GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Magnetospirillum magneticum AMB-1

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 (45 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) AMB_RS15010
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) AMB_RS09135 AMB_RS08455
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) AMB_RS09130 AMB_RS08460
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) AMB_RS09125 AMB_RS08465
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) AMB_RS09120 AMB_RS10230
ltaE L-threonine aldolase AMB_RS11815
adh acetaldehyde dehydrogenase (not acylating) AMB_RS18195 AMB_RS06710
acs acetyl-CoA synthetase, AMP-forming AMB_RS21140 AMB_RS11645
gcvP glycine cleavage system, P component (glycine decarboxylase) AMB_RS03940 AMB_RS03935
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) AMB_RS03925
gcvH glycine cleavage system, H component (lipoyl protein) AMB_RS03930
lpd dihydrolipoyl dehydrogenase AMB_RS11730 AMB_RS20050
Alternative steps:
ackA acetate kinase AMB_RS12860
acn (2R,3S)-2-methylcitrate dehydratase AMB_RS22255 AMB_RS18485
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) AMB_RS18485
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase AMB_RS01425 AMB_RS06710
D-LDH D-lactate dehydrogenase AMB_RS20900 AMB_RS15030
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component AMB_RS20895
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components AMB_RS20890
epi methylmalonyl-CoA epimerase AMB_RS12960
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) AMB_RS15030 AMB_RS18795
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE)
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I AMB_RS12480
gloB hydroxyacylglutathione hydrolase (glyoxalase II) AMB_RS21210 AMB_RS06135
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 AMB_RS03265 AMB_RS13040
iolA malonate semialdehyde dehydrogenase (CoA-acylating) AMB_RS04115 AMB_RS06710
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) AMB_RS08510 AMB_RS13875
L-LDH L-lactate dehydrogenase AMB_RS20025 AMB_RS22540
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit AMB_RS16305 AMB_RS19755
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component AMB_RS15030 AMB_RS18795
lctO L-lactate oxidase or 2-monooxygenase AMB_RS22540
lldE L-lactate dehydrogenase, LldE subunit AMB_RS20885
lldF L-lactate dehydrogenase, LldF subunit AMB_RS20890
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit AMB_RS20885
lutB L-lactate dehydrogenase, LutB subunit AMB_RS20890
lutC L-lactate dehydrogenase, LutC subunit AMB_RS20895
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit AMB_RS01570
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit AMB_RS01570
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components AMB_RS01570
pccA propionyl-CoA carboxylase, alpha subunit AMB_RS21445 AMB_RS03465
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit AMB_RS21445 AMB_RS13620
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit AMB_RS21450 AMB_RS03475
pco propanyl-CoA oxidase AMB_RS16315 AMB_RS03480
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase AMB_RS14105
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase AMB_RS01270
pta phosphate acetyltransferase AMB_RS12865 AMB_RS01465
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
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase
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 Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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