GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Pseudomonas litoralis 2SM5

Best path

braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd

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 (37 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) BLU11_RS03770
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BLU11_RS03765
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) BLU11_RS03760
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BLU11_RS03755 BLU11_RS01420
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BLU11_RS03750 BLU11_RS01420
ltaE L-threonine aldolase BLU11_RS12220
adh acetaldehyde dehydrogenase (not acylating) BLU11_RS01865 BLU11_RS14925
ackA acetate kinase BLU11_RS01770 BLU11_RS12900
pta phosphate acetyltransferase BLU11_RS12905
gcvP glycine cleavage system, P component (glycine decarboxylase) BLU11_RS13295
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) BLU11_RS13305
gcvH glycine cleavage system, H component (lipoyl protein) BLU11_RS13300
lpd dihydrolipoyl dehydrogenase BLU11_RS04775 BLU11_RS17200
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase BLU11_RS05825 BLU11_RS08620
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BLU11_RS05825 BLU11_RS05430
acs acetyl-CoA synthetase, AMP-forming BLU11_RS00320 BLU11_RS01910
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase BLU11_RS01865 BLU11_RS07260
D-LDH D-lactate dehydrogenase BLU11_RS13390 BLU11_RS00695
dddA 3-hydroxypropionate dehydrogenase BLU11_RS15245
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)
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE)
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I BLU11_RS05210
gloB hydroxyacylglutathione hydrolase (glyoxalase II) BLU11_RS04005 BLU11_RS05955
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 BLU11_RS15435 BLU11_RS12290
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BLU11_RS18585 BLU11_RS12285
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) BLU11_RS01345
L-LDH L-lactate dehydrogenase BLU11_RS13640
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component BLU11_RS13390
lctO L-lactate oxidase or 2-monooxygenase BLU11_RS13640
lldE L-lactate dehydrogenase, LldE subunit
lldF L-lactate dehydrogenase, LldF subunit
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit
lutB L-lactate dehydrogenase, LutB subunit
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 BLU11_RS15495 BLU11_RS15720
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BLU11_RS16535 BLU11_RS02630
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit BLU11_RS10715
pccB propionyl-CoA carboxylase, beta subunit BLU11_RS15485 BLU11_RS15710
pco propanyl-CoA oxidase BLU11_RS13665
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase BLU11_RS05815
prpC 2-methylcitrate synthase BLU11_RS05820 BLU11_RS04740
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase BLU11_RS05830
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase BLU11_RS13360
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase BLU11_RS17735 BLU11_RS16230
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent)

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 24 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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