GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Ochrobactrum thiophenivorans DSM 7216

Best path

braC, braD, braE, braF, braG, 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 (48 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) CEV31_RS05815 CEV31_RS03660
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) CEV31_RS03685 CEV31_RS13110
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) CEV31_RS03680
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) CEV31_RS14825 CEV31_RS03675
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) CEV31_RS03670 CEV31_RS14820
ltaE L-threonine aldolase CEV31_RS20650 CEV31_RS10015
adh acetaldehyde dehydrogenase (not acylating) CEV31_RS18595 CEV31_RS06610
acs acetyl-CoA synthetase, AMP-forming CEV31_RS03785 CEV31_RS03440
gcvP glycine cleavage system, P component (glycine decarboxylase) CEV31_RS15325
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) CEV31_RS15335 CEV31_RS06730
gcvH glycine cleavage system, H component (lipoyl protein) CEV31_RS15330
lpd dihydrolipoyl dehydrogenase CEV31_RS15020 CEV31_RS11945
Alternative steps:
ackA acetate kinase CEV31_RS13070
acn (2R,3S)-2-methylcitrate dehydratase CEV31_RS06075
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) CEV31_RS06075
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase CEV31_RS01730 CEV31_RS16855
D-LDH D-lactate dehydrogenase CEV31_RS01355 CEV31_RS07780
dddA 3-hydroxypropionate dehydrogenase CEV31_RS02710 CEV31_RS08355
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase CEV31_RS10320
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) CEV31_RS19915 CEV31_RS01355
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) CEV31_RS19910
glcF D-lactate dehydrogenase, FeS subunit GlcF CEV31_RS19905
gloA glyoxylase I CEV31_RS00805 CEV31_RS18660
gloB hydroxyacylglutathione hydrolase (glyoxalase II) CEV31_RS01985 CEV31_RS04745
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 CEV31_RS04900 CEV31_RS05620
iolA malonate semialdehyde dehydrogenase (CoA-acylating) CEV31_RS03890 CEV31_RS08350
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) CEV31_RS07370
L-LDH L-lactate dehydrogenase CEV31_RS02535 CEV31_RS04710
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit CEV31_RS04320
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component CEV31_RS19915 CEV31_RS01355
lctO L-lactate oxidase or 2-monooxygenase CEV31_RS02535 CEV31_RS20515
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 CEV31_RS12240
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit CEV31_RS12240
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components CEV31_RS12240
pccA propionyl-CoA carboxylase, alpha subunit CEV31_RS12235 CEV31_RS05800
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit CEV31_RS12235 CEV31_RS10995
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit CEV31_RS12230 CEV31_RS05795
pco propanyl-CoA oxidase CEV31_RS11735 CEV31_RS05790
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase CEV31_RS15595
prpC 2-methylcitrate synthase CEV31_RS12050
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase CEV31_RS04090
pta phosphate acetyltransferase CEV31_RS11445 CEV31_RS06335
RR42_RS28305 L-threonine:H+ symporter CEV31_RS20665 CEV31_RS18290
serP1 L-threonine uptake transporter SerP1 CEV31_RS20665 CEV31_RS18290
snatA L-threonine transporter snatA CEV31_RS11825 CEV31_RS04115
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase CEV31_RS11600 CEV31_RS19095
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase CEV31_RS17940 CEV31_RS20765
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) CEV31_RS19890 CEV31_RS14710

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