GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Saccharomonospora cyanea NA-134

Best path

RR42_RS28305, 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 (50 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
RR42_RS28305 L-threonine:H+ symporter SACCYDRAFT_RS13365 SACCYDRAFT_RS20860
ltaE L-threonine aldolase SACCYDRAFT_RS24440 SACCYDRAFT_RS07700
adh acetaldehyde dehydrogenase (not acylating) SACCYDRAFT_RS03230 SACCYDRAFT_RS19650
acs acetyl-CoA synthetase, AMP-forming SACCYDRAFT_RS23100 SACCYDRAFT_RS14620
gcvP glycine cleavage system, P component (glycine decarboxylase) SACCYDRAFT_RS07685
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) SACCYDRAFT_RS07690 SACCYDRAFT_RS11615
gcvH glycine cleavage system, H component (lipoyl protein) SACCYDRAFT_RS07695 SACCYDRAFT_RS14605
lpd dihydrolipoyl dehydrogenase SACCYDRAFT_RS06380 SACCYDRAFT_RS10840
Alternative steps:
ackA acetate kinase SACCYDRAFT_RS14850
acn (2R,3S)-2-methylcitrate dehydratase SACCYDRAFT_RS14425
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) SACCYDRAFT_RS14425
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase SACCYDRAFT_RS23730 SACCYDRAFT_RS03230
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) SACCYDRAFT_RS18990
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) SACCYDRAFT_RS15010
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) SACCYDRAFT_RS15025 SACCYDRAFT_RS10270
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) SACCYDRAFT_RS15020 SACCYDRAFT_RS20255
D-LDH D-lactate dehydrogenase SACCYDRAFT_RS24560 SACCYDRAFT_RS19665
dddA 3-hydroxypropionate dehydrogenase SACCYDRAFT_RS20575 SACCYDRAFT_RS15820
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components SACCYDRAFT_RS23710
epi methylmalonyl-CoA epimerase SACCYDRAFT_RS18435
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) SACCYDRAFT_RS01495 SACCYDRAFT_RS24560
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) SACCYDRAFT_RS01490 SACCYDRAFT_RS24560
glcF D-lactate dehydrogenase, FeS subunit GlcF SACCYDRAFT_RS01485
gloA glyoxylase I SACCYDRAFT_RS11645 SACCYDRAFT_RS22435
gloB hydroxyacylglutathione hydrolase (glyoxalase II) SACCYDRAFT_RS16735 SACCYDRAFT_RS09180
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 SACCYDRAFT_RS18310 SACCYDRAFT_RS03705
iolA malonate semialdehyde dehydrogenase (CoA-acylating) SACCYDRAFT_RS20580 SACCYDRAFT_RS15225
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) SACCYDRAFT_RS05770
L-LDH L-lactate dehydrogenase SACCYDRAFT_RS07750
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit SACCYDRAFT_RS18140
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component SACCYDRAFT_RS19665 SACCYDRAFT_RS24560
lctO L-lactate oxidase or 2-monooxygenase SACCYDRAFT_RS07750
lldE L-lactate dehydrogenase, LldE subunit SACCYDRAFT_RS23715
lldF L-lactate dehydrogenase, LldF subunit SACCYDRAFT_RS23710
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit SACCYDRAFT_RS23715 SACCYDRAFT_RS01485
lutB L-lactate dehydrogenase, LutB subunit SACCYDRAFT_RS23710
lutC L-lactate dehydrogenase, LutC subunit
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit SACCYDRAFT_RS03315 SACCYDRAFT_RS16070
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit SACCYDRAFT_RS03315
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components SACCYDRAFT_RS03315 SACCYDRAFT_RS16070
pccA propionyl-CoA carboxylase, alpha subunit SACCYDRAFT_RS03395 SACCYDRAFT_RS19840
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit SACCYDRAFT_RS03395 SACCYDRAFT_RS19840
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit SACCYDRAFT_RS19840
pccB propionyl-CoA carboxylase, beta subunit SACCYDRAFT_RS03415 SACCYDRAFT_RS19845
pco propanyl-CoA oxidase SACCYDRAFT_RS20625 SACCYDRAFT_RS04895
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase SACCYDRAFT_RS18195 SACCYDRAFT_RS18415
prpC 2-methylcitrate synthase SACCYDRAFT_RS21740 SACCYDRAFT_RS21820
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase
serP1 L-threonine uptake transporter SerP1 SACCYDRAFT_RS13365 SACCYDRAFT_RS20860
snatA L-threonine transporter snatA
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase SACCYDRAFT_RS15285 SACCYDRAFT_RS20685
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase SACCYDRAFT_RS14705 SACCYDRAFT_RS07490
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) SACCYDRAFT_RS12560

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