GapMind for catabolism of small carbon sources


L-threonine catabolism in Photobacterium jeanii R-40508

Best path

sstT, tdh, kbl, grdA, grdE, grdB, grdD, grdC, ackA


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 (47 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
sstT L-threonine:Na+ symporter SstT A3K86_RS19835
tdh L-threonine 3-dehydrogenase A3K86_RS20580 A3K86_RS13845
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) A3K86_RS20585 A3K86_RS04555
grdA glycine reductase component A1 A3K86_RS16180 A3K86_RS16175
grdE glycine reductase component B, precursor to alpha/beta subunits A3K86_RS16225
grdB glycine reductase component B, gamma subunit A3K86_RS16220
grdD glycine reductase component C, alpha subunit A3K86_RS16165
grdC glycine reductase component C, beta subunit A3K86_RS16170
ackA acetate kinase A3K86_RS07230 A3K86_RS03265
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase A3K86_RS10550
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
acs acetyl-CoA synthetase, AMP-forming A3K86_RS09595
adh acetaldehyde dehydrogenase (not acylating) A3K86_RS19720 A3K86_RS06055
ald-dh-CoA acetaldehyde dehydrogenase, acylating A3K86_RS06055 A3K86_RS16475
aldA lactaldehyde dehydrogenase A3K86_RS19720 A3K86_RS14375
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) A3K86_RS10225 A3K86_RS12240
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) A3K86_RS10225 A3K86_RS04635
D-LDH D-lactate dehydrogenase A3K86_RS18455 A3K86_RS13975
dddA 3-hydroxypropionate dehydrogenase A3K86_RS04400
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components A3K86_RS04595
epi methylmalonyl-CoA epimerase
gcvH glycine cleavage system, H component (lipoyl protein) A3K86_RS17495 A3K86_RS20760
gcvP glycine cleavage system, P component (glycine decarboxylase) A3K86_RS20755 A3K86_RS03830
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) A3K86_RS20770
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 A3K86_RS13750 A3K86_RS21770
gloB hydroxyacylglutathione hydrolase (glyoxalase II) A3K86_RS07790 A3K86_RS04710
hpcD 3-hydroxypropionyl-CoA dehydratase A3K86_RS15920 A3K86_RS06710
iolA malonate semialdehyde dehydrogenase (CoA-acylating) A3K86_RS15930 A3K86_RS14375
L-LDH L-lactate dehydrogenase
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit A3K86_RS15855
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit A3K86_RS04590
lldF L-lactate dehydrogenase, LldF subunit A3K86_RS04595
lldG L-lactate dehydrogenase, LldG subunit
lpd dihydrolipoyl dehydrogenase A3K86_RS10525 A3K86_RS01850
ltaE L-threonine aldolase A3K86_RS12120
lutA L-lactate dehydrogenase, LutA subunit A3K86_RS04590
lutB L-lactate dehydrogenase, LutB subunit A3K86_RS04595
lutC L-lactate dehydrogenase, LutC subunit A3K86_RS04600
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit A3K86_RS10020
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
pccA propionyl-CoA carboxylase, alpha subunit A3K86_RS09575
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit A3K86_RS09575
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit A3K86_RS07920
pccB propionyl-CoA carboxylase, beta subunit A3K86_RS15950
pco propanyl-CoA oxidase
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase A3K86_RS11865 A3K86_RS02430
prpC 2-methylcitrate synthase A3K86_RS02435 A3K86_RS06340
prpD 2-methylcitrate dehydratase A3K86_RS02440
prpF methylaconitate isomerase
pta phosphate acetyltransferase A3K86_RS07235 A3K86_RS16445
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA A3K86_RS06060 A3K86_RS22190
tdcB L-threonine dehydratase A3K86_RS17175
tdcC L-threonine:H+ symporter TdcC A3K86_RS03730 A3K86_RS05090
tdcE 2-ketobutyrate formate-lyase A3K86_RS07115
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 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