GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Bacillus altitudinis 41KF2b

Best path

serP1, 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 (48 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
serP1 L-threonine uptake transporter SerP1 BA79_RS16380 BA79_RS12105
ltaE L-threonine aldolase BA79_RS08870
adh acetaldehyde dehydrogenase (not acylating) BA79_RS13175 BA79_RS15800
ackA acetate kinase BA79_RS07620
pta phosphate acetyltransferase BA79_RS09250 BA79_RS11095
gcvP glycine cleavage system, P component (glycine decarboxylase) BA79_RS10900 BA79_RS10895
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) BA79_RS10890
gcvH glycine cleavage system, H component (lipoyl protein) BA79_RS04965
lpd dihydrolipoyl dehydrogenase BA79_RS01965 BA79_RS11110
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase BA79_RS03665
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BA79_RS03665
acs acetyl-CoA synthetase, AMP-forming BA79_RS07825 BA79_RS18200
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase BA79_RS13175 BA79_RS04010
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) BA79_RS17265 BA79_RS08110
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BA79_RS06410 BA79_RS08570
D-LDH D-lactate dehydrogenase BA79_RS18270 BA79_RS11625
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components BA79_RS03525
epi methylmalonyl-CoA epimerase BA79_RS11170
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) BA79_RS18270
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) BA79_RS18270
glcF D-lactate dehydrogenase, FeS subunit GlcF BA79_RS18275
gloA glyoxylase I BA79_RS17830 BA79_RS09595
gloB hydroxyacylglutathione hydrolase (glyoxalase II) BA79_RS10790
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 BA79_RS07305 BA79_RS18210
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BA79_RS03900 BA79_RS13175
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) BA79_RS03210
L-LDH L-lactate dehydrogenase BA79_RS12635 BA79_RS07500
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit BA79_RS07295
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component BA79_RS18270
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit BA79_RS03520
lldF L-lactate dehydrogenase, LldF subunit BA79_RS03525
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit BA79_RS03520
lutB L-lactate dehydrogenase, LutB subunit BA79_RS03525
lutC L-lactate dehydrogenase, LutC subunit BA79_RS03530
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BA79_RS00335
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
pccA propionyl-CoA carboxylase, alpha subunit BA79_RS11005 BA79_RS18225
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BA79_RS18225 BA79_RS11005
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit BA79_RS11175 BA79_RS18205
pco propanyl-CoA oxidase BA79_RS04975 BA79_RS09030
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase BA79_RS13120
prpC 2-methylcitrate synthase BA79_RS13130 BA79_RS07510
prpD 2-methylcitrate dehydratase BA79_RS13125
prpF methylaconitate isomerase BA79_RS07240
RR42_RS28305 L-threonine:H+ symporter BA79_RS12105 BA79_RS16380
snatA L-threonine transporter snatA BA79_RS05450
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase BA79_RS13430
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase BA79_RS03205 BA79_RS04005
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) BA79_RS05245 BA79_RS12255

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