GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Oceanisphaera arctica V1-41

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 UN63_RS04550
tdh L-threonine 3-dehydrogenase UN63_RS11715 UN63_RS01050
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) UN63_RS11710 UN63_RS13755
gcvP glycine cleavage system, P component (glycine decarboxylase) UN63_RS08250
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) UN63_RS08235
gcvH glycine cleavage system, H component (lipoyl protein) UN63_RS08240
lpd dihydrolipoyl dehydrogenase UN63_RS13455 UN63_RS12615
Alternative steps:
ackA acetate kinase UN63_RS08110 UN63_RS08075
acn (2R,3S)-2-methylcitrate dehydratase UN63_RS13445 UN63_RS09715
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) UN63_RS09715
acs acetyl-CoA synthetase, AMP-forming UN63_RS07990 UN63_RS15435
adh acetaldehyde dehydrogenase (not acylating) UN63_RS03525 UN63_RS03450
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase UN63_RS14965 UN63_RS08875
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) UN63_RS11720
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) UN63_RS11725
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) UN63_RS11730
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) UN63_RS11735 UN63_RS06410
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) UN63_RS11740 UN63_RS06410
D-LDH D-lactate dehydrogenase UN63_RS04435 UN63_RS05590
dddA 3-hydroxypropionate dehydrogenase UN63_RS03420
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components UN63_RS04445
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 UN63_RS15225 UN63_RS16280
gloB hydroxyacylglutathione hydrolase (glyoxalase II) UN63_RS10105 UN63_RS00115
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 UN63_RS10750 UN63_RS10745
iolA malonate semialdehyde dehydrogenase (CoA-acylating) UN63_RS16535 UN63_RS08995
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 UN63_RS08955
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit UN63_RS04450
lldF L-lactate dehydrogenase, LldF subunit UN63_RS04445
lldG L-lactate dehydrogenase, LldG subunit
ltaE L-threonine aldolase UN63_RS07960 UN63_RS16715
lutA L-lactate dehydrogenase, LutA subunit UN63_RS04450
lutB L-lactate dehydrogenase, LutB subunit UN63_RS04445
lutC L-lactate dehydrogenase, LutC subunit UN63_RS04440
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit UN63_RS11590
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
pccA propionyl-CoA carboxylase, alpha subunit UN63_RS13355 UN63_RS08005
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit UN63_RS08005 UN63_RS13355
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit UN63_RS08790
pccB propionyl-CoA carboxylase, beta subunit UN63_RS13345
pco propanyl-CoA oxidase
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase UN63_RS01190
prpC 2-methylcitrate synthase UN63_RS01195 UN63_RS07100
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase UN63_RS08115 UN63_RS06755
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA
tdcB L-threonine dehydratase UN63_RS11405
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) UN63_RS16055

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