GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Flavobacterium sp. LM5

Best path

snatA, ltaE, adh, ackA, pta, 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 BXU11_RS04800
ltaE L-threonine aldolase BXU11_RS08210 BXU11_RS14300
adh acetaldehyde dehydrogenase (not acylating) BXU11_RS01185 BXU11_RS12805
ackA acetate kinase BXU11_RS08385
pta phosphate acetyltransferase BXU11_RS08380 BXU11_RS03485
gcvP glycine cleavage system, P component (glycine decarboxylase) BXU11_RS04370
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) BXU11_RS12605
gcvH glycine cleavage system, H component (lipoyl protein) BXU11_RS03500
lpd dihydrolipoyl dehydrogenase BXU11_RS12530 BXU11_RS08250
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase BXU11_RS10770
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
acs acetyl-CoA synthetase, AMP-forming BXU11_RS15515 BXU11_RS13450
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase BXU11_RS01185 BXU11_RS04005
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) BXU11_RS05265
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BXU11_RS05265 BXU11_RS06900
D-LDH* D-lactate dehydrogenase BXU11_RS01240 with BXU11_RS01235 BXU11_RS02295
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase BXU11_RS02910
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
gloB hydroxyacylglutathione hydrolase (glyoxalase II)
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 BXU11_RS02105
iolA malonate semialdehyde dehydrogenase (CoA-acylating)
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) BXU11_RS00340 BXU11_RS09195
L-LDH L-lactate dehydrogenase BXU11_RS06540
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit
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
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 BXU11_RS09065
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BXU11_RS09065 BXU11_RS11800
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components BXU11_RS09065
pccA propionyl-CoA carboxylase, alpha subunit BXU11_RS09415 BXU11_RS02955
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BXU11_RS09415 BXU11_RS02955
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit BXU11_RS09410 BXU11_RS08190
pco propanyl-CoA oxidase BXU11_RS00155 BXU11_RS04315
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase BXU11_RS02765
prpC 2-methylcitrate synthase BXU11_RS04785
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase BXU11_RS11050 BXU11_RS12485
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase BXU11_RS13740
tdh L-threonine 3-dehydrogenase BXU11_RS01305
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent)

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