GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Rhizorhabdus wittichii RW1

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 (45 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
snatA L-threonine transporter snatA SWIT_RS14540
ltaE L-threonine aldolase SWIT_RS05990 SWIT_RS05765
adh acetaldehyde dehydrogenase (not acylating) SWIT_RS03590 SWIT_RS08815
acs acetyl-CoA synthetase, AMP-forming SWIT_RS17565 SWIT_RS03515
gcvP glycine cleavage system, P component (glycine decarboxylase) SWIT_RS13650 SWIT_RS13645
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) SWIT_RS13635 SWIT_RS04805
gcvH glycine cleavage system, H component (lipoyl protein) SWIT_RS13640
lpd dihydrolipoyl dehydrogenase SWIT_RS06910 SWIT_RS24900
Alternative steps:
ackA acetate kinase SWIT_RS22145
acn (2R,3S)-2-methylcitrate dehydratase SWIT_RS24185 SWIT_RS13825
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) SWIT_RS24185 SWIT_RS13825
ald-dh-CoA acetaldehyde dehydrogenase, acylating SWIT_RS26330 SWIT_RS10665
aldA lactaldehyde dehydrogenase SWIT_RS01135 SWIT_RS08815
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) SWIT_RS14705 SWIT_RS00070
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) SWIT_RS14705 SWIT_RS04010
D-LDH D-lactate dehydrogenase SWIT_RS05855 SWIT_RS09455
dddA 3-hydroxypropionate dehydrogenase SWIT_RS22820 SWIT_RS24305
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase SWIT_RS14635 SWIT_RS11415
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) SWIT_RS05050 SWIT_RS05855
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) SWIT_RS05055 SWIT_RS05855
glcF D-lactate dehydrogenase, FeS subunit GlcF SWIT_RS05060
gloA glyoxylase I SWIT_RS10055 SWIT_RS08400
gloB hydroxyacylglutathione hydrolase (glyoxalase II) SWIT_RS17970 SWIT_RS10035
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 SWIT_RS03300 SWIT_RS09105
iolA malonate semialdehyde dehydrogenase (CoA-acylating) SWIT_RS03320 SWIT_RS26765
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) SWIT_RS19310 SWIT_RS19710
L-LDH L-lactate dehydrogenase SWIT_RS23415 SWIT_RS08305
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit SWIT_RS16135
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component SWIT_RS05050 SWIT_RS26905
lctO L-lactate oxidase or 2-monooxygenase SWIT_RS21500 SWIT_RS21400
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 SWIT_RS14630
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit SWIT_RS14630 SWIT_RS12140
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components SWIT_RS14630
pccA propionyl-CoA carboxylase, alpha subunit SWIT_RS14620 SWIT_RS10920
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit SWIT_RS14620 SWIT_RS23720
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit SWIT_RS14645 SWIT_RS10915
pco propanyl-CoA oxidase SWIT_RS04185 SWIT_RS21415
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase SWIT_RS24205 SWIT_RS21870
prpC 2-methylcitrate synthase SWIT_RS24200 SWIT_RS16220
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase SWIT_RS24190
pta phosphate acetyltransferase SWIT_RS13975
RR42_RS28305 L-threonine:H+ symporter SWIT_RS03485
serP1 L-threonine uptake transporter SerP1 SWIT_RS03485
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase SWIT_RS12115 SWIT_RS20935
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase SWIT_RS01430 SWIT_RS07295
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 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