GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Halomonas xinjiangensis TRM 0175

Best path

braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, 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 (47 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) JH15_RS14375
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) JH15_RS14385 JH15_RS09310
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) JH15_RS14395 JH15_RS16675
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) JH15_RS14390 JH15_RS09325
ltaE L-threonine aldolase JH15_RS06290 JH15_RS13185
adh acetaldehyde dehydrogenase (not acylating) JH15_RS05155 JH15_RS10710
ackA acetate kinase JH15_RS10545
pta phosphate acetyltransferase JH15_RS10540
gcvP glycine cleavage system, P component (glycine decarboxylase) JH15_RS00330
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) JH15_RS00345 JH15_RS13170
gcvH glycine cleavage system, H component (lipoyl protein) JH15_RS00335
lpd dihydrolipoyl dehydrogenase JH15_RS04405 JH15_RS04195
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase JH15_RS12220 JH15_RS01405
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) JH15_RS12220 JH15_RS08095
acs acetyl-CoA synthetase, AMP-forming JH15_RS06450 JH15_RS00950
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase JH15_RS05310 JH15_RS03035
D-LDH D-lactate dehydrogenase JH15_RS17065 JH15_RS10220
dddA 3-hydroxypropionate dehydrogenase JH15_RS13880 JH15_RS03245
DVU3032 L-lactate dehydrogenase, LutC-like component JH15_RS17070
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components JH15_RS17075
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) JH15_RS09970 JH15_RS15340
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) JH15_RS09965 JH15_RS15065
glcF D-lactate dehydrogenase, FeS subunit GlcF JH15_RS09960
gloA glyoxylase I JH15_RS14300 JH15_RS08790
gloB hydroxyacylglutathione hydrolase (glyoxalase II) JH15_RS00990 JH15_RS05910
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 JH15_RS10685 JH15_RS15755
iolA malonate semialdehyde dehydrogenase (CoA-acylating) JH15_RS10815 JH15_RS09670
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase)
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 JH15_RS02515
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component JH15_RS09970 JH15_RS10220
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit JH15_RS17080
lldF L-lactate dehydrogenase, LldF subunit JH15_RS17075
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit JH15_RS17080
lutB L-lactate dehydrogenase, LutB subunit JH15_RS17075
lutC L-lactate dehydrogenase, LutC subunit JH15_RS17070
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit JH15_RS00745
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
pccA propionyl-CoA carboxylase, alpha subunit JH15_RS02135 JH15_RS16470
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit JH15_RS16470 JH15_RS16340
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit JH15_RS06980 JH15_RS02135
pccB propionyl-CoA carboxylase, beta subunit JH15_RS02125
pco propanyl-CoA oxidase JH15_RS01445 JH15_RS02120
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase JH15_RS12210
prpC 2-methylcitrate synthase JH15_RS12215 JH15_RS04440
prpD 2-methylcitrate dehydratase JH15_RS12230
prpF methylaconitate isomerase JH15_RS12225
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase JH15_RS13820 JH15_RS05020
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase JH15_RS09795 JH15_RS13190
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) JH15_RS09395 JH15_RS05605

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