GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Sphingomonas indica Dd16

Best path

snatA, 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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
snatA L-threonine transporter snatA B9N75_RS07265
ltaE L-threonine aldolase B9N75_RS05140 B9N75_RS01275
adh acetaldehyde dehydrogenase (not acylating) B9N75_RS09175 B9N75_RS04360
acs acetyl-CoA synthetase, AMP-forming B9N75_RS08675 B9N75_RS00190
gcvP glycine cleavage system, P component (glycine decarboxylase) B9N75_RS01355 B9N75_RS01360
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) B9N75_RS01370
gcvH glycine cleavage system, H component (lipoyl protein) B9N75_RS01365
lpd dihydrolipoyl dehydrogenase B9N75_RS05895 B9N75_RS05035
Alternative steps:
ackA acetate kinase B9N75_RS13485
acn (2R,3S)-2-methylcitrate dehydratase B9N75_RS04320
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) B9N75_RS04320
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase B9N75_RS04360 B9N75_RS09590
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) B9N75_RS06875 B9N75_RS12690
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) B9N75_RS06875 B9N75_RS05840
D-LDH D-lactate dehydrogenase B9N75_RS02270 B9N75_RS08140
dddA 3-hydroxypropionate dehydrogenase B9N75_RS13465
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase B9N75_RS06780
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 B9N75_RS06290
gloB hydroxyacylglutathione hydrolase (glyoxalase II) B9N75_RS02620 B9N75_RS03520
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 B9N75_RS13460 B9N75_RS11255
iolA malonate semialdehyde dehydrogenase (CoA-acylating) B9N75_RS13435 B9N75_RS04360
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) B9N75_RS01260 B9N75_RS10785
L-LDH L-lactate dehydrogenase B9N75_RS05000 B9N75_RS04945
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit B9N75_RS04280
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component
lctO L-lactate oxidase or 2-monooxygenase B9N75_RS04945
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 B9N75_RS06775
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit B9N75_RS06775
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components B9N75_RS06775
pccA propionyl-CoA carboxylase, alpha subunit B9N75_RS06755 B9N75_RS13145
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit B9N75_RS11080 B9N75_RS06755
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit B9N75_RS06795 B9N75_RS13150
pco propanyl-CoA oxidase B9N75_RS12195
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase B9N75_RS04185
prpC 2-methylcitrate synthase B9N75_RS11750
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase B9N75_RS05700 B9N75_RS00120
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase B9N75_RS10675 B9N75_RS09065
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