GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Methylocella silvestris BL2

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 (48 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) MSIL_RS10660
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) MSIL_RS10635 MSIL_RS00340
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) MSIL_RS10640
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) MSIL_RS00330 MSIL_RS10230
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) MSIL_RS10650 MSIL_RS00325
ltaE L-threonine aldolase MSIL_RS19680 MSIL_RS10775
adh acetaldehyde dehydrogenase (not acylating) MSIL_RS11965 MSIL_RS19705
acs acetyl-CoA synthetase, AMP-forming MSIL_RS06300 MSIL_RS17440
gcvP glycine cleavage system, P component (glycine decarboxylase) MSIL_RS06240 MSIL_RS06245
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) MSIL_RS06255 MSIL_RS18315
gcvH glycine cleavage system, H component (lipoyl protein) MSIL_RS06250
lpd dihydrolipoyl dehydrogenase MSIL_RS02655 MSIL_RS12790
Alternative steps:
ackA acetate kinase MSIL_RS15165 MSIL_RS13775
acn (2R,3S)-2-methylcitrate dehydratase MSIL_RS17810
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) MSIL_RS17810
ald-dh-CoA acetaldehyde dehydrogenase, acylating MSIL_RS07560
aldA lactaldehyde dehydrogenase MSIL_RS19705 MSIL_RS11965
D-LDH D-lactate dehydrogenase MSIL_RS03770 MSIL_RS08635
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components MSIL_RS12410
epi methylmalonyl-CoA epimerase MSIL_RS14930
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) MSIL_RS08635 MSIL_RS03770
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) MSIL_RS12955
glcF D-lactate dehydrogenase, FeS subunit GlcF MSIL_RS12950
gloA glyoxylase I MSIL_RS01020
gloB hydroxyacylglutathione hydrolase (glyoxalase II) MSIL_RS09685 MSIL_RS13470
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 MSIL_RS07135 MSIL_RS04665
iolA malonate semialdehyde dehydrogenase (CoA-acylating) MSIL_RS17445 MSIL_RS19705
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) MSIL_RS10890 MSIL_RS10370
L-LDH L-lactate dehydrogenase MSIL_RS12765
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit MSIL_RS18370
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit MSIL_RS18365 MSIL_RS19195
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component MSIL_RS08635 MSIL_RS03770
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit MSIL_RS12405
lldF L-lactate dehydrogenase, LldF subunit MSIL_RS12410
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit MSIL_RS12405
lutB L-lactate dehydrogenase, LutB subunit MSIL_RS12410
lutC L-lactate dehydrogenase, LutC subunit
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit MSIL_RS19215
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit MSIL_RS19215
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components MSIL_RS19215
pccA propionyl-CoA carboxylase, alpha subunit MSIL_RS19225 MSIL_RS17455
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit MSIL_RS19225 MSIL_RS19590
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit MSIL_RS06960
pccB propionyl-CoA carboxylase, beta subunit MSIL_RS19230 MSIL_RS17450
pco propanyl-CoA oxidase
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase MSIL_RS08565
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase MSIL_RS13770 MSIL_RS15160
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 MSIL_RS09280
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase MSIL_RS09285 MSIL_RS17435
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) MSIL_RS12490

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 Apr 09 2024. 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