GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Paraburkholderia bryophila 376MFSha3.1

Best path

braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd

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 (57 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) H281DRAFT_02161 H281DRAFT_06096
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) H281DRAFT_04062 H281DRAFT_06397
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) H281DRAFT_04061 H281DRAFT_04452
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) H281DRAFT_02375 H281DRAFT_04060
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) H281DRAFT_06394 H281DRAFT_04059
ltaE L-threonine aldolase H281DRAFT_04448 H281DRAFT_04726
adh acetaldehyde dehydrogenase (not acylating) H281DRAFT_01117 H281DRAFT_02299
acs acetyl-CoA synthetase, AMP-forming H281DRAFT_04953 H281DRAFT_05523
gcvP glycine cleavage system, P component (glycine decarboxylase) H281DRAFT_02409
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) H281DRAFT_02411 H281DRAFT_06542
gcvH glycine cleavage system, H component (lipoyl protein) H281DRAFT_02410
lpd dihydrolipoyl dehydrogenase H281DRAFT_00468 H281DRAFT_05115
Alternative steps:
ackA acetate kinase H281DRAFT_00303 H281DRAFT_01409
acn (2R,3S)-2-methylcitrate dehydratase H281DRAFT_02981 H281DRAFT_06606
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) H281DRAFT_02981 H281DRAFT_06210
ald-dh-CoA acetaldehyde dehydrogenase, acylating H281DRAFT_01665
aldA lactaldehyde dehydrogenase H281DRAFT_00972 H281DRAFT_03016
D-LDH D-lactate dehydrogenase H281DRAFT_04684 H281DRAFT_04746
dddA 3-hydroxypropionate dehydrogenase H281DRAFT_02374 H281DRAFT_00975
DVU3032 L-lactate dehydrogenase, LutC-like component H281DRAFT_04331
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components H281DRAFT_00473 H281DRAFT_02904
epi methylmalonyl-CoA epimerase H281DRAFT_04643
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) H281DRAFT_04683 H281DRAFT_04684
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) H281DRAFT_04682 H281DRAFT_04684
glcF D-lactate dehydrogenase, FeS subunit GlcF H281DRAFT_04681
gloA glyoxylase I H281DRAFT_04643
gloB hydroxyacylglutathione hydrolase (glyoxalase II) H281DRAFT_04399 H281DRAFT_02154
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 H281DRAFT_05725 H281DRAFT_02514
iolA malonate semialdehyde dehydrogenase (CoA-acylating) H281DRAFT_02373 H281DRAFT_03264
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) H281DRAFT_03587 H281DRAFT_02095
L-LDH L-lactate dehydrogenase H281DRAFT_05436 H281DRAFT_02928
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit H281DRAFT_04285 H281DRAFT_03367
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component H281DRAFT_04684 H281DRAFT_04480
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit H281DRAFT_02905 H281DRAFT_00472
lldF L-lactate dehydrogenase, LldF subunit H281DRAFT_02904 H281DRAFT_00473
lldG L-lactate dehydrogenase, LldG subunit H281DRAFT_02903
lutA L-lactate dehydrogenase, LutA subunit H281DRAFT_00472 H281DRAFT_02905
lutB L-lactate dehydrogenase, LutB subunit H281DRAFT_00473 H281DRAFT_02904
lutC L-lactate dehydrogenase, LutC subunit H281DRAFT_04331
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit H281DRAFT_01038 H281DRAFT_02110
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit H281DRAFT_01038 H281DRAFT_02076
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components H281DRAFT_02110 H281DRAFT_01038
pccA propionyl-CoA carboxylase, alpha subunit H281DRAFT_01343 H281DRAFT_06283
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit H281DRAFT_06283 H281DRAFT_01343
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit H281DRAFT_01345
pco propanyl-CoA oxidase H281DRAFT_05174 H281DRAFT_04737
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase H281DRAFT_00580 H281DRAFT_02542
prpC 2-methylcitrate synthase H281DRAFT_06634 H281DRAFT_06327
prpD 2-methylcitrate dehydratase H281DRAFT_06607
prpF methylaconitate isomerase H281DRAFT_02982 H281DRAFT_01376
pta phosphate acetyltransferase H281DRAFT_01410 H281DRAFT_06308
RR42_RS28305 L-threonine:H+ symporter H281DRAFT_04042 H281DRAFT_01668
serP1 L-threonine uptake transporter SerP1 H281DRAFT_04042
snatA L-threonine transporter snatA H281DRAFT_05656 H281DRAFT_06268
sstT L-threonine:Na+ symporter SstT
tdcB* L-threonine dehydratase H281DRAFT_01887 with H281DRAFT_04606 H281DRAFT_05256
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase H281DRAFT_03586 H281DRAFT_03803
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) H281DRAFT_00358 H281DRAFT_04096

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