GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Brucella inopinata BO1

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) BIBO1_RS12225 BIBO1_RS06815
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BIBO1_RS12250 BIBO1_RS14975
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) BIBO1_RS12245
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BIBO1_RS19765 BIBO1_RS12240
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BIBO1_RS12235 BIBO1_RS14990
ltaE L-threonine aldolase BIBO1_RS14860 BIBO1_RS07260
adh acetaldehyde dehydrogenase (not acylating) BIBO1_RS10835 BIBO1_RS11605
acs acetyl-CoA synthetase, AMP-forming BIBO1_RS12340 BIBO1_RS12015
gcvP glycine cleavage system, P component (glycine decarboxylase) BIBO1_RS16930
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) BIBO1_RS16920 BIBO1_RS12740
gcvH glycine cleavage system, H component (lipoyl protein) BIBO1_RS16925
lpd dihydrolipoyl dehydrogenase BIBO1_RS17510 BIBO1_RS08610
Alternative steps:
ackA acetate kinase BIBO1_RS16460
acn (2R,3S)-2-methylcitrate dehydratase BIBO1_RS10365
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BIBO1_RS10365
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase BIBO1_RS19460 BIBO1_RS14100
D-LDH D-lactate dehydrogenase BIBO1_RS10100 BIBO1_RS13480
dddA 3-hydroxypropionate dehydrogenase BIBO1_RS19010 BIBO1_RS15375
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase BIBO1_RS07490
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) BIBO1_RS15670 BIBO1_RS10100
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) BIBO1_RS15675
glcF D-lactate dehydrogenase, FeS subunit GlcF BIBO1_RS15680
gloA glyoxylase I BIBO1_RS19195 BIBO1_RS09435
gloB hydroxyacylglutathione hydrolase (glyoxalase II) BIBO1_RS05750 BIBO1_RS11085
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 BIBO1_RS06755 BIBO1_RS15870
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BIBO1_RS12430 BIBO1_RS10860
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) BIBO1_RS13145 BIBO1_RS17370
L-LDH L-lactate dehydrogenase BIBO1_RS18825 BIBO1_RS05715
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit BIBO1_RS05850
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component BIBO1_RS15670 BIBO1_RS13480
lctO L-lactate oxidase or 2-monooxygenase BIBO1_RS18825
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 BIBO1_RS09070
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BIBO1_RS09070
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components BIBO1_RS09070
pccA propionyl-CoA carboxylase, alpha subunit BIBO1_RS09065 BIBO1_RS06830
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BIBO1_RS09065 BIBO1_RS07715
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit BIBO1_RS12215
pccB propionyl-CoA carboxylase, beta subunit BIBO1_RS09060 BIBO1_RS06835
pco propanyl-CoA oxidase BIBO1_RS08430 BIBO1_RS17185
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase BIBO1_RS11515
prpC 2-methylcitrate synthase BIBO1_RS08705
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase BIBO1_RS10585 BIBO1_RS08120
RR42_RS28305 L-threonine:H+ symporter BIBO1_RS14845
serP1 L-threonine uptake transporter SerP1 BIBO1_RS14845
snatA L-threonine transporter snatA BIBO1_RS08495
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase BIBO1_RS08275
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase BIBO1_RS10840 BIBO1_RS16475
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) BIBO1_RS15685

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