GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Phaeacidiphilus oryzae TH49

Best path

braC, braD, braE, braF, braG, tdcB, tdcE, pccA, pccB, epi, mcm-large, mcm-small

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 (49 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
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) BS73_RS29125 BS73_RS13625
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) BS73_RS29120
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BS73_RS00335 BS73_RS29115
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BS73_RS00340 BS73_RS29110
tdcB L-threonine dehydratase BS73_RS16930 BS73_RS17825
tdcE 2-ketobutyrate formate-lyase BS73_RS30625
pccA propionyl-CoA carboxylase, alpha subunit BS73_RS23635 BS73_RS25280
pccB propionyl-CoA carboxylase, beta subunit BS73_RS07330 BS73_RS24900
epi methylmalonyl-CoA epimerase BS73_RS15090
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit BS73_RS07325 BS73_RS15040
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BS73_RS23175 BS73_RS11855
Alternative steps:
ackA acetate kinase BS73_RS15005
acn (2R,3S)-2-methylcitrate dehydratase BS73_RS12710
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BS73_RS12710
acs acetyl-CoA synthetase, AMP-forming BS73_RS20690 BS73_RS01530
adh acetaldehyde dehydrogenase (not acylating) BS73_RS04090 BS73_RS04035
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase BS73_RS10620 BS73_RS23595
D-LDH D-lactate dehydrogenase BS73_RS04910 BS73_RS24465
dddA 3-hydroxypropionate dehydrogenase BS73_RS13540 BS73_RS01415
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components BS73_RS03925 BS73_RS10140
gcvH glycine cleavage system, H component (lipoyl protein) BS73_RS14875
gcvP glycine cleavage system, P component (glycine decarboxylase)
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) BS73_RS14870
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) BS73_RS24465 BS73_RS04750
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) BS73_RS04750
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I
gloB hydroxyacylglutathione hydrolase (glyoxalase II) BS73_RS10415 BS73_RS08575
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 BS73_RS20300 BS73_RS14910
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BS73_RS14210 BS73_RS14255
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) BS73_RS00515 BS73_RS34050
L-LDH L-lactate dehydrogenase BS73_RS07640 BS73_RS01430
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit BS73_RS09575
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component BS73_RS24465 BS73_RS04750
lctO L-lactate oxidase or 2-monooxygenase BS73_RS10185 BS73_RS07640
lldE L-lactate dehydrogenase, LldE subunit BS73_RS10145 BS73_RS03920
lldF L-lactate dehydrogenase, LldF subunit BS73_RS10140 BS73_RS03925
lldG L-lactate dehydrogenase, LldG subunit
lpd dihydrolipoyl dehydrogenase BS73_RS01320 BS73_RS28205
ltaE L-threonine aldolase BS73_RS09615 BS73_RS14880
lutA L-lactate dehydrogenase, LutA subunit BS73_RS10145 BS73_RS03920
lutB L-lactate dehydrogenase, LutB subunit BS73_RS10140 BS73_RS03925
lutC L-lactate dehydrogenase, LutC subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components BS73_RS07325 BS73_RS15040
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BS73_RS23635 BS73_RS06500
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase BS73_RS32915
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase BS73_RS29705 BS73_RS10660
prpC 2-methylcitrate synthase BS73_RS25400 BS73_RS17760
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase BS73_RS10825 BS73_RS31830
pta phosphate acetyltransferase
RR42_RS28305 L-threonine:H+ symporter BS73_RS16535 BS73_RS25710
serP1 L-threonine uptake transporter SerP1 BS73_RS10785 BS73_RS16535
snatA L-threonine transporter snatA
sstT L-threonine:Na+ symporter SstT
tdcC L-threonine:H+ symporter TdcC
tdh L-threonine 3-dehydrogenase BS73_RS16880 BS73_RS10410
tynA aminoacetone oxidase BS73_RS10580
yvgN methylglyoxal reductase (NADPH-dependent) BS73_RS07605 BS73_RS39300

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