GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Rhizobium etli CFN 42

Best path

braC, braD, braE, braF, braG, 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 (49 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) RHE_RS16985 RHE_RS15820
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) RHE_RS17010 RHE_RS25480
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) RHE_RS17005
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) RHE_RS17000 RHE_RS25470
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) RHE_RS16995 RHE_RS25475
ltaE L-threonine aldolase RHE_RS18230 RHE_RS07695
adh acetaldehyde dehydrogenase (not acylating) RHE_RS19035 RHE_RS20725
acs acetyl-CoA synthetase, AMP-forming RHE_RS21025 RHE_RS21035
gcvP glycine cleavage system, P component (glycine decarboxylase) RHE_RS11470
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) RHE_RS11460 RHE_RS26195
gcvH glycine cleavage system, H component (lipoyl protein) RHE_RS11465
lpd dihydrolipoyl dehydrogenase RHE_RS23215 RHE_RS09895
Alternative steps:
ackA acetate kinase RHE_RS17585
acn (2R,3S)-2-methylcitrate dehydratase RHE_RS20170
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) RHE_RS20170
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase RHE_RS25545 RHE_RS16180
D-LDH D-lactate dehydrogenase RHE_RS14345 RHE_RS04520
dddA 3-hydroxypropionate dehydrogenase RHE_RS25490 RHE_RS22360
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase RHE_RS08290
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) RHE_RS04070 RHE_RS14345
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) RHE_RS04075
glcF D-lactate dehydrogenase, FeS subunit GlcF RHE_RS04080
gloA glyoxylase I RHE_RS01750 RHE_RS09630
gloB hydroxyacylglutathione hydrolase (glyoxalase II) RHE_RS15415 RHE_RS19490
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 RHE_RS01800 RHE_RS08795
iolA malonate semialdehyde dehydrogenase (CoA-acylating) RHE_RS03695 RHE_RS16180
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) RHE_RS15100 RHE_RS28965
L-LDH L-lactate dehydrogenase RHE_RS16015 RHE_RS19905
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit RHE_RS30500
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit RHE_RS30505 RHE_RS28535
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component RHE_RS04070 RHE_RS14345
lctO L-lactate oxidase or 2-monooxygenase RHE_RS16015 RHE_RS02155
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 RHE_RS22800
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit RHE_RS22800
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components RHE_RS22800
pccA propionyl-CoA carboxylase, alpha subunit RHE_RS11385 RHE_RS23155
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit RHE_RS11385 RHE_RS09550
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit RHE_RS23155
pccB propionyl-CoA carboxylase, beta subunit RHE_RS11415 RHE_RS23160
pco propanyl-CoA oxidase RHE_RS25445
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase RHE_RS03605
prpC 2-methylcitrate synthase RHE_RS09835 RHE_RS11160
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase RHE_RS01970 RHE_RS12030
RR42_RS28305 L-threonine:H+ symporter RHE_RS25845
serP1 L-threonine uptake transporter SerP1 RHE_RS25845
snatA L-threonine transporter snatA RHE_RS10800
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase RHE_RS08995 RHE_RS20915
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase RHE_RS15095 RHE_RS15165
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) RHE_RS20275 RHE_RS14260

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