GapMind for catabolism of small carbon sources


L-threonine catabolism in Burkholderia phytofirmans PsJN

Best path

snatA, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd

Also see fitness data for the top candidates


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 (58 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
snatA L-threonine transporter snatA BPHYT_RS17695
ltaE L-threonine aldolase BPHYT_RS13965 BPHYT_RS29600
adh acetaldehyde dehydrogenase (not acylating) BPHYT_RS25810 BPHYT_RS00120
ackA acetate kinase BPHYT_RS06125 BPHYT_RS26200
pta phosphate acetyltransferase BPHYT_RS21700 BPHYT_RS27695
gcvP glycine cleavage system, P component (glycine decarboxylase) BPHYT_RS19330
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) BPHYT_RS19320 BPHYT_RS24765
gcvH glycine cleavage system, H component (lipoyl protein) BPHYT_RS19325
lpd dihydrolipoyl dehydrogenase BPHYT_RS12830 BPHYT_RS08120
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase BPHYT_RS30145 BPHYT_RS10160
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BPHYT_RS30145 BPHYT_RS33980
acs acetyl-CoA synthetase, AMP-forming BPHYT_RS07000 BPHYT_RS27780
ald-dh-CoA acetaldehyde dehydrogenase, acylating BPHYT_RS07245 BPHYT_RS21770
aldA lactaldehyde dehydrogenase BPHYT_RS09875 BPHYT_RS09900
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) BPHYT_RS01885 BPHYT_RS26525
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BPHYT_RS15605 BPHYT_RS31740
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) BPHYT_RS31745 BPHYT_RS15600
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BPHYT_RS15595 BPHYT_RS31750
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BPHYT_RS15590 BPHYT_RS31755
D-LDH D-lactate dehydrogenase BPHYT_RS03515 BPHYT_RS03835
dddA 3-hydroxypropionate dehydrogenase BPHYT_RS19495 BPHYT_RS21745
DVU3032 L-lactate dehydrogenase, LutC-like component BPHYT_RS14530
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components BPHYT_RS12805 BPHYT_RS26970
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) BPHYT_RS31645 BPHYT_RS03510
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) BPHYT_RS31650 BPHYT_RS03505
glcF D-lactate dehydrogenase, FeS subunit GlcF BPHYT_RS31655 BPHYT_RS03500
gloA glyoxylase I BPHYT_RS03320 BPHYT_RS22605
gloB hydroxyacylglutathione hydrolase (glyoxalase II) BPHYT_RS14210 BPHYT_RS00495
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 BPHYT_RS25360 BPHYT_RS17335
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BPHYT_RS19500 BPHYT_RS28825
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) BPHYT_RS34655 BPHYT_RS02160
L-LDH L-lactate dehydrogenase BPHYT_RS31690 BPHYT_RS27110
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit BPHYT_RS20830 BPHYT_RS14800
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component BPHYT_RS31645 BPHYT_RS03515
lctO L-lactate oxidase or 2-monooxygenase BPHYT_RS31690
lldE L-lactate dehydrogenase, LldE subunit BPHYT_RS26975 BPHYT_RS12810
lldF L-lactate dehydrogenase, LldF subunit BPHYT_RS26970 BPHYT_RS12805
lldG L-lactate dehydrogenase, LldG subunit BPHYT_RS26965
lutA L-lactate dehydrogenase, LutA subunit BPHYT_RS12810 BPHYT_RS26975
lutB L-lactate dehydrogenase, LutB subunit BPHYT_RS12805 BPHYT_RS26970
lutC L-lactate dehydrogenase, LutC subunit BPHYT_RS14530
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit BPHYT_RS02085
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BPHYT_RS02305
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components BPHYT_RS02085
pccA propionyl-CoA carboxylase, alpha subunit BPHYT_RS23275 BPHYT_RS17015
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BPHYT_RS17015 BPHYT_RS25975
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit BPHYT_RS23265
pco propanyl-CoA oxidase BPHYT_RS11475 BPHYT_RS03780
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase BPHYT_RS12285 BPHYT_RS26855
prpC 2-methylcitrate synthase BPHYT_RS33965 BPHYT_RS30150
prpD 2-methylcitrate dehydratase BPHYT_RS33975
prpF methylaconitate isomerase BPHYT_RS30140 BPHYT_RS27420
RR42_RS28305 L-threonine:H+ symporter BPHYT_RS15500 BPHYT_RS07280
serP1 L-threonine uptake transporter SerP1 BPHYT_RS15500 BPHYT_RS21680
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase BPHYT_RS03145 BPHYT_RS11065
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase BPHYT_RS34650 BPHYT_RS20205
tynA aminoacetone oxidase BPHYT_RS09910
yvgN methylglyoxal reductase (NADPH-dependent) BPHYT_RS08410 BPHYT_RS15795

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 17 2021. The underlying query database was built on Sep 17 2021.



Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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