GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Herbaspirillum seropedicae SmR1

Best path

braC, braD, braE, braF, braG, tdcB, tdcE, prpC, acnD, prpF, acn, prpB

Also see fitness data for the top candidates

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 (42 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) HSERO_RS08270 HSERO_RS17350
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) HSERO_RS08275 HSERO_RS05960
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) HSERO_RS08280 HSERO_RS05965
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) HSERO_RS08285 HSERO_RS05970
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) HSERO_RS08290 HSERO_RS14710
tdcB L-threonine dehydratase HSERO_RS19510 HSERO_RS00265
tdcE 2-ketobutyrate formate-lyase
prpC 2-methylcitrate synthase HSERO_RS15655 HSERO_RS14890
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) HSERO_RS11425 HSERO_RS14940
prpF methylaconitate isomerase HSERO_RS11420 HSERO_RS07335
acn (2R,3S)-2-methylcitrate dehydratase HSERO_RS11425 HSERO_RS14940
prpB 2-methylisocitrate lyase HSERO_RS10565 HSERO_RS15660
Alternative steps:
ackA acetate kinase HSERO_RS01305 HSERO_RS11090
acs acetyl-CoA synthetase, AMP-forming HSERO_RS07770 HSERO_RS23535
adh acetaldehyde dehydrogenase (not acylating) HSERO_RS05115 HSERO_RS09465
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase HSERO_RS22235 HSERO_RS09465
D-LDH D-lactate dehydrogenase HSERO_RS19115 HSERO_RS12550
dddA 3-hydroxypropionate dehydrogenase HSERO_RS24000 HSERO_RS23855
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase
gcvH glycine cleavage system, H component (lipoyl protein) HSERO_RS07915
gcvP glycine cleavage system, P component (glycine decarboxylase)
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase)
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) HSERO_RS19105 HSERO_RS19115
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) HSERO_RS19100
glcF D-lactate dehydrogenase, FeS subunit GlcF HSERO_RS19095
gloA glyoxylase I HSERO_RS03550 HSERO_RS14410
gloB hydroxyacylglutathione hydrolase (glyoxalase II) HSERO_RS17120 HSERO_RS13610
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 HSERO_RS19405 HSERO_RS12745
iolA malonate semialdehyde dehydrogenase (CoA-acylating) HSERO_RS24005 HSERO_RS23245
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) HSERO_RS12245
L-LDH L-lactate dehydrogenase HSERO_RS12985 HSERO_RS01205
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit HSERO_RS14220
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit HSERO_RS14225 HSERO_RS07560
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component HSERO_RS19115 HSERO_RS16560
lctO L-lactate oxidase or 2-monooxygenase HSERO_RS01205 HSERO_RS12985
lldE L-lactate dehydrogenase, LldE subunit
lldF L-lactate dehydrogenase, LldF subunit
lldG L-lactate dehydrogenase, LldG subunit
lpd dihydrolipoyl dehydrogenase HSERO_RS07315 HSERO_RS14875
ltaE L-threonine aldolase HSERO_RS06140
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
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit HSERO_RS21740
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
pccA propionyl-CoA carboxylase, alpha subunit HSERO_RS23460 HSERO_RS01925
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit HSERO_RS01925 HSERO_RS20550
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit HSERO_RS23455
pco propanyl-CoA oxidase HSERO_RS23440
phtA L-threonine uptake permease PhtA
prpD 2-methylcitrate dehydratase
pta phosphate acetyltransferase HSERO_RS12030 HSERO_RS01300
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA
sstT L-threonine:Na+ symporter SstT
tdcC L-threonine:H+ symporter TdcC
tdh L-threonine 3-dehydrogenase HSERO_RS00730 HSERO_RS05485
tynA aminoacetone oxidase HSERO_RS17625
yvgN methylglyoxal reductase (NADPH-dependent) HSERO_RS01485

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