GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Sedimenticola selenatireducens DSM 17993

Best path

braC, braD, braE, braF, braG, 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 (51 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) A3GO_RS0114190 A3GO_RS0114160
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) A3GO_RS0114215 A3GO_RS0114165
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) A3GO_RS0114210 A3GO_RS0114170
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) A3GO_RS0114175 A3GO_RS0114425
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) A3GO_RS0114200 A3GO_RS0114180
ltaE L-threonine aldolase A3GO_RS0100345
adh acetaldehyde dehydrogenase (not acylating) A3GO_RS0105360 A3GO_RS0115130
ackA acetate kinase A3GO_RS0105460
pta phosphate acetyltransferase A3GO_RS0105465 A3GO_RS0103715
gcvP glycine cleavage system, P component (glycine decarboxylase) A3GO_RS0118780 A3GO_RS24555
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) A3GO_RS0118765
gcvH glycine cleavage system, H component (lipoyl protein) A3GO_RS0118770 A3GO_RS0108180
lpd dihydrolipoyl dehydrogenase A3GO_RS0106805 A3GO_RS0102625
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase A3GO_RS0104620 A3GO_RS0104540
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) A3GO_RS0104540
acs acetyl-CoA synthetase, AMP-forming A3GO_RS0111360 A3GO_RS0103965
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase A3GO_RS0115130 A3GO_RS0114560
D-LDH D-lactate dehydrogenase A3GO_RS0106070 A3GO_RS0103695
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component A3GO_RS0106035
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components A3GO_RS0106040
epi methylmalonyl-CoA epimerase A3GO_RS0103990 A3GO_RS0105820
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) A3GO_RS0119890 A3GO_RS0102525
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) A3GO_RS0119895
glcF D-lactate dehydrogenase, FeS subunit GlcF A3GO_RS0119900 A3GO_RS0118680
gloA glyoxylase I A3GO_RS0119755
gloB hydroxyacylglutathione hydrolase (glyoxalase II) A3GO_RS0101820 A3GO_RS0114765
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 A3GO_RS0114405 A3GO_RS0115400
iolA malonate semialdehyde dehydrogenase (CoA-acylating) A3GO_RS0108930 A3GO_RS0120300
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) A3GO_RS0114490 A3GO_RS0108800
L-LDH L-lactate dehydrogenase A3GO_RS0103720
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit A3GO_RS0114810
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component A3GO_RS0119890 A3GO_RS0102525
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit A3GO_RS0106045
lldF L-lactate dehydrogenase, LldF subunit A3GO_RS0106040
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit A3GO_RS0106045
lutB L-lactate dehydrogenase, LutB subunit A3GO_RS0106040
lutC L-lactate dehydrogenase, LutC subunit A3GO_RS0106035
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit A3GO_RS0103970 A3GO_RS0114395
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit A3GO_RS0103970
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components A3GO_RS0103970 A3GO_RS0114395
pccA propionyl-CoA carboxylase, alpha subunit A3GO_RS0103980 A3GO_RS0114350
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit A3GO_RS0103980 A3GO_RS0119025
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit A3GO_RS0103975 A3GO_RS0114360
pco propanyl-CoA oxidase A3GO_RS0115815 A3GO_RS0114380
phtA L-threonine uptake permease PhtA A3GO_RS0120380
prpB 2-methylisocitrate lyase A3GO_RS0109300 A3GO_RS0103960
prpC 2-methylcitrate synthase A3GO_RS0103745 A3GO_RS0101980
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase A3GO_RS0100145
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA A3GO_RS0114825
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase A3GO_RS0118715 A3GO_RS0117900
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase A3GO_RS0114485
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent)

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