GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Pseudomonas fluorescens FW300-N1B4

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 (53 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) Pf1N1B4_3218 Pf1N1B4_1382
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) Pf1N1B4_3217 Pf1N1B4_1381
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) Pf1N1B4_3216 Pf1N1B4_1380
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) Pf1N1B4_3215 Pf1N1B4_1346
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) Pf1N1B4_3214 Pf1N1B4_1378
ltaE L-threonine aldolase Pf1N1B4_2451 Pf1N1B4_2778
adh acetaldehyde dehydrogenase (not acylating) Pf1N1B4_4502 Pf1N1B4_2673
ackA acetate kinase Pf1N1B4_879
pta phosphate acetyltransferase Pf1N1B4_1055
gcvP glycine cleavage system, P component (glycine decarboxylase) Pf1N1B4_621 Pf1N1B4_2236
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) Pf1N1B4_623 Pf1N1B4_2234
gcvH glycine cleavage system, H component (lipoyl protein) Pf1N1B4_2235 Pf1N1B4_620
lpd dihydrolipoyl dehydrogenase Pf1N1B4_4477 Pf1N1B4_3683
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase Pf1N1B4_3821 Pf1N1B4_4564
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Pf1N1B4_3821 Pf1N1B4_3888
acs acetyl-CoA synthetase, AMP-forming Pf1N1B4_3430 Pf1N1B4_2849
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase Pf1N1B4_5695 Pf1N1B4_171
D-LDH D-lactate dehydrogenase Pf1N1B4_1190 Pf1N1B4_3500
dddA 3-hydroxypropionate dehydrogenase Pf1N1B4_4450 Pf1N1B4_2416
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components Pf1N1B4_1188
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) Pf1N1B4_5862 Pf1N1B4_2274
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) Pf1N1B4_5863
glcF D-lactate dehydrogenase, FeS subunit GlcF Pf1N1B4_5864
gloA glyoxylase I Pf1N1B4_5009
gloB hydroxyacylglutathione hydrolase (glyoxalase II) Pf1N1B4_4596 Pf1N1B4_2963
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 Pf1N1B4_4788 Pf1N1B4_5593
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Pf1N1B4_4277 Pf1N1B4_1238
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) Pf1N1B4_2488
L-LDH L-lactate dehydrogenase Pf1N1B4_4705 Pf1N1B4_5979
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit Pf1N1B4_391 Pf1N1B4_5613
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component Pf1N1B4_5862 Pf1N1B4_2274
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit Pf1N1B4_1187
lldF L-lactate dehydrogenase, LldF subunit Pf1N1B4_1188
lldG L-lactate dehydrogenase, LldG subunit Pf1N1B4_1189
lutA L-lactate dehydrogenase, LutA subunit Pf1N1B4_1187
lutB L-lactate dehydrogenase, LutB subunit Pf1N1B4_1188
lutC L-lactate dehydrogenase, LutC subunit Pf1N1B4_1189
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 Pf1N1B4_225 Pf1N1B4_3984
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Pf1N1B4_2010 Pf1N1B4_1309
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit Pf1N1B4_3986 Pf1N1B4_222
pco propanyl-CoA oxidase Pf1N1B4_1816
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase Pf1N1B4_3819 Pf1N1B4_4042
prpC 2-methylcitrate synthase Pf1N1B4_3820 Pf1N1B4_3676
prpD 2-methylcitrate dehydratase Pf1N1B4_3823
prpF methylaconitate isomerase Pf1N1B4_3822 Pf1N1B4_4463
RR42_RS28305 L-threonine:H+ symporter Pf1N1B4_801 Pf1N1B4_1580
serP1 L-threonine uptake transporter SerP1 Pf1N1B4_4976 Pf1N1B4_1580
snatA L-threonine transporter snatA Pf1N1B4_1320
sstT L-threonine:Na+ symporter SstT Pf1N1B4_3934
tdcB L-threonine dehydratase Pf1N1B4_2280 Pf1N1B4_4257
tdcC L-threonine:H+ symporter TdcC Pf1N1B4_4562 Pf1N1B4_1014
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase Pf1N1B4_3270 Pf1N1B4_4506
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) Pf1N1B4_128 Pf1N1B4_85

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 Aug 02 2021. The underlying query database was built on Aug 02 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