GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Pontibacter ramchanderi LP43

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 (40 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
snatA L-threonine transporter snatA BD749_RS07320
ltaE L-threonine aldolase BD749_RS01230 BD749_RS11795
adh acetaldehyde dehydrogenase (not acylating) BD749_RS08950 BD749_RS10835
acs acetyl-CoA synthetase, AMP-forming BD749_RS07975 BD749_RS07980
gcvP glycine cleavage system, P component (glycine decarboxylase) BD749_RS12725
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) BD749_RS07855
gcvH glycine cleavage system, H component (lipoyl protein) BD749_RS17075
lpd dihydrolipoyl dehydrogenase BD749_RS18705 BD749_RS14590
Alternative steps:
ackA acetate kinase
acn (2R,3S)-2-methylcitrate dehydratase
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
ald-dh-CoA acetaldehyde dehydrogenase, acylating
aldA lactaldehyde dehydrogenase BD749_RS10835 BD749_RS08950
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) BD749_RS11320 BD749_RS14880
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BD749_RS11320 BD749_RS12890
D-LDH D-lactate dehydrogenase BD749_RS06090 BD749_RS16365
dddA 3-hydroxypropionate dehydrogenase
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components BD749_RS12620
epi methylmalonyl-CoA epimerase BD749_RS06500
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) BD749_RS15860
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE)
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I BD749_RS01065 BD749_RS04290
gloB hydroxyacylglutathione hydrolase (glyoxalase II) BD749_RS17115 BD749_RS00480
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 BD749_RS17005 BD749_RS07655
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BD749_RS10835
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) BD749_RS10390 BD749_RS04505
L-LDH L-lactate dehydrogenase BD749_RS15730
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component BD749_RS15860
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit BD749_RS13090
lldF L-lactate dehydrogenase, LldF subunit BD749_RS12620
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit BD749_RS13090
lutB L-lactate dehydrogenase, LutB subunit BD749_RS12620
lutC L-lactate dehydrogenase, LutC subunit BD749_RS08530
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit BD749_RS08120 BD749_RS03410
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BD749_RS08120
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components BD749_RS03410 BD749_RS08120
pccA propionyl-CoA carboxylase, alpha subunit BD749_RS02955 BD749_RS03880
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BD749_RS02955 BD749_RS03880
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit BD749_RS15550 BD749_RS08175
pco propanyl-CoA oxidase BD749_RS08765 BD749_RS11220
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase BD749_RS13120
prpC 2-methylcitrate synthase BD749_RS03380
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase BD749_RS17060
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
sstT L-threonine:Na+ symporter SstT
tdcB L-threonine dehydratase BD749_RS13335
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase BD749_RS10400 BD749_RS04745
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) BD749_RS12640

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