GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Pseudomonas fluorescens GW456-L13

Best path

braC, braD, braE, braF, braG, 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 (52 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) PfGW456L13_4606 PfGW456L13_124
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) PfGW456L13_4608 PfGW456L13_123
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) PfGW456L13_4609 PfGW456L13_122
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) PfGW456L13_4610 PfGW456L13_84
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) PfGW456L13_4611 PfGW456L13_120
ltaE L-threonine aldolase PfGW456L13_1114 PfGW456L13_2685
adh acetaldehyde dehydrogenase (not acylating) PfGW456L13_3517 PfGW456L13_1342
ackA acetate kinase PfGW456L13_4820
pta phosphate acetyltransferase PfGW456L13_4990
gcvP glycine cleavage system, P component (glycine decarboxylase) PfGW456L13_1868 PfGW456L13_904
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) PfGW456L13_1866 PfGW456L13_902
gcvH glycine cleavage system, H component (lipoyl protein) PfGW456L13_903 PfGW456L13_1869
lpd dihydrolipoyl dehydrogenase PfGW456L13_3543 PfGW456L13_4267
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase PfGW456L13_4116 PfGW456L13_3378
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) PfGW456L13_4116 PfGW456L13_4052
acs acetyl-CoA synthetase, AMP-forming PfGW456L13_1963 PfGW456L13_1517
ald-dh-CoA acetaldehyde dehydrogenase, acylating PfGW456L13_2505
aldA lactaldehyde dehydrogenase PfGW456L13_3932 PfGW456L13_2360
D-LDH D-lactate dehydrogenase PfGW456L13_5118 PfGW456L13_2028
dddA 3-hydroxypropionate dehydrogenase PfGW456L13_3561 PfGW456L13_1082
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components PfGW456L13_5116
epi methylmalonyl-CoA epimerase PfGW456L13_3114 PfGW456L13_1425
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 PfGW456L13_2929
gloB hydroxyacylglutathione hydrolase (glyoxalase II) PfGW456L13_3340 PfGW456L13_1623
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 PfGW456L13_3427 PfGW456L13_2984
iolA malonate semialdehyde dehydrogenase (CoA-acylating) PfGW456L13_2 PfGW456L13_5146
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) PfGW456L13_1148
L-LDH L-lactate dehydrogenase PfGW456L13_2974
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit PfGW456L13_2137
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit PfGW456L13_5115
lldF L-lactate dehydrogenase, LldF subunit PfGW456L13_5116
lldG L-lactate dehydrogenase, LldG subunit PfGW456L13_5117
lutA L-lactate dehydrogenase, LutA subunit PfGW456L13_5115
lutB L-lactate dehydrogenase, LutB subunit PfGW456L13_5116
lutC L-lactate dehydrogenase, LutC subunit PfGW456L13_5117
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 PfGW456L13_2284 PfGW456L13_2588
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit PfGW456L13_728 PfGW456L13_52
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit PfGW456L13_2590 PfGW456L13_2287
pco propanyl-CoA oxidase PfGW456L13_554 PfGW456L13_2983
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase PfGW456L13_4118 PfGW456L13_2633
prpC 2-methylcitrate synthase PfGW456L13_4117 PfGW456L13_4274
prpD 2-methylcitrate dehydratase PfGW456L13_4114
prpF methylaconitate isomerase PfGW456L13_4115
RR42_RS28305 L-threonine:H+ symporter PfGW456L13_4790 PfGW456L13_318
serP1 L-threonine uptake transporter SerP1 PfGW456L13_4291 PfGW456L13_4400
snatA L-threonine transporter snatA PfGW456L13_60
sstT L-threonine:Na+ symporter SstT PfGW456L13_2541
tdcB L-threonine dehydratase PfGW456L13_949 PfGW456L13_3031
tdcC L-threonine:H+ symporter TdcC PfGW456L13_3379
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase PfGW456L13_3512 PfGW456L13_1214
tynA aminoacetone oxidase PfGW456L13_2439
yvgN methylglyoxal reductase (NADPH-dependent) PfGW456L13_2401 PfGW456L13_1417

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