GapMind for catabolism of small carbon sources

 

L-threonine catabolism in Azospirillum sp. B510

Best path

braC, braD, braE, braF, braG, tdcB, tdcE, pccA, pccB, epi, mcmA

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 (57 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) AZL_RS26820 AZL_RS31475
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) AZL_RS31500 AZL_RS12750
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) AZL_RS31495 AZL_RS29465
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) AZL_RS31490 AZL_RS29470
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) AZL_RS31485 AZL_RS16120
tdcB L-threonine dehydratase AZL_RS23080 AZL_RS25790
tdcE 2-ketobutyrate formate-lyase AZL_RS26860
pccA propionyl-CoA carboxylase, alpha subunit AZL_RS27040 AZL_RS16595
pccB propionyl-CoA carboxylase, beta subunit AZL_RS27045 AZL_RS16585
epi methylmalonyl-CoA epimerase AZL_RS11340
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components AZL_RS27035
Alternative steps:
ackA acetate kinase AZL_RS22905 AZL_RS03675
acn (2R,3S)-2-methylcitrate dehydratase AZL_RS26840 AZL_RS13010
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) AZL_RS13010
acs acetyl-CoA synthetase, AMP-forming AZL_RS12975 AZL_RS11460
adh acetaldehyde dehydrogenase (not acylating) AZL_RS28845 AZL_RS19620
ald-dh-CoA acetaldehyde dehydrogenase, acylating AZL_RS19645
aldA lactaldehyde dehydrogenase AZL_RS20100 AZL_RS28845
D-LDH D-lactate dehydrogenase AZL_RS32085 AZL_RS04840
dddA 3-hydroxypropionate dehydrogenase AZL_RS27190 AZL_RS09520
DVU3032 L-lactate dehydrogenase, LutC-like component AZL_RS32100
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components AZL_RS32095
gcvH glycine cleavage system, H component (lipoyl protein) AZL_RS08400
gcvP glycine cleavage system, P component (glycine decarboxylase) AZL_RS08390 AZL_RS08395
gcvT glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) AZL_RS08405 AZL_RS25435
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) AZL_RS02630 AZL_RS04840
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) AZL_RS02635
glcF D-lactate dehydrogenase, FeS subunit GlcF AZL_RS02640
gloA glyoxylase I AZL_RS08525 AZL_RS26050
gloB hydroxyacylglutathione hydrolase (glyoxalase II) AZL_RS31360 AZL_RS26715
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 AZL_RS14255 AZL_RS21160
iolA malonate semialdehyde dehydrogenase (CoA-acylating) AZL_RS19190 AZL_RS29835
kbl glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) AZL_RS01705
L-LDH L-lactate dehydrogenase AZL_RS17080 AZL_RS14350
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit AZL_RS03410
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit AZL_RS03415 AZL_RS22205
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component AZL_RS04840 AZL_RS02630
lctO L-lactate oxidase or 2-monooxygenase AZL_RS17080 AZL_RS21195
lldE L-lactate dehydrogenase, LldE subunit AZL_RS32090
lldF L-lactate dehydrogenase, LldF subunit AZL_RS32095
lldG L-lactate dehydrogenase, LldG subunit
lpd dihydrolipoyl dehydrogenase AZL_RS08045 AZL_RS13320
ltaE L-threonine aldolase AZL_RS29725 AZL_RS05335
lutA L-lactate dehydrogenase, LutA subunit AZL_RS32090
lutB L-lactate dehydrogenase, LutB subunit AZL_RS32095
lutC L-lactate dehydrogenase, LutC subunit AZL_RS32100
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit AZL_RS27035
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit AZL_RS27035
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit AZL_RS27040 AZL_RS05680
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit AZL_RS23315 AZL_RS16595
pco propanyl-CoA oxidase AZL_RS29505
phtA L-threonine uptake permease PhtA
prpB 2-methylisocitrate lyase AZL_RS27755
prpC 2-methylcitrate synthase AZL_RS08510 AZL_RS32055
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
pta phosphate acetyltransferase AZL_RS22910 AZL_RS03670
RR42_RS28305 L-threonine:H+ symporter
serP1 L-threonine uptake transporter SerP1
snatA L-threonine transporter snatA AZL_RS27015
sstT L-threonine:Na+ symporter SstT
tdcC L-threonine:H+ symporter TdcC AZL_RS23395
tdh L-threonine 3-dehydrogenase AZL_RS19645 AZL_RS31225
tynA aminoacetone oxidase
yvgN methylglyoxal reductase (NADPH-dependent) AZL_RS31900

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