GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Bacteroides fluxus YIT 12057

Best path

snatA, 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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
snatA L-threonine transporter snatA HMPREF9446_RS06265
tdh L-threonine 3-dehydrogenase HMPREF9446_RS04240 HMPREF9446_RS03595
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) HMPREF9446_RS04235 HMPREF9446_RS00275
gcvP glycine cleavage system, P component (glycine decarboxylase) HMPREF9446_RS17780
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) HMPREF9446_RS00020
gcvH glycine cleavage system, H component (lipoyl protein) HMPREF9446_RS13280
lpd dihydrolipoyl dehydrogenase HMPREF9446_RS12300 HMPREF9446_RS05445
Alternative steps:
ackA acetate kinase HMPREF9446_RS14790 HMPREF9446_RS02125
acn (2R,3S)-2-methylcitrate dehydratase
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
acs acetyl-CoA synthetase, AMP-forming HMPREF9446_RS14965
adh acetaldehyde dehydrogenase (not acylating) HMPREF9446_RS11430
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase
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) HMPREF9446_RS09630 HMPREF9446_RS02955
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) HMPREF9446_RS09630 HMPREF9446_RS13805
D-LDH D-lactate dehydrogenase HMPREF9446_RS14625 HMPREF9446_RS07845
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase HMPREF9446_RS00075
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 HMPREF9446_RS07825
gloB hydroxyacylglutathione hydrolase (glyoxalase II) HMPREF9446_RS17785
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 HMPREF9446_RS13610
iolA malonate semialdehyde dehydrogenase (CoA-acylating)
L-LDH L-lactate dehydrogenase HMPREF9446_RS11070
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit HMPREF9446_RS00555
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit HMPREF9446_RS00550
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit
lldF L-lactate dehydrogenase, LldF subunit
lldG L-lactate dehydrogenase, LldG subunit
ltaE L-threonine aldolase HMPREF9446_RS00530 HMPREF9446_RS11625
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 HMPREF9446_RS11995
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit HMPREF9446_RS11995
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components HMPREF9446_RS11995 HMPREF9446_RS11990
pccA propionyl-CoA carboxylase, alpha subunit HMPREF9446_RS10475
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit HMPREF9446_RS10475
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit HMPREF9446_RS00070 HMPREF9446_RS10485
pco propanyl-CoA oxidase
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase HMPREF9446_RS05250
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase HMPREF9446_RS14785 HMPREF9446_RS01515
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase HMPREF9446_RS04595
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) HMPREF9446_RS11000

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