GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Duganella sacchari Sac-22

Best path

RR42_RS28305, 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
RR42_RS28305 L-threonine:H+ symporter BUA36_RS06065 BUA36_RS24700
ltaE L-threonine aldolase BUA36_RS01325 BUA36_RS16260
adh acetaldehyde dehydrogenase (not acylating) BUA36_RS13005 BUA36_RS02795
acs acetyl-CoA synthetase, AMP-forming BUA36_RS11840 BUA36_RS28615
gcvP glycine cleavage system, P component (glycine decarboxylase) BUA36_RS11125 BUA36_RS17885
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) BUA36_RS11135
gcvH glycine cleavage system, H component (lipoyl protein) BUA36_RS11130
lpd dihydrolipoyl dehydrogenase BUA36_RS22760 BUA36_RS01790
Alternative steps:
ackA acetate kinase BUA36_RS04825 BUA36_RS05735
acn (2R,3S)-2-methylcitrate dehydratase BUA36_RS28625 BUA36_RS06375
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BUA36_RS28625 BUA36_RS01905
ald-dh-CoA acetaldehyde dehydrogenase, acylating BUA36_RS24730
aldA lactaldehyde dehydrogenase BUA36_RS15000 BUA36_RS13005
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) BUA36_RS04095 BUA36_RS27625
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BUA36_RS22500 BUA36_RS26910
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) BUA36_RS22495 BUA36_RS26915
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BUA36_RS26915 BUA36_RS22490
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BUA36_RS26920 BUA36_RS22485
D-LDH D-lactate dehydrogenase BUA36_RS09525 BUA36_RS27965
dddA 3-hydroxypropionate dehydrogenase BUA36_RS07265
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase BUA36_RS08655
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) BUA36_RS13895 BUA36_RS27965
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) BUA36_RS13890
glcF D-lactate dehydrogenase, FeS subunit GlcF BUA36_RS13885
gloA glyoxylase I BUA36_RS14815
gloB hydroxyacylglutathione hydrolase (glyoxalase II) BUA36_RS28065 BUA36_RS10090
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 BUA36_RS19960 BUA36_RS12660
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BUA36_RS12915 BUA36_RS12670
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) BUA36_RS04305 BUA36_RS15370
L-LDH L-lactate dehydrogenase BUA36_RS24315
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit BUA36_RS21035
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component BUA36_RS27965
lctO L-lactate oxidase or 2-monooxygenase BUA36_RS24315
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 BUA36_RS08685 BUA36_RS23520
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BUA36_RS08685
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components BUA36_RS08685 BUA36_RS23520
pccA propionyl-CoA carboxylase, alpha subunit BUA36_RS07760 BUA36_RS28720
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BUA36_RS28720 BUA36_RS07760
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit BUA36_RS07795
pco propanyl-CoA oxidase BUA36_RS15230
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase BUA36_RS09240 BUA36_RS28635
prpC 2-methylcitrate synthase BUA36_RS28630 BUA36_RS01855
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase BUA36_RS28620
pta phosphate acetyltransferase BUA36_RS04820 BUA36_RS15335
serP1 L-threonine uptake transporter SerP1 BUA36_RS06065 BUA36_RS24700
snatA L-threonine transporter snatA
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase BUA36_RS18985 BUA36_RS25770
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase BUA36_RS04310 BUA36_RS07230
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) BUA36_RS30010 BUA36_RS26930

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.

Links

Downloads

Related tools

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