GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Marivita geojedonensis DPG-138

Best path

braC, braD, braE, braF, braG, ltaE, adh, acs, 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 (46 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) MGEO_RS14450
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) MGEO_RS14465 MGEO_RS19850
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) MGEO_RS14470 MGEO_RS19845
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) MGEO_RS19860 MGEO_RS14455
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) MGEO_RS14460 MGEO_RS19855
ltaE L-threonine aldolase MGEO_RS04160 MGEO_RS16680
adh acetaldehyde dehydrogenase (not acylating) MGEO_RS02095 MGEO_RS02570
acs acetyl-CoA synthetase, AMP-forming MGEO_RS21005 MGEO_RS10460
gcvP glycine cleavage system, P component (glycine decarboxylase) MGEO_RS16605
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) MGEO_RS16615 MGEO_RS09725
gcvH glycine cleavage system, H component (lipoyl protein) MGEO_RS16610
lpd dihydrolipoyl dehydrogenase MGEO_RS09565 MGEO_RS18755
Alternative steps:
ackA acetate kinase MGEO_RS02500
acn (2R,3S)-2-methylcitrate dehydratase MGEO_RS14690
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) MGEO_RS14690
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase MGEO_RS07470 MGEO_RS02095
D-LDH D-lactate dehydrogenase MGEO_RS08420 MGEO_RS06960
dddA 3-hydroxypropionate dehydrogenase MGEO_RS07505 MGEO_RS02655
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase MGEO_RS18700
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) MGEO_RS02315 MGEO_RS08420
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) MGEO_RS02320
glcF D-lactate dehydrogenase, FeS subunit GlcF MGEO_RS02325
gloA glyoxylase I MGEO_RS09920
gloB hydroxyacylglutathione hydrolase (glyoxalase II) MGEO_RS10060 MGEO_RS01450
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 MGEO_RS17480 MGEO_RS00470
iolA malonate semialdehyde dehydrogenase (CoA-acylating) MGEO_RS13860 MGEO_RS17260
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) MGEO_RS17650 MGEO_RS06180
L-LDH L-lactate dehydrogenase MGEO_RS07910 MGEO_RS00265
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit MGEO_RS18025
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component MGEO_RS08420 MGEO_RS02315
lctO L-lactate oxidase or 2-monooxygenase MGEO_RS07910 MGEO_RS05345
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 MGEO_RS05505 MGEO_RS00155
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit MGEO_RS05505 MGEO_RS00155
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components MGEO_RS05505 MGEO_RS00155
pccA propionyl-CoA carboxylase, alpha subunit MGEO_RS05495 MGEO_RS05760
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit MGEO_RS05495 MGEO_RS14815
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit MGEO_RS05475 MGEO_RS05755
pco propanyl-CoA oxidase MGEO_RS11945
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase MGEO_RS11935
prpC 2-methylcitrate synthase MGEO_RS02490 MGEO_RS11295
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase MGEO_RS06775
pta phosphate acetyltransferase MGEO_RS02495
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA MGEO_RS06320
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase MGEO_RS12755 MGEO_RS01815
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase MGEO_RS02630 MGEO_RS05355
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) MGEO_RS06720

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