GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Klebsiella michiganensis M5al

Best path

sstT, ltaE, adh, ackA, pta, 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 (44 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
sstT L-threonine:Na+ symporter SstT BWI76_RS24715
ltaE L-threonine aldolase BWI76_RS09550 BWI76_RS21225
adh acetaldehyde dehydrogenase (not acylating) BWI76_RS21985 BWI76_RS15205
ackA acetate kinase BWI76_RS20235 BWI76_RS23200
pta phosphate acetyltransferase BWI76_RS20240 BWI76_RS20805
gcvP glycine cleavage system, P component (glycine decarboxylase) BWI76_RS23870
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) BWI76_RS23880
gcvH glycine cleavage system, H component (lipoyl protein) BWI76_RS23875
lpd dihydrolipoyl dehydrogenase BWI76_RS04890 BWI76_RS14145
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase BWI76_RS04910 BWI76_RS11940
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BWI76_RS11940
acs acetyl-CoA synthetase, AMP-forming BWI76_RS02095 BWI76_RS17800
ald-dh-CoA acetaldehyde dehydrogenase, acylating BWI76_RS17250 BWI76_RS20790
aldA lactaldehyde dehydrogenase BWI76_RS13210 BWI76_RS10695
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) BWI76_RS26350 BWI76_RS26365
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BWI76_RS26345 BWI76_RS07280
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) BWI76_RS26340 BWI76_RS07275
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BWI76_RS26335 BWI76_RS05980
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BWI76_RS26330 BWI76_RS05975
D-LDH D-lactate dehydrogenase BWI76_RS12790 BWI76_RS26540
dddA 3-hydroxypropionate dehydrogenase BWI76_RS07610
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD)
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE)
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I BWI76_RS16480
gloB hydroxyacylglutathione hydrolase (glyoxalase II) BWI76_RS19670 BWI76_RS09865
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 BWI76_RS13115 BWI76_RS13120
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BWI76_RS03070 BWI76_RS02840
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) BWI76_RS27255 BWI76_RS08765
L-LDH L-lactate dehydrogenase BWI76_RS15220 BWI76_RS16775
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component
lctO L-lactate oxidase or 2-monooxygenase
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 BWI76_RS23935
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BWI76_RS23935
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components BWI76_RS23935
pccA propionyl-CoA carboxylase, alpha subunit BWI76_RS25540 BWI76_RS13985
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BWI76_RS25540 BWI76_RS13985
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase BWI76_RS01665
prpC 2-methylcitrate synthase BWI76_RS08385 BWI76_RS19140
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase BWI76_RS04370 BWI76_RS14180
RR42_RS28305 L-threonine:H+ symporter BWI76_RS01140 BWI76_RS02700
serP1 L-threonine uptake transporter SerP1 BWI76_RS02700 BWI76_RS07360
snatA L-threonine transporter snatA BWI76_RS17245
tdcB L-threonine dehydratase BWI76_RS00980
tdcC L-threonine:H+ symporter TdcC BWI76_RS14475 BWI76_RS22875
tdcE 2-ketobutyrate formate-lyase BWI76_RS09735
tdh L-threonine 3-dehydrogenase BWI76_RS27250 BWI76_RS00645
tynA aminoacetone oxidase BWI76_RS13080
yvgN methylglyoxal reductase (NADPH-dependent) BWI76_RS24305 BWI76_RS05410

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, 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