GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Pseudomonas benzenivorans DSM 8628

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 (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) BLS63_RS09655 BLS63_RS23775
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BLS63_RS09650 BLS63_RS23780
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) BLS63_RS09645 BLS63_RS23785
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BLS63_RS09640 BLS63_RS23790
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BLS63_RS09635 BLS63_RS23795
ltaE L-threonine aldolase BLS63_RS26060 BLS63_RS04015
adh acetaldehyde dehydrogenase (not acylating) BLS63_RS17270 BLS63_RS19270
ackA acetate kinase BLS63_RS09000 BLS63_RS21520
pta phosphate acetyltransferase BLS63_RS21525
gcvP glycine cleavage system, P component (glycine decarboxylase) BLS63_RS24800 BLS63_RS11160
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) BLS63_RS24785 BLS63_RS11170
gcvH glycine cleavage system, H component (lipoyl protein) BLS63_RS11165 BLS63_RS24805
lpd dihydrolipoyl dehydrogenase BLS63_RS00200 BLS63_RS25065
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase BLS63_RS00675 BLS63_RS00850
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BLS63_RS00675 BLS63_RS00030
acs acetyl-CoA synthetase, AMP-forming BLS63_RS26090 BLS63_RS23690
ald-dh-CoA acetaldehyde dehydrogenase, acylating BLS63_RS02455 BLS63_RS17010
aldA lactaldehyde dehydrogenase BLS63_RS22155 BLS63_RS03170
D-LDH D-lactate dehydrogenase BLS63_RS14300 BLS63_RS16595
dddA 3-hydroxypropionate dehydrogenase BLS63_RS09135 BLS63_RS14560
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components BLS63_RS14310
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) BLS63_RS18815 BLS63_RS10140
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) BLS63_RS18820 BLS63_RS10140
glcF D-lactate dehydrogenase, FeS subunit GlcF BLS63_RS18825
gloA glyoxylase I BLS63_RS23180 BLS63_RS17660
gloB hydroxyacylglutathione hydrolase (glyoxalase II) BLS63_RS09480 BLS63_RS01065
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 BLS63_RS06660 BLS63_RS21705
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BLS63_RS14055 BLS63_RS21720
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) BLS63_RS04165
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 BLS63_RS18395
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component BLS63_RS18815 BLS63_RS16595
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit BLS63_RS14315
lldF L-lactate dehydrogenase, LldF subunit BLS63_RS14310
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit BLS63_RS14315
lutB L-lactate dehydrogenase, LutB subunit BLS63_RS14310
lutC L-lactate dehydrogenase, LutC subunit BLS63_RS14305
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
pccA propionyl-CoA carboxylase, alpha subunit BLS63_RS18330 BLS63_RS24345
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BLS63_RS15655 BLS63_RS04465
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit BLS63_RS24335 BLS63_RS18315
pco propanyl-CoA oxidase BLS63_RS14585
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase BLS63_RS00665 BLS63_RS21130
prpC 2-methylcitrate synthase BLS63_RS00670 BLS63_RS00165
prpD 2-methylcitrate dehydratase BLS63_RS00685
prpF methylaconitate isomerase BLS63_RS00680 BLS63_RS13860
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA BLS63_RS04515
sstT L-threonine:Na+ symporter SstT BLS63_RS19390
tdcB L-threonine dehydratase BLS63_RS16565
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase BLS63_RS17235 BLS63_RS10745
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) BLS63_RS12250 BLS63_RS22095

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