iolA malonate semialdehyde dehydrogenase (CoA-acylating) B5D49_RS13965 B5D49_RS04205
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
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component B5D49_RS10975 B5D49_RS13100
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit B5D49_RS13125
lldF L-lactate dehydrogenase, LldF subunit B5D49_RS13125
lldG L-lactate dehydrogenase, LldG subunit B5D49_RS13120
ltaE L-threonine aldolase B5D49_RS01980
lutA L-lactate dehydrogenase, LutA subunit B5D49_RS13125 B5D49_RS13105
lutB L-lactate dehydrogenase, LutB subunit B5D49_RS13125
lutC L-lactate dehydrogenase, LutC subunit B5D49_RS13120
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
pccA propionyl-CoA carboxylase, alpha subunit B5D49_RS12550 B5D49_RS04650
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit B5D49_RS12550 B5D49_RS04650
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase B5D49_RS00370
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase B5D49_RS13110 B5D49_RS05450
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
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
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 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