GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Alkalihalobacterium alkalinitrilicum DSM 22532

Best path

tdcC, 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 (49 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
tdcC L-threonine:H+ symporter TdcC
ltaE L-threonine aldolase BK574_RS06730 BK574_RS19235
adh acetaldehyde dehydrogenase (not acylating) BK574_RS07475 BK574_RS03925
ackA acetate kinase BK574_RS22225 BK574_RS01080
pta phosphate acetyltransferase BK574_RS19005 BK574_RS11510
gcvP glycine cleavage system, P component (glycine decarboxylase) BK574_RS11740 BK574_RS11745
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) BK574_RS11750
gcvH glycine cleavage system, H component (lipoyl protein) BK574_RS20890
lpd dihydrolipoyl dehydrogenase BK574_RS25485 BK574_RS11495
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase BK574_RS00360
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BK574_RS00360
acs acetyl-CoA synthetase, AMP-forming BK574_RS22105 BK574_RS14010
ald-dh-CoA acetaldehyde dehydrogenase, acylating BK574_RS16280
aldA lactaldehyde dehydrogenase BK574_RS07735 BK574_RS14530
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) BK574_RS14065 BK574_RS08070
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) BK574_RS14060
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BK574_RS08060 BK574_RS14075
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BK574_RS08055 BK574_RS14050
D-LDH D-lactate dehydrogenase BK574_RS17260 BK574_RS12965
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components BK574_RS13515
epi methylmalonyl-CoA epimerase BK574_RS11400
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) BK574_RS12965 BK574_RS17260
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) BK574_RS12965 BK574_RS17260
glcF D-lactate dehydrogenase, FeS subunit GlcF BK574_RS12960
gloA glyoxylase I BK574_RS05690 BK574_RS01160
gloB hydroxyacylglutathione hydrolase (glyoxalase II) BK574_RS11785 BK574_RS06450
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 BK574_RS03985 BK574_RS22580
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BK574_RS05715 BK574_RS14950
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase)
L-LDH L-lactate dehydrogenase BK574_RS12390 BK574_RS22390
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit BK574_RS05855
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit BK574_RS05850 BK574_RS04000
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component BK574_RS12965 BK574_RS17260
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit BK574_RS13520
lldF L-lactate dehydrogenase, LldF subunit BK574_RS13515
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit BK574_RS13520 BK574_RS12960
lutB L-lactate dehydrogenase, LutB subunit BK574_RS13515
lutC L-lactate dehydrogenase, LutC subunit BK574_RS13510
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit BK574_RS23320 BK574_RS19110
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BK574_RS23320
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components BK574_RS23320 BK574_RS19110
pccA propionyl-CoA carboxylase, alpha subunit BK574_RS23295 BK574_RS11610
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BK574_RS23295 BK574_RS14035
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit BK574_RS23310 BK574_RS08385
pco propanyl-CoA oxidase BK574_RS19095 BK574_RS21840
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase BK574_RS25365 BK574_RS06655
prpC 2-methylcitrate synthase BK574_RS22380
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
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 BK574_RS09650
tdcE 2-ketobutyrate formate-lyase BK574_RS08720
tdh L-threonine 3-dehydrogenase BK574_RS05080 BK574_RS08030
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) BK574_RS01040 BK574_RS16455

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 Apr 09 2024. 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