GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Pseudomonas fluorescens FW300-N2C3

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) AO356_05320 AO356_08500
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) AO356_05325 AO356_08495
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) AO356_05330 AO356_08490
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) AO356_05335 AO356_29020
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) AO356_05340 AO356_08480
ltaE L-threonine aldolase AO356_13955 AO356_15725
adh acetaldehyde dehydrogenase (not acylating) AO356_28025 AO356_15225
ackA acetate kinase AO356_17605
pta phosphate acetyltransferase AO356_16680
gcvP glycine cleavage system, P component (glycine decarboxylase) AO356_18170
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) AO356_18160 AO356_13035
gcvH glycine cleavage system, H component (lipoyl protein) AO356_13040 AO356_18175
lpd dihydrolipoyl dehydrogenase AO356_22975 AO356_19705
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase AO356_20875 AO356_24390
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) AO356_20875 AO356_02385
acs acetyl-CoA synthetase, AMP-forming AO356_18695 AO356_16045
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase AO356_26145 AO356_28685
D-LDH D-lactate dehydrogenase AO356_07570 AO356_19040
dddA 3-hydroxypropionate dehydrogenase AO356_21730 AO356_30225
DVU3032 L-lactate dehydrogenase, LutC-like component AO356_07560
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components AO356_07560
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) AO356_01090 AO356_24000
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) AO356_01095
glcF D-lactate dehydrogenase, FeS subunit GlcF AO356_01100
gloA glyoxylase I AO356_22815
gloB hydroxyacylglutathione hydrolase (glyoxalase II) AO356_24480 AO356_05915
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 AO356_26360 AO356_30355
iolA malonate semialdehyde dehydrogenase (CoA-acylating) AO356_23175 AO356_07950
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) AO356_14140
L-LDH L-lactate dehydrogenase AO356_26080
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit AO356_20325 AO356_21850
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component AO356_01090 AO356_24000
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit AO356_07555
lldF L-lactate dehydrogenase, LldF subunit AO356_07560
lldG L-lactate dehydrogenase, LldG subunit AO356_07565
lutA L-lactate dehydrogenase, LutA subunit AO356_07555
lutB L-lactate dehydrogenase, LutB subunit AO356_07560
lutC L-lactate dehydrogenase, LutC subunit AO356_07565
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 AO356_01595 AO356_02930
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit AO356_12020 AO356_08195
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit AO356_01585 AO356_02920
pco propanyl-CoA oxidase AO356_10850 AO356_26355
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase AO356_20865 AO356_22080
prpC 2-methylcitrate synthase AO356_20870 AO356_19670
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase AO356_20880 AO356_28890
RR42_RS28305 L-threonine:H+ symporter AO356_17670 AO356_18530
serP1 L-threonine uptake transporter SerP1 AO356_29455 AO356_18530
snatA L-threonine transporter snatA AO356_08255
sstT L-threonine:Na+ symporter SstT AO356_01815
tdcB L-threonine dehydratase AO356_10330 AO356_27710
tdcC L-threonine:H+ symporter TdcC AO356_24385
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase AO356_04765 AO356_28020
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) AO356_01320

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, 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