GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Halostagnicola larsenii XH-48

Best path

tdcC, 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 (40 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
tdcC L-threonine:H+ symporter TdcC
ltaE L-threonine aldolase HALLA_RS05870
adh acetaldehyde dehydrogenase (not acylating) HALLA_RS14430 HALLA_RS18050
acs acetyl-CoA synthetase, AMP-forming HALLA_RS04270 HALLA_RS04260
gcvP glycine cleavage system, P component (glycine decarboxylase) HALLA_RS10160 HALLA_RS10165
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) HALLA_RS10000 HALLA_RS18255
gcvH glycine cleavage system, H component (lipoyl protein) HALLA_RS10005
lpd dihydrolipoyl dehydrogenase HALLA_RS14380 HALLA_RS18420
Alternative steps:
ackA acetate kinase
acn (2R,3S)-2-methylcitrate dehydratase HALLA_RS10910
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase HALLA_RS14710 HALLA_RS14430
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) HALLA_RS14500 HALLA_RS00025
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) HALLA_RS14490 HALLA_RS00010
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) HALLA_RS14485 HALLA_RS00005
D-LDH D-lactate dehydrogenase HALLA_RS07515 HALLA_RS07995
dddA 3-hydroxypropionate dehydrogenase HALLA_RS18055 HALLA_RS18060
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components HALLA_RS14700
epi methylmalonyl-CoA epimerase HALLA_RS07465 HALLA_RS14475
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) HALLA_RS07515 HALLA_RS07995
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE)
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I HALLA_RS03715 HALLA_RS09270
gloB hydroxyacylglutathione hydrolase (glyoxalase II) HALLA_RS18985 HALLA_RS08665
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 HALLA_RS14450 HALLA_RS09800
iolA malonate semialdehyde dehydrogenase (CoA-acylating) HALLA_RS17055 HALLA_RS16180
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) HALLA_RS09750
L-LDH L-lactate dehydrogenase HALLA_RS09785 HALLA_RS13870
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit HALLA_RS11585
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component HALLA_RS07515 HALLA_RS07995
lctO L-lactate oxidase or 2-monooxygenase HALLA_RS09785
lldE L-lactate dehydrogenase, LldE subunit
lldF L-lactate dehydrogenase, LldF subunit HALLA_RS14360 HALLA_RS14700
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit
lutB L-lactate dehydrogenase, LutB subunit HALLA_RS14700 HALLA_RS14360
lutC L-lactate dehydrogenase, LutC subunit
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit HALLA_RS08365 HALLA_RS18720
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit HALLA_RS02715
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components HALLA_RS08365 HALLA_RS18720
pccA propionyl-CoA carboxylase, alpha subunit HALLA_RS05450 HALLA_RS19235
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit HALLA_RS05450 HALLA_RS19235
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit HALLA_RS03905 HALLA_RS05460
pco propanyl-CoA oxidase HALLA_RS17630 HALLA_RS09810
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase HALLA_RS11180
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase HALLA_RS09975 HALLA_RS08450
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 HALLA_RS11190 HALLA_RS14105
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase HALLA_RS18085 HALLA_RS18025
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) HALLA_RS07885 HALLA_RS17095

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