GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Pseudomonas fluorescens FW300-N2E2

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 (49 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) Pf6N2E2_2921 Pf6N2E2_3580
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) Pf6N2E2_2923 Pf6N2E2_3579
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) Pf6N2E2_2924 Pf6N2E2_3578
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) Pf6N2E2_2925 Pf6N2E2_1433
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) Pf6N2E2_2926 Pf6N2E2_3576
ltaE L-threonine aldolase Pf6N2E2_4715 Pf6N2E2_5082
adh acetaldehyde dehydrogenase (not acylating) Pf6N2E2_1381 Pf6N2E2_4979
ackA acetate kinase Pf6N2E2_5444
pta phosphate acetyltransferase Pf6N2E2_5260
gcvP glycine cleavage system, P component (glycine decarboxylase) Pf6N2E2_5558
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) Pf6N2E2_5556 Pf6N2E2_4485
gcvH glycine cleavage system, H component (lipoyl protein) Pf6N2E2_4486 Pf6N2E2_5559
lpd dihydrolipoyl dehydrogenase Pf6N2E2_478 Pf6N2E2_5857
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase Pf6N2E2_6063 Pf6N2E2_564
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Pf6N2E2_6063 Pf6N2E2_2301
acs acetyl-CoA synthetase, AMP-forming Pf6N2E2_5659 Pf6N2E2_5149
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase Pf6N2E2_1102 Pf6N2E2_1751
D-LDH D-lactate dehydrogenase Pf6N2E2_3385 Pf6N2E2_5719
dddA 3-hydroxypropionate dehydrogenase Pf6N2E2_2094 Pf6N2E2_4677
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) Pf6N2E2_137 Pf6N2E2_1497
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) Pf6N2E2_136
glcF D-lactate dehydrogenase, FeS subunit GlcF Pf6N2E2_135
gloA glyoxylase I Pf6N2E2_449
gloB hydroxyacylglutathione hydrolase (glyoxalase II) Pf6N2E2_587 Pf6N2E2_3043
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 Pf6N2E2_1147 Pf6N2E2_1934
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Pf6N2E2_515 Pf6N2E2_3462
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) Pf6N2E2_4761
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 Pf6N2E2_5984
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component Pf6N2E2_137 Pf6N2E2_1497
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit Pf6N2E2_3381
lldF L-lactate dehydrogenase, LldF subunit
lldG L-lactate dehydrogenase, LldG subunit Pf6N2E2_3384
lutA L-lactate dehydrogenase, LutA subunit Pf6N2E2_3381
lutB* L-lactate dehydrogenase, LutB subunit Pf6N2E2_3383 with Pf6N2E2_3382
lutC L-lactate dehydrogenase, LutC subunit Pf6N2E2_3384
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 Pf6N2E2_2194 Pf6N2E2_2411
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Pf6N2E2_4278 Pf6N2E2_3512
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit Pf6N2E2_2192 Pf6N2E2_2409
pco propanyl-CoA oxidase Pf6N2E2_4036 Pf6N2E2_1146
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase Pf6N2E2_6061 Pf6N2E2_279
prpC 2-methylcitrate synthase Pf6N2E2_6062 Pf6N2E2_5850
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase Pf6N2E2_6064
RR42_RS28305 L-threonine:H+ symporter Pf6N2E2_5459 Pf6N2E2_5633
serP1 L-threonine uptake transporter SerP1 Pf6N2E2_5633 Pf6N2E2_5459
snatA L-threonine transporter snatA Pf6N2E2_3525
sstT L-threonine:Na+ symporter SstT Pf6N2E2_2230
tdcB L-threonine dehydratase Pf6N2E2_3938 Pf6N2E2_802
tdcC L-threonine:H+ symporter TdcC Pf6N2E2_563
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase Pf6N2E2_2802 Pf6N2E2_1380
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) Pf6N2E2_2136

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