GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Halioglobus japonicus S1-36

Best path

sstT, tdh, kbl, 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 (42 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
sstT L-threonine:Na+ symporter SstT C0029_RS04155
tdh L-threonine 3-dehydrogenase C0029_RS08250 C0029_RS12995
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) C0029_RS08245 C0029_RS16525
gcvP glycine cleavage system, P component (glycine decarboxylase) C0029_RS07925
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) C0029_RS16435 C0029_RS01720
gcvH glycine cleavage system, H component (lipoyl protein) C0029_RS12605
lpd dihydrolipoyl dehydrogenase C0029_RS10915 C0029_RS12865
Alternative steps:
ackA acetate kinase
acn (2R,3S)-2-methylcitrate dehydratase C0029_RS10190
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
acs acetyl-CoA synthetase, AMP-forming C0029_RS18225 C0029_RS09450
adh acetaldehyde dehydrogenase (not acylating) C0029_RS01440 C0029_RS01835
ald-dh-CoA acetaldehyde dehydrogenase, acylating C0029_RS08555 C0029_RS01665
aldA lactaldehyde dehydrogenase C0029_RS01835 C0029_RS01440
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB)
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD)
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC)
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) C0029_RS00525 C0029_RS13145
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) C0029_RS00525 C0029_RS18690
D-LDH D-lactate dehydrogenase C0029_RS05565 C0029_RS16560
dddA 3-hydroxypropionate dehydrogenase C0029_RS03565 C0029_RS09135
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components C0029_RS02450
epi methylmalonyl-CoA epimerase C0029_RS11180 C0029_RS05365
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) C0029_RS09320
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) C0029_RS09315
glcF D-lactate dehydrogenase, FeS subunit GlcF C0029_RS09310
gloA glyoxylase I C0029_RS12105
gloB hydroxyacylglutathione hydrolase (glyoxalase II) C0029_RS04100 C0029_RS05740
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 C0029_RS09615 C0029_RS01675
iolA malonate semialdehyde dehydrogenase (CoA-acylating) C0029_RS01440 C0029_RS01630
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
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit C0029_RS02455
lldF L-lactate dehydrogenase, LldF subunit C0029_RS02450
lldG L-lactate dehydrogenase, LldG subunit
ltaE L-threonine aldolase C0029_RS03550 C0029_RS17200
lutA L-lactate dehydrogenase, LutA subunit C0029_RS02455
lutB L-lactate dehydrogenase, LutB subunit C0029_RS02450
lutC L-lactate dehydrogenase, LutC subunit C0029_RS02445
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit C0029_RS11185
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit C0029_RS11185
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components C0029_RS11185
pccA propionyl-CoA carboxylase, alpha subunit C0029_RS03860 C0029_RS16990
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit C0029_RS15355 C0029_RS16990
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit C0029_RS02495
pccB propionyl-CoA carboxylase, beta subunit C0029_RS16980 C0029_RS11170
pco propanyl-CoA oxidase C0029_RS13310
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase C0029_RS13155 C0029_RS10890
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA C0029_RS01795
tdcB L-threonine dehydratase C0029_RS12560 C0029_RS16810
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
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