GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Shewanella sp. ANA-3

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 (42 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
sstT L-threonine:Na+ symporter SstT Shewana3_1426
ltaE L-threonine aldolase Shewana3_1208 Shewana3_1094
adh acetaldehyde dehydrogenase (not acylating) Shewana3_0250 Shewana3_1788
ackA acetate kinase Shewana3_1552 Shewana3_3197
pta phosphate acetyltransferase Shewana3_1551
gcvP glycine cleavage system, P component (glycine decarboxylase) Shewana3_3499
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) Shewana3_3501
gcvH glycine cleavage system, H component (lipoyl protein) Shewana3_3500
lpd dihydrolipoyl dehydrogenase Shewana3_0428 Shewana3_4345
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase Shewana3_3827 Shewana3_0433
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Shewana3_3827
acs acetyl-CoA synthetase, AMP-forming Shewana3_2523 Shewana3_1675
ald-dh-CoA acetaldehyde dehydrogenase, acylating Shewana3_1788
aldA lactaldehyde dehydrogenase Shewana3_3105 Shewana3_0250
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) Shewana3_0673 Shewana3_1620
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) Shewana3_0673 Shewana3_0880
D-LDH D-lactate dehydrogenase Shewana3_2905 Shewana3_3319
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component Shewana3_2908
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components Shewana3_2907
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 Shewana3_2232 Shewana3_2721
gloB hydroxyacylglutathione hydrolase (glyoxalase II) Shewana3_2369 Shewana3_1493
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 Shewana3_2768 Shewana3_1461
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Shewana3_3107 Shewana3_2770
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) Shewana3_4104 Shewana3_2518
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 Shewana3_1406
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit Shewana3_2906
lldF L-lactate dehydrogenase, LldF subunit Shewana3_2907
lldG L-lactate dehydrogenase, LldG subunit Shewana3_2908
lutA L-lactate dehydrogenase, LutA subunit Shewana3_2906
lutB L-lactate dehydrogenase, LutB subunit Shewana3_2907
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 Shewana3_1669 Shewana3_3438
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Shewana3_1669 Shewana3_3438
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit Shewana3_1671
pco propanyl-CoA oxidase
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase Shewana3_3825 Shewana3_2942
prpC 2-methylcitrate synthase Shewana3_3826 Shewana3_1705
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase Shewana3_3828
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA Shewana3_1789
tdcB L-threonine dehydratase Shewana3_0359
tdcC L-threonine:H+ symporter TdcC Shewana3_3365
tdcE 2-ketobutyrate formate-lyase Shewana3_1555
tdh L-threonine 3-dehydrogenase Shewana3_4105 Shewana3_2938
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) Shewana3_3599

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