GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Nocardioides dokdonensis FR1436

Best path

braC, braD, braE, braF, braG, 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 (45 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) I601_RS18165
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) I601_RS18185 I601_RS10450
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) I601_RS18180 I601_RS05895
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) I601_RS18175 I601_RS19350
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) I601_RS18170 I601_RS10465
ltaE L-threonine aldolase I601_RS13330 I601_RS14510
adh acetaldehyde dehydrogenase (not acylating) I601_RS01590 I601_RS05735
acs acetyl-CoA synthetase, AMP-forming I601_RS07695 I601_RS18315
gcvP glycine cleavage system, P component (glycine decarboxylase) I601_RS16090
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) I601_RS14275
gcvH glycine cleavage system, H component (lipoyl protein) I601_RS16065
lpd dihydrolipoyl dehydrogenase I601_RS01085 I601_RS05875
Alternative steps:
ackA acetate kinase
acn (2R,3S)-2-methylcitrate dehydratase I601_RS17670
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) I601_RS17670
ald-dh-CoA acetaldehyde dehydrogenase, acylating I601_RS02750 I601_RS17195
aldA lactaldehyde dehydrogenase I601_RS01130 I601_RS12775
D-LDH D-lactate dehydrogenase I601_RS05925 I601_RS19110
dddA 3-hydroxypropionate dehydrogenase I601_RS09160 I601_RS02690
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components I601_RS07400
epi methylmalonyl-CoA epimerase I601_RS19255
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) I601_RS19110 I601_RS05925
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) I601_RS19110 I601_RS05925
glcF D-lactate dehydrogenase, FeS subunit GlcF
gloA glyoxylase I
gloB hydroxyacylglutathione hydrolase (glyoxalase II) I601_RS14740 I601_RS01675
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 I601_RS16330 I601_RS19165
iolA malonate semialdehyde dehydrogenase (CoA-acylating) I601_RS07030 I601_RS08960
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase)
L-LDH L-lactate dehydrogenase I601_RS05920 I601_RS19710
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit I601_RS19150
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component I601_RS19110 I601_RS05925
lctO L-lactate oxidase or 2-monooxygenase I601_RS19710 I601_RS18465
lldE L-lactate dehydrogenase, LldE subunit I601_RS07395
lldF L-lactate dehydrogenase, LldF subunit I601_RS07400
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit I601_RS07395
lutB L-lactate dehydrogenase, LutB subunit I601_RS07400
lutC L-lactate dehydrogenase, LutC subunit
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit I601_RS01215 I601_RS19390
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit I601_RS01215 I601_RS19390
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components I601_RS01215 I601_RS08155
pccA propionyl-CoA carboxylase, alpha subunit I601_RS00935 I601_RS06760
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit I601_RS00950 I601_RS00935
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit I601_RS05415
pccB propionyl-CoA carboxylase, beta subunit I601_RS00885 I601_RS18425
pco propanyl-CoA oxidase I601_RS08210 I601_RS10230
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase I601_RS09645 I601_RS03455
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase
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 I601_RS07215 I601_RS09980
tdcC L-threonine:H+ symporter TdcC
tdcE 2-ketobutyrate formate-lyase
tdh L-threonine 3-dehydrogenase I601_RS03520 I601_RS01680
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) I601_RS04705

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