GapMind for catabolism of small carbon sources


L-threonine catabolism in Belnapia rosea CPCC 100156

Best path

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


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 (50 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) BLR02_RS12505
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BLR02_RS12525 BLR02_RS19370
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) BLR02_RS12520 BLR02_RS25430
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BLR02_RS12515 BLR02_RS03485
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BLR02_RS12510 BLR02_RS10300
ltaE L-threonine aldolase BLR02_RS01970 BLR02_RS04215
adh acetaldehyde dehydrogenase (not acylating) BLR02_RS07320 BLR02_RS18460
acs acetyl-CoA synthetase, AMP-forming BLR02_RS09295 BLR02_RS17730
gcvP glycine cleavage system, P component (glycine decarboxylase) BLR02_RS15325
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) BLR02_RS15335
gcvH glycine cleavage system, H component (lipoyl protein) BLR02_RS15330
lpd dihydrolipoyl dehydrogenase BLR02_RS01950 BLR02_RS16900
Alternative steps:
ackA acetate kinase BLR02_RS16785
acn (2R,3S)-2-methylcitrate dehydratase BLR02_RS06435
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BLR02_RS06435
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase BLR02_RS04250 BLR02_RS07320
D-LDH D-lactate dehydrogenase BLR02_RS13975 BLR02_RS19165
dddA 3-hydroxypropionate dehydrogenase BLR02_RS18510 BLR02_RS02205
DVU3032 L-lactate dehydrogenase, LutC-like component BLR02_RS08915
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components BLR02_RS08910
epi methylmalonyl-CoA epimerase
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) BLR02_RS08760 BLR02_RS13975
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) BLR02_RS08765 BLR02_RS18505
glcF D-lactate dehydrogenase, FeS subunit GlcF BLR02_RS08785 BLR02_RS18265
gloA glyoxylase I BLR02_RS05210 BLR02_RS16530
gloB hydroxyacylglutathione hydrolase (glyoxalase II) BLR02_RS00015 BLR02_RS17670
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 BLR02_RS23955 BLR02_RS08090
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BLR02_RS18460 BLR02_RS07320
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) BLR02_RS13350 BLR02_RS19580
L-LDH L-lactate dehydrogenase BLR02_RS22460 BLR02_RS22355
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit BLR02_RS25820
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component BLR02_RS13975 BLR02_RS08760
lctO L-lactate oxidase or 2-monooxygenase BLR02_RS05520
lldE L-lactate dehydrogenase, LldE subunit BLR02_RS18265
lldF L-lactate dehydrogenase, LldF subunit BLR02_RS08910
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit BLR02_RS18265
lutB L-lactate dehydrogenase, LutB subunit BLR02_RS08910
lutC L-lactate dehydrogenase, LutC subunit BLR02_RS08915
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 BLR02_RS03535 BLR02_RS01010
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BLR02_RS01010 BLR02_RS23135
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit BLR02_RS03535
pccB propionyl-CoA carboxylase, beta subunit BLR02_RS03530 BLR02_RS23125
pco propanyl-CoA oxidase BLR02_RS06730
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase BLR02_RS15615 BLR02_RS04390
prpC 2-methylcitrate synthase BLR02_RS19010 BLR02_RS05735
prpD 2-methylcitrate dehydratase BLR02_RS19020
prpF methylaconitate isomerase BLR02_RS04850 BLR02_RS20970
pta phosphate acetyltransferase BLR02_RS16780 BLR02_RS20655
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 BLR02_RS18970 BLR02_RS15635
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase BLR02_RS07915 BLR02_RS05380
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) BLR02_RS23585 BLR02_RS01590

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.



Related tools

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