GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Streptococcus massiliensis 4401825

Best path

serP1, tdcB, tdcE, pccA, pccB, epi, mcmA

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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
serP1 L-threonine uptake transporter SerP1 BN415_RS05555
tdcB L-threonine dehydratase BN415_RS05905 BN415_RS09095
tdcE 2-ketobutyrate formate-lyase BN415_RS07680
pccA propionyl-CoA carboxylase, alpha subunit BN415_RS08050
pccB propionyl-CoA carboxylase, beta subunit
epi methylmalonyl-CoA epimerase
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
Alternative steps:
ackA acetate kinase BN415_RS06580 BN415_RS07820
acn (2R,3S)-2-methylcitrate dehydratase
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
acs acetyl-CoA synthetase, AMP-forming
adh acetaldehyde dehydrogenase (not acylating) BN415_RS08155 BN415_RS07850
ald-dh-CoA acetaldehyde dehydrogenase, acylating BN415_RS08155 BN415_RS07850
aldA lactaldehyde dehydrogenase
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) BN415_RS07295
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BN415_RS07285
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) BN415_RS07280
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BN415_RS07275 BN415_RS07270
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BN415_RS07270 BN415_RS07275
D-LDH D-lactate dehydrogenase
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
gcvH glycine cleavage system, H component (lipoyl protein)
gcvP glycine cleavage system, P component (glycine decarboxylase)
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase)
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 BN415_RS03185
gloB hydroxyacylglutathione hydrolase (glyoxalase II) BN415_RS07245
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
iolA malonate semialdehyde dehydrogenase (CoA-acylating)
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase)
L-LDH L-lactate dehydrogenase BN415_RS01525
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
lpd dihydrolipoyl dehydrogenase BN415_RS01990 BN415_RS00555
ltaE L-threonine aldolase BN415_RS01220
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
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BN415_RS08050
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase BN415_RS01595 BN415_RS07865
RR42_RS28305 L-threonine:H+ symporter BN415_RS05555
snatA L-threonine transporter snatA
sstT L-threonine:Na+ symporter SstT
tdcC L-threonine:H+ symporter TdcC
tdh L-threonine 3-dehydrogenase BN415_RS08155 BN415_RS07845
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) BN415_RS05670 BN415_RS08590

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