GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Chryseobacterium viscerum 687B-08

Best path

RR42_RS28305, tdh, kbl, 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 (37 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
RR42_RS28305 L-threonine:H+ symporter C1634_RS09660
tdh L-threonine 3-dehydrogenase C1634_RS07115 C1634_RS22675
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) C1634_RS06780 C1634_RS08690
gcvP glycine cleavage system, P component (glycine decarboxylase) C1634_RS12275
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) C1634_RS07210 C1634_RS24635
gcvH glycine cleavage system, H component (lipoyl protein) C1634_RS23630 C1634_RS24640
lpd dihydrolipoyl dehydrogenase C1634_RS13265 C1634_RS05600
Alternative steps:
ackA acetate kinase
acn (2R,3S)-2-methylcitrate dehydratase C1634_RS21970
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
acs acetyl-CoA synthetase, AMP-forming C1634_RS07705 C1634_RS07710
adh acetaldehyde dehydrogenase (not acylating) C1634_RS19425 C1634_RS04075
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase C1634_RS04075 C1634_RS08590
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB)
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD)
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) C1634_RS11570 C1634_RS05280
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) C1634_RS11570 C1634_RS09390
D-LDH D-lactate dehydrogenase C1634_RS21995 C1634_RS07230
dddA 3-hydroxypropionate dehydrogenase C1634_RS05380
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase C1634_RS16040
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD)
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE)
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I C1634_RS13340 C1634_RS05300
gloB hydroxyacylglutathione hydrolase (glyoxalase II) C1634_RS10145 C1634_RS06695
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 C1634_RS22030 C1634_RS25300
iolA malonate semialdehyde dehydrogenase (CoA-acylating) C1634_RS25320 C1634_RS04075
L-LDH L-lactate dehydrogenase C1634_RS03690
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit C1634_RS13775
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit
lldF L-lactate dehydrogenase, LldF subunit
lldG L-lactate dehydrogenase, LldG subunit
ltaE L-threonine aldolase C1634_RS11295
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 C1634_RS21620 C1634_RS19875
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit C1634_RS21620 C1634_RS19875
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components C1634_RS19875 C1634_RS21620
pccA propionyl-CoA carboxylase, alpha subunit C1634_RS20040
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit C1634_RS20040
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit C1634_RS16490
pco propanyl-CoA oxidase C1634_RS21750 C1634_RS08940
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase C1634_RS10620 C1634_RS25335
prpC 2-methylcitrate synthase C1634_RS25330 C1634_RS00260
prpD 2-methylcitrate dehydratase C1634_RS25325
prpF methylaconitate isomerase
pta phosphate acetyltransferase C1634_RS23645
serP1 L-threonine uptake transporter SerP1 C1634_RS09660
snatA L-threonine transporter snatA
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase C1634_RS17595 C1634_RS18260
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) C1634_RS14680 C1634_RS12965

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