GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Shewanella amazonensis SB2B

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 (41 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
sstT L-threonine:Na+ symporter SstT Sama_2200
ltaE L-threonine aldolase Sama_2462 Sama_1014
adh acetaldehyde dehydrogenase (not acylating) Sama_3435 Sama_1693
ackA acetate kinase Sama_1495 Sama_2807
pta phosphate acetyltransferase Sama_1494
gcvP glycine cleavage system, P component (glycine decarboxylase) Sama_2719
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) Sama_2721
gcvH glycine cleavage system, H component (lipoyl protein) Sama_2720
lpd dihydrolipoyl dehydrogenase Sama_0377 Sama_3543
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase Sama_3296 Sama_0382
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Sama_3296
acs acetyl-CoA synthetase, AMP-forming Sama_2079 Sama_1364
ald-dh-CoA acetaldehyde dehydrogenase, acylating Sama_1693
aldA lactaldehyde dehydrogenase Sama_2648 Sama_3435
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB)
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD)
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC)
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) Sama_3087 Sama_3588
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) Sama_3087 Sama_3588
D-LDH D-lactate dehydrogenase Sama_2440 Sama_0612
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components Sama_2442
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 Sama_1837
gloB hydroxyacylglutathione hydrolase (glyoxalase II) Sama_1884 Sama_2142
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 Sama_1378 Sama_2167
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Sama_2650 Sama_1376
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) Sama_0098 Sama_1439
L-LDH L-lactate dehydrogenase
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit Sama_1170
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit Sama_2441
lldF L-lactate dehydrogenase, LldF subunit Sama_2442
lldG L-lactate dehydrogenase, LldG subunit Sama_2443
lutA L-lactate dehydrogenase, LutA subunit Sama_2441
lutB L-lactate dehydrogenase, LutB subunit Sama_2442
lutC L-lactate dehydrogenase, LutC subunit
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
pccA propionyl-CoA carboxylase, alpha subunit Sama_1359 Sama_3196
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Sama_1359 Sama_3196
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit Sama_1361
pco propanyl-CoA oxidase Sama_2796
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase Sama_2380 Sama_3294
prpC 2-methylcitrate synthase Sama_3295 Sama_1422
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase Sama_3297
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA Sama_1694
tdcB L-threonine dehydratase Sama_3278
tdcC L-threonine:H+ symporter TdcC Sama_2772
tdcE 2-ketobutyrate formate-lyase Sama_1498
tdh L-threonine 3-dehydrogenase Sama_0097 Sama_2455
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