GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Sinorhizobium fredii NGR234

Best path

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

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 (49 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) NGR_RS23720 NGR_RS14075
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) NGR_RS23745 NGR_RS28280
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) NGR_RS23740 NGR_RS10930
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) NGR_RS21550 NGR_RS07890
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) NGR_RS23730 NGR_RS10940
ltaE L-threonine aldolase NGR_RS25500 NGR_RS03350
adh acetaldehyde dehydrogenase (not acylating) NGR_RS06135 NGR_RS22740
acs acetyl-CoA synthetase, AMP-forming NGR_RS27780 NGR_RS27800
gcvP glycine cleavage system, P component (glycine decarboxylase) NGR_RS18990
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) NGR_RS19000 NGR_RS22090
gcvH glycine cleavage system, H component (lipoyl protein) NGR_RS18995
lpd dihydrolipoyl dehydrogenase NGR_RS26095 NGR_RS17710
Alternative steps:
ackA acetate kinase NGR_RS06510
acn (2R,3S)-2-methylcitrate dehydratase NGR_RS27315 NGR_RS03745
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) NGR_RS27315 NGR_RS03745
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase NGR_RS12570 NGR_RS30435
D-LDH D-lactate dehydrogenase NGR_RS21525 NGR_RS04255
dddA 3-hydroxypropionate dehydrogenase NGR_RS02360 NGR_RS03665
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase NGR_RS16610
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) NGR_RS13330 NGR_RS09400
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) NGR_RS13335 NGR_RS09395
glcF D-lactate dehydrogenase, FeS subunit GlcF NGR_RS13345 NGR_RS09390
gloA glyoxylase I NGR_RS18320 NGR_RS23785
gloB hydroxyacylglutathione hydrolase (glyoxalase II) NGR_RS22585 NGR_RS24700
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 NGR_RS29675 NGR_RS27640
iolA malonate semialdehyde dehydrogenase (CoA-acylating) NGR_RS13065 NGR_RS23205
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) NGR_RS22520 NGR_RS12410
L-LDH L-lactate dehydrogenase NGR_RS23125 NGR_RS26785
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit NGR_RS30345
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit NGR_RS30350 NGR_RS21415
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component NGR_RS09400 NGR_RS13330
lctO L-lactate oxidase or 2-monooxygenase NGR_RS23125
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 NGR_RS10040
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit NGR_RS10040
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components NGR_RS10040
pccA propionyl-CoA carboxylase, alpha subunit NGR_RS10035 NGR_RS05540
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit NGR_RS10035 NGR_RS16825
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit NGR_RS10025 NGR_RS05530
pco propanyl-CoA oxidase NGR_RS06370
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase NGR_RS18405
prpC 2-methylcitrate synthase NGR_RS18005
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase NGR_RS02985
pta phosphate acetyltransferase NGR_RS06505 NGR_RS11510
RR42_RS28305 L-threonine:H+ symporter NGR_RS11085
serP1 L-threonine uptake transporter SerP1 NGR_RS11085
snatA L-threonine transporter snatA NGR_RS19050
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase NGR_RS18695 NGR_RS03160
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase NGR_RS22515 NGR_RS14365
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) NGR_RS14925 NGR_RS21275

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 Apr 09 2024. 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