GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Best path

snatA, ltaE, adh, acs, 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 (46 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
snatA L-threonine transporter snatA HTA01S_RS09085
ltaE L-threonine aldolase HTA01S_RS21310 HTA01S_RS18870
adh acetaldehyde dehydrogenase (not acylating) HTA01S_RS03325 HTA01S_RS11515
acs acetyl-CoA synthetase, AMP-forming HTA01S_RS22665 HTA01S_RS06610
gcvP glycine cleavage system, P component (glycine decarboxylase) HTA01S_RS02260
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) HTA01S_RS02250
gcvH glycine cleavage system, H component (lipoyl protein) HTA01S_RS02255
lpd dihydrolipoyl dehydrogenase HTA01S_RS00005 HTA01S_RS07650
Alternative steps:
ackA acetate kinase HTA01S_RS04935
acn (2R,3S)-2-methylcitrate dehydratase HTA01S_RS17335 HTA01S_RS17285
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) HTA01S_RS17335
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase HTA01S_RS10225 HTA01S_RS03325
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) HTA01S_RS07615
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) HTA01S_RS16520 HTA01S_RS12260
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) HTA01S_RS16515 HTA01S_RS04365
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) HTA01S_RS16510 HTA01S_RS04370
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) HTA01S_RS16505 HTA01S_RS14300
D-LDH D-lactate dehydrogenase HTA01S_RS10365 HTA01S_RS02835
dddA 3-hydroxypropionate dehydrogenase HTA01S_RS09515 HTA01S_RS06370
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
epi methylmalonyl-CoA epimerase HTA01S_RS06740
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) HTA01S_RS20820 HTA01S_RS10365
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) HTA01S_RS09775 HTA01S_RS10365
glcF D-lactate dehydrogenase, FeS subunit GlcF HTA01S_RS09770
gloA glyoxylase I HTA01S_RS17570
gloB hydroxyacylglutathione hydrolase (glyoxalase II) HTA01S_RS07255 HTA01S_RS09210
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 HTA01S_RS03890 HTA01S_RS03885
iolA malonate semialdehyde dehydrogenase (CoA-acylating) HTA01S_RS06165 HTA01S_RS16360
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) HTA01S_RS00505
L-LDH L-lactate dehydrogenase HTA01S_RS20150 HTA01S_RS00900
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit HTA01S_RS15330
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit HTA01S_RS15335 HTA01S_RS01940
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component HTA01S_RS10365 HTA01S_RS20820
lctO L-lactate oxidase or 2-monooxygenase HTA01S_RS00900 HTA01S_RS20150
lldE L-lactate dehydrogenase, LldE subunit
lldF L-lactate dehydrogenase, LldF subunit
lldG L-lactate dehydrogenase, LldG subunit
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 HTA01S_RS06715 HTA01S_RS04855
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit HTA01S_RS06715 HTA01S_RS09875
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components HTA01S_RS06715 HTA01S_RS04855
pccA propionyl-CoA carboxylase, alpha subunit HTA01S_RS06730 HTA01S_RS11160
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit HTA01S_RS06730 HTA01S_RS04010
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit HTA01S_RS06725 HTA01S_RS11130
pco propanyl-CoA oxidase HTA01S_RS14830 HTA01S_RS11035
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase HTA01S_RS22560
prpC 2-methylcitrate synthase HTA01S_RS17235
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase HTA01S_RS19850 HTA01S_RS18160
pta phosphate acetyltransferase HTA01S_RS23970
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase HTA01S_RS16595 HTA01S_RS10060
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase HTA01S_RS08210 HTA01S_RS06450
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent)

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