GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Marinomonas arctica 328

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 (41 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
sstT L-threonine:Na+ symporter SstT DK187_RS11345
tdh L-threonine 3-dehydrogenase DK187_RS14770 DK187_RS00285
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) DK187_RS14775 DK187_RS00730
gcvP glycine cleavage system, P component (glycine decarboxylase) DK187_RS11630
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) DK187_RS11615
gcvH glycine cleavage system, H component (lipoyl protein) DK187_RS11625
lpd dihydrolipoyl dehydrogenase DK187_RS04750 DK187_RS02350
Alternative steps:
ackA acetate kinase DK187_RS12110
acn (2R,3S)-2-methylcitrate dehydratase DK187_RS10545 DK187_RS13240
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) DK187_RS10545
acs acetyl-CoA synthetase, AMP-forming DK187_RS06350 DK187_RS08760
adh acetaldehyde dehydrogenase (not acylating) DK187_RS00035 DK187_RS07470
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase DK187_RS16485 DK187_RS17920
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) DK187_RS07505
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) DK187_RS07510 DK187_RS18835
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) DK187_RS07515
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) DK187_RS09960 DK187_RS07520
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) DK187_RS07525 DK187_RS18820
D-LDH D-lactate dehydrogenase DK187_RS02280 DK187_RS06240
dddA 3-hydroxypropionate dehydrogenase DK187_RS17925
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 DK187_RS05330 DK187_RS10630
gloB hydroxyacylglutathione hydrolase (glyoxalase II) DK187_RS12390 DK187_RS16245
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 DK187_RS04965 DK187_RS04960
iolA malonate semialdehyde dehydrogenase (CoA-acylating) DK187_RS07670 DK187_RS08870
L-LDH L-lactate dehydrogenase DK187_RS04980 DK187_RS16410
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit DK187_RS06305 DK187_RS08780
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component
lctO L-lactate oxidase or 2-monooxygenase DK187_RS16410 DK187_RS04980
lldE L-lactate dehydrogenase, LldE subunit
lldF L-lactate dehydrogenase, LldF subunit
lldG L-lactate dehydrogenase, LldG subunit
ltaE L-threonine aldolase DK187_RS04365 DK187_RS11620
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 DK187_RS07855
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit DK187_RS07855 DK187_RS12875
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components DK187_RS07855
pccA propionyl-CoA carboxylase, alpha subunit DK187_RS06470 DK187_RS09690
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit DK187_RS09690 DK187_RS06470
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase DK187_RS09220 DK187_RS06645
prpC 2-methylcitrate synthase DK187_RS09225 DK187_RS04785
prpD 2-methylcitrate dehydratase DK187_RS09230
prpF methylaconitate isomerase DK187_RS04090 DK187_RS09720
pta phosphate acetyltransferase DK187_RS12115
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA DK187_RS11460
tdcB L-threonine dehydratase DK187_RS19550
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) DK187_RS09090

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