GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Nocardiopsis baichengensis YIM 90130

Best path

braC, braD, braE, braF, braG, 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 (47 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) C892_RS0115140
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) C892_RS0115120 C892_RS0104280
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) C892_RS0115125 C892_RS0110670
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) C892_RS0115130 C892_RS0110655
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) C892_RS0115135 C892_RS0110660
ltaE L-threonine aldolase C892_RS0111390 C892_RS0108035
adh acetaldehyde dehydrogenase (not acylating) C892_RS0114890 C892_RS0112195
ackA acetate kinase C892_RS0110465
pta phosphate acetyltransferase C892_RS0120525
gcvP glycine cleavage system, P component (glycine decarboxylase) C892_RS0125155
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) C892_RS0108045 C892_RS0127070
gcvH glycine cleavage system, H component (lipoyl protein) C892_RS0108040
lpd dihydrolipoyl dehydrogenase C892_RS0123470 C892_RS0114110
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase C892_RS0113040
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) C892_RS0113040
acs acetyl-CoA synthetase, AMP-forming C892_RS0121690 C892_RS0108070
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase C892_RS0122405 C892_RS0112195
D-LDH D-lactate dehydrogenase C892_RS0109975 C892_RS0122000
dddA 3-hydroxypropionate dehydrogenase C892_RS0105225
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components C892_RS0124830
epi methylmalonyl-CoA epimerase C892_RS0118240
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) C892_RS0109975 C892_RS0109530
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) C892_RS0109980
glcF D-lactate dehydrogenase, FeS subunit GlcF C892_RS0109985
gloA glyoxylase I
gloB hydroxyacylglutathione hydrolase (glyoxalase II) C892_RS0108850 C892_RS0123535
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 C892_RS0126825 C892_RS0107320
iolA malonate semialdehyde dehydrogenase (CoA-acylating) C892_RS0108545 C892_RS0126085
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) C892_RS0112095
L-LDH L-lactate dehydrogenase
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit C892_RS0126835
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit C892_RS0126840
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit C892_RS0124825
lldF L-lactate dehydrogenase, LldF subunit C892_RS0124830
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit C892_RS0124825
lutB L-lactate dehydrogenase, LutB subunit C892_RS0124830
lutC L-lactate dehydrogenase, LutC subunit
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit C892_RS0104600 C892_RS0118195
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit C892_RS0128095 C892_RS0104600
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components C892_RS0104600 C892_RS0118195
pccA propionyl-CoA carboxylase, alpha subunit C892_RS0123485 C892_RS0127295
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit C892_RS0127295 C892_RS0123485
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit C892_RS0123495 C892_RS0127290
pco propanyl-CoA oxidase C892_RS0110455 C892_RS0114500
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase C892_RS0122210
prpC 2-methylcitrate synthase C892_RS0125305 C892_RS0103950
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
RR42_RS28305 L-threonine:H+ symporter C892_RS0102390
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase C892_RS0100740 C892_RS0100860
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase C892_RS0103360 C892_RS0123530
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) C892_RS0121920 C892_RS0111005

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