GapMind for catabolism of small carbon sources


L-threonine catabolism in Algoriphagus machipongonensis PR1

Best path

snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd


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 (40 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
snatA L-threonine transporter snatA ALPR1_RS14825
ltaE L-threonine aldolase ALPR1_RS17895 ALPR1_RS00385
adh acetaldehyde dehydrogenase (not acylating) ALPR1_RS18135 ALPR1_RS00010
acs acetyl-CoA synthetase, AMP-forming ALPR1_RS02860 ALPR1_RS19255
gcvP glycine cleavage system, P component (glycine decarboxylase) ALPR1_RS04320
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) ALPR1_RS14795
gcvH glycine cleavage system, H component (lipoyl protein) ALPR1_RS16345
lpd dihydrolipoyl dehydrogenase ALPR1_RS03970 ALPR1_RS17920
Alternative steps:
ackA acetate kinase
acn (2R,3S)-2-methylcitrate dehydratase ALPR1_RS07835
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) ALPR1_RS07835
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase ALPR1_RS05645 ALPR1_RS05690
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) ALPR1_RS03040
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) ALPR1_RS03040 ALPR1_RS06390
D-LDH D-lactate dehydrogenase ALPR1_RS07965 ALPR1_RS12870
dddA 3-hydroxypropionate dehydrogenase ALPR1_RS01365
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components ALPR1_RS05625
epi methylmalonyl-CoA epimerase ALPR1_RS14785
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 ALPR1_RS18410 ALPR1_RS14785
gloB hydroxyacylglutathione hydrolase (glyoxalase II) ALPR1_RS16385 ALPR1_RS07910
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 ALPR1_RS16285 ALPR1_RS05015
iolA malonate semialdehyde dehydrogenase (CoA-acylating) ALPR1_RS01205 ALPR1_RS06860
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) ALPR1_RS15305 ALPR1_RS12525
L-LDH L-lactate dehydrogenase ALPR1_RS18485 ALPR1_RS04625
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 ALPR1_RS05630
lldF L-lactate dehydrogenase, LldF subunit ALPR1_RS05625
lldG L-lactate dehydrogenase, LldG subunit ALPR1_RS05620
lutA L-lactate dehydrogenase, LutA subunit ALPR1_RS05630
lutB L-lactate dehydrogenase, LutB subunit ALPR1_RS05625
lutC L-lactate dehydrogenase, LutC subunit
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit ALPR1_RS17365 ALPR1_RS12840
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit ALPR1_RS17365
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components ALPR1_RS12840 ALPR1_RS17365
pccA propionyl-CoA carboxylase, alpha subunit ALPR1_RS12520 ALPR1_RS12915
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit ALPR1_RS12520 ALPR1_RS12915
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit ALPR1_RS04635 ALPR1_RS14955
pco propanyl-CoA oxidase ALPR1_RS19490 ALPR1_RS12195
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase ALPR1_RS08615
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase ALPR1_RS16330
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase ALPR1_RS03120
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase ALPR1_RS15310 ALPR1_RS16070
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) ALPR1_RS12360

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