GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Sinorhizobium meliloti 1021

Best path

braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd

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 (48 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) SMc01946 SMc00078
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) SMc01951 SMc02359
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) SMc01950
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) SMc01949 SMc03120
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) SMc01948 SMc02358
ltaE L-threonine aldolase SMc04029 SMc01770
adh acetaldehyde dehydrogenase (not acylating) SM_b21301 SM_b21539
ackA acetate kinase SM_b21184
pta phosphate acetyltransferase SM_b21532 SMc01126
gcvP glycine cleavage system, P component (glycine decarboxylase) SMc02049
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) SMc02047 SMc04148
gcvH glycine cleavage system, H component (lipoyl protein) SMc02048
lpd dihydrolipoyl dehydrogenase SMc03204 SMc01035
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase SMc03846
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) SMc03846
acs acetyl-CoA synthetase, AMP-forming SMc04093 SMc04095
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase SMc02322 SMa2213
D-LDH D-lactate dehydrogenase SMc01455 SMa0244
dddA 3-hydroxypropionate dehydrogenase SMc03116 SM_b20496
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase SMc01930
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) SMc00832 SMc01455
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) SMc00833 SM_b21129
glcF D-lactate dehydrogenase, FeS subunit GlcF SMc00926
gloA glyoxylase I SMc00290 SMc01961
gloB hydroxyacylglutathione hydrolase (glyoxalase II) SM_b20171 SMc01587
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 SMc01153 SMc04398
iolA malonate semialdehyde dehydrogenase (CoA-acylating) SMc00781 SM_b20891
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) SMc01565 SMc03104
L-LDH L-lactate dehydrogenase SM_b20850 SMa0404
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit SMa0822
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit SMa0819 SMc00728
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component SMc01455 SMc00832
lctO L-lactate oxidase or 2-monooxygenase SM_b20850 SMc01712
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 SM_b20757
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit SM_b20757
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components SM_b20757
pccA propionyl-CoA carboxylase, alpha subunit SM_b20756 SM_b21124
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit SM_b20756 SMc01345
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit SMc03895
pccB propionyl-CoA carboxylase, beta subunit SM_b20755 SM_b21122
pco propanyl-CoA oxidase SM_b21181 SM_b21121
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase SMc00768
prpC 2-methylcitrate synthase SMc02087
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase SMc00497
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA SMc01232
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase SMc00936 SMa1872
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase SMc01564 SMc01582
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) SMc00101 SMa1410

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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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