GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Cereibacter sphaeroides ATCC 17029

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 (46 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
snatA L-threonine transporter snatA RSPH17029_RS07790
ltaE L-threonine aldolase RSPH17029_RS00510 RSPH17029_RS04985
adh acetaldehyde dehydrogenase (not acylating) RSPH17029_RS17490 RSPH17029_RS13480
acs acetyl-CoA synthetase, AMP-forming RSPH17029_RS11250 RSPH17029_RS01250
gcvP glycine cleavage system, P component (glycine decarboxylase) RSPH17029_RS04430
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) RSPH17029_RS04420 RSPH17029_RS06825
gcvH glycine cleavage system, H component (lipoyl protein) RSPH17029_RS04425
lpd dihydrolipoyl dehydrogenase RSPH17029_RS08165 RSPH17029_RS13225
Alternative steps:
ackA acetate kinase RSPH17029_RS14695
acn (2R,3S)-2-methylcitrate dehydratase RSPH17029_RS02300
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) RSPH17029_RS02300
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase RSPH17029_RS16005 RSPH17029_RS04350
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) RSPH17029_RS07930
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) RSPH17029_RS07945 RSPH17029_RS17970
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) RSPH17029_RS17975 RSPH17029_RS04845
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) RSPH17029_RS07935 RSPH17029_RS14865
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) RSPH17029_RS07940 RSPH17029_RS04835
D-LDH D-lactate dehydrogenase RSPH17029_RS04045 RSPH17029_RS09160
dddA 3-hydroxypropionate dehydrogenase RSPH17029_RS20315 RSPH17029_RS04355
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase RSPH17029_RS12460
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) RSPH17029_RS13520 RSPH17029_RS04045
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) RSPH17029_RS13515
glcF D-lactate dehydrogenase, FeS subunit GlcF RSPH17029_RS13510
gloA glyoxylase I RSPH17029_RS20070 RSPH17029_RS19105
gloB hydroxyacylglutathione hydrolase (glyoxalase II) RSPH17029_RS04945 RSPH17029_RS12665
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 RSPH17029_RS00050 RSPH17029_RS06550
iolA malonate semialdehyde dehydrogenase (CoA-acylating) RSPH17029_RS08140 RSPH17029_RS04350
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) RSPH17029_RS05290 RSPH17029_RS08245
L-LDH L-lactate dehydrogenase RSPH17029_RS12550 RSPH17029_RS13255
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit RSPH17029_RS01640
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component RSPH17029_RS04045 RSPH17029_RS13520
lctO L-lactate oxidase or 2-monooxygenase RSPH17029_RS12550
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 RSPH17029_RS04415 RSPH17029_RS18485
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit RSPH17029_RS04415 RSPH17029_RS18470
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components RSPH17029_RS04415 RSPH17029_RS18485
pccA propionyl-CoA carboxylase, alpha subunit RSPH17029_RS04405 RSPH17029_RS05950
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit RSPH17029_RS04405 RSPH17029_RS09225
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit RSPH17029_RS09220
pccB propionyl-CoA carboxylase, beta subunit RSPH17029_RS04380 RSPH17029_RS05945
pco propanyl-CoA oxidase RSPH17029_RS14905
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase RSPH17029_RS03595
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase RSPH17029_RS18095 RSPH17029_RS18235
pta phosphate acetyltransferase RSPH17029_RS14700 RSPH17029_RS14510
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase RSPH17029_RS14480 RSPH17029_RS04715
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase RSPH17029_RS05295 RSPH17029_RS05055
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) RSPH17029_RS05040

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 10 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