GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Azospirillum brasilense Sp245

Best path

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

Also see fitness data for the top candidates

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 (57 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) AZOBR_RS08260
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) AZOBR_RS08235 AZOBR_RS03565
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) AZOBR_RS08240 AZOBR_RS25635
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) AZOBR_RS08245 AZOBR_RS04130
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) AZOBR_RS08250 AZOBR_RS29685
tdcB L-threonine dehydratase AZOBR_RS06795
tdcE 2-ketobutyrate formate-lyase AZOBR_RS21180 AZOBR_RS30195
pccA propionyl-CoA carboxylase, alpha subunit AZOBR_RS21105 AZOBR_RS22285
pccB propionyl-CoA carboxylase, beta subunit AZOBR_RS21100 AZOBR_RS22295
epi methylmalonyl-CoA epimerase AZOBR_RS07250
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit AZOBR_RS24250 AZOBR_RS21115
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit AZOBR_RS24250 AZOBR_RS21115
Alternative steps:
ackA acetate kinase AZOBR_RS12495 AZOBR_RS04605
acn (2R,3S)-2-methylcitrate dehydratase AZOBR_RS17090 AZOBR_RS02985
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) AZOBR_RS02985
acs acetyl-CoA synthetase, AMP-forming AZOBR_RS00270 AZOBR_RS06340
adh acetaldehyde dehydrogenase (not acylating) AZOBR_RS22315 AZOBR_RS26825
ald-dh-CoA acetaldehyde dehydrogenase, acylating AZOBR_RS32240 AZOBR_RS32475
aldA lactaldehyde dehydrogenase AZOBR_RS29185 AZOBR_RS19635
D-LDH D-lactate dehydrogenase AZOBR_RS25120 AZOBR_RS12240
dddA 3-hydroxypropionate dehydrogenase AZOBR_RS26815
DVU3032 L-lactate dehydrogenase, LutC-like component AZOBR_RS01625 AZOBR_RS01620
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components AZOBR_RS25110 AZOBR_RS01620
gcvH glycine cleavage system, H component (lipoyl protein) AZOBR_RS10465
gcvP glycine cleavage system, P component (glycine decarboxylase) AZOBR_RS10455 AZOBR_RS10460
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) AZOBR_RS10470
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) AZOBR_RS05725 AZOBR_RS29745
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) AZOBR_RS05730
glcF D-lactate dehydrogenase, FeS subunit GlcF AZOBR_RS05735
gloA glyoxylase I AZOBR_RS07390 AZOBR_RS29310
gloB hydroxyacylglutathione hydrolase (glyoxalase II) AZOBR_RS20450 AZOBR_RS19250
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 AZOBR_RS26485 AZOBR_RS01260
iolA malonate semialdehyde dehydrogenase (CoA-acylating) AZOBR_RS22500 AZOBR_RS29750
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) AZOBR_RS31105 AZOBR_RS03625
L-LDH L-lactate dehydrogenase AZOBR_RS01310 AZOBR_RS14060
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit AZOBR_RS05480
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit AZOBR_RS05475 AZOBR_RS29735
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component AZOBR_RS12240 AZOBR_RS05725
lctO L-lactate oxidase or 2-monooxygenase AZOBR_RS19085 AZOBR_RS27055
lldE L-lactate dehydrogenase, LldE subunit AZOBR_RS01615 AZOBR_RS25115
lldF L-lactate dehydrogenase, LldF subunit AZOBR_RS25110 AZOBR_RS01620
lldG L-lactate dehydrogenase, LldG subunit
lpd dihydrolipoyl dehydrogenase AZOBR_RS14390 AZOBR_RS03960
ltaE L-threonine aldolase AZOBR_RS10015
lutA L-lactate dehydrogenase, LutA subunit AZOBR_RS25115 AZOBR_RS01615
lutB L-lactate dehydrogenase, LutB subunit AZOBR_RS25110 AZOBR_RS01620
lutC L-lactate dehydrogenase, LutC subunit AZOBR_RS25105 AZOBR_RS01625
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components AZOBR_RS24250 AZOBR_RS21115
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit AZOBR_RS21105 AZOBR_RS12015
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit AZOBR_RS22285
pco propanyl-CoA oxidase AZOBR_RS19670
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase AZOBR_RS02405 AZOBR_RS27820
prpC 2-methylcitrate synthase AZOBR_RS24300 AZOBR_RS25925
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase AZOBR_RS24310 AZOBR_RS28105
pta phosphate acetyltransferase AZOBR_RS04600 AZOBR_RS12500
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA AZOBR_RS25935 AZOBR_RS31980
sstT L-threonine:Na+ symporter SstT
tdcC L-threonine:H+ symporter TdcC
tdh L-threonine 3-dehydrogenase AZOBR_RS28580 AZOBR_RS32240
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) AZOBR_RS19710 AZOBR_RS02275

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.

Links

Downloads

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 preprint 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