GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Paraburkholderia phymatum STM815

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 (56 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) BPHY_RS00550 BPHY_RS32955
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BPHY_RS02955 BPHY_RS15515
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) BPHY_RS02960
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BPHY_RS15530 BPHY_RS02965
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BPHY_RS02970 BPHY_RS15485
ltaE L-threonine aldolase BPHY_RS08205 BPHY_RS19160
adh acetaldehyde dehydrogenase (not acylating) BPHY_RS23385 BPHY_RS00050
ackA acetate kinase BPHY_RS18625 BPHY_RS10635
pta phosphate acetyltransferase BPHY_RS30920 BPHY_RS18620
gcvP glycine cleavage system, P component (glycine decarboxylase) BPHY_RS15315
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) BPHY_RS15305 BPHY_RS29800
gcvH glycine cleavage system, H component (lipoyl protein) BPHY_RS15310
lpd dihydrolipoyl dehydrogenase BPHY_RS07480 BPHY_RS08755
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase BPHY_RS33395 BPHY_RS29285
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BPHY_RS33395 BPHY_RS34220
acs acetyl-CoA synthetase, AMP-forming BPHY_RS09860 BPHY_RS34900
ald-dh-CoA acetaldehyde dehydrogenase, acylating BPHY_RS17785 BPHY_RS22820
aldA lactaldehyde dehydrogenase BPHY_RS19265 BPHY_RS23615
D-LDH D-lactate dehydrogenase BPHY_RS12755 BPHY_RS12320
dddA 3-hydroxypropionate dehydrogenase BPHY_RS15535 BPHY_RS12090
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components BPHY_RS07455 BPHY_RS26895
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) BPHY_RS36905 BPHY_RS28260
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) BPHY_RS28255 BPHY_RS36910
glcF D-lactate dehydrogenase, FeS subunit GlcF BPHY_RS28250 BPHY_RS12770
gloA glyoxylase I BPHY_RS02000 BPHY_RS22525
gloB hydroxyacylglutathione hydrolase (glyoxalase II) BPHY_RS04410 BPHY_RS00590
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 BPHY_RS13655 BPHY_RS33205
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BPHY_RS28450 BPHY_RS25705
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) BPHY_RS20935 BPHY_RS00855
L-LDH L-lactate dehydrogenase BPHY_RS12155 BPHY_RS25845
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit BPHY_RS38180
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit BPHY_RS38175 BPHY_RS29775
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component BPHY_RS28260 BPHY_RS36905
lctO L-lactate oxidase or 2-monooxygenase BPHY_RS25845 BPHY_RS30720
lldE L-lactate dehydrogenase, LldE subunit BPHY_RS07460 BPHY_RS26905
lldF L-lactate dehydrogenase, LldF subunit BPHY_RS26895 BPHY_RS07455
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit BPHY_RS26905 BPHY_RS07460
lutB L-lactate dehydrogenase, LutB subunit BPHY_RS26895 BPHY_RS07455
lutC L-lactate dehydrogenase, LutC subunit BPHY_RS26900 BPHY_RS04090
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit BPHY_RS22975 BPHY_RS00775
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BPHY_RS22975 BPHY_RS00950
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components BPHY_RS22975 BPHY_RS00775
pccA propionyl-CoA carboxylase, alpha subunit BPHY_RS18000 BPHY_RS13340
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BPHY_RS13340 BPHY_RS18000
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit BPHY_RS18010
pco propanyl-CoA oxidase BPHY_RS06510 BPHY_RS12365
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase BPHY_RS06940 BPHY_RS21910
prpC 2-methylcitrate synthase BPHY_RS21905 BPHY_RS33390
prpD 2-methylcitrate dehydratase BPHY_RS21895
prpF methylaconitate isomerase BPHY_RS33400 BPHY_RS30045
RR42_RS28305 L-threonine:H+ symporter BPHY_RS03010 BPHY_RS32965
serP1 L-threonine uptake transporter SerP1 BPHY_RS03010 BPHY_RS32965
snatA L-threonine transporter snatA BPHY_RS14015 BPHY_RS13410
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase BPHY_RS01840 BPHY_RS27245
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase BPHY_RS20940 BPHY_RS34090
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) BPHY_RS02780

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