GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Burkholderia vietnamiensis G4

Best path

lysP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB

Rules

Overview: Lysine degradation in GapMind is based on many metacyc pathways (link), including L-lysine degradation I via cadaverine (link), pathway IV via lysine monooxygenase (link), pathway V via D-lysine (link), pathway VI via lysine 6-aminotransferase (link), pathway VIII via lysine 6-dehydrogenase (link), and fermentation to acetate and butanoate (link). Pathway X (link) is similar to pathway I (with cadaverine and glutarate as intermediates), but glutarate is consumed via glutaryl-CoA (as in pathway IV); it does not introduce any new steps. Pathways II (L-pipecolate pathway) and III (via N6-acetyllysine) and VII (via 6-amino-2-oxohexanoate) and IX (similar to pathway IV) and XI (via saccharopine) are not thought to occur in prokaryotes and are not included in GapMind.

44 steps (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP WP_011881451.1 WP_011881650.1
cadA lysine decarboxylase WP_011885706.1 WP_011882700.1
patA cadaverine aminotransferase WP_011881939.1 WP_011879744.1
patD 5-aminopentanal dehydrogenase WP_011880783.1 WP_011879745.1
davT 5-aminovalerate aminotransferase WP_011880937.1 WP_011884023.1
davD glutarate semialdehyde dehydrogenase WP_011880938.1 WP_011880486.1
gcdG succinyl-CoA:glutarate CoA-transferase WP_011884420.1 WP_011882039.1
gcdH glutaryl-CoA dehydrogenase WP_011883419.1 WP_011880846.1
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase WP_011883164.1 WP_011881868.1
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase WP_011885989.1 WP_011886130.1
atoB acetyl-CoA C-acetyltransferase WP_011884947.1 WP_011879792.1
Alternative steps:
alr lysine racemase WP_011885163.1 WP_011876059.1
amaA L-pipecolate oxidase WP_011882022.1 WP_011886241.1
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) WP_011880871.1 WP_011876068.1
amaD D-lysine oxidase WP_011880730.1 WP_011880475.1
argT L-lysine ABC transporter, substrate-binding component ArgT WP_034192590.1 WP_011881551.1
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit WP_011880691.1 WP_011880846.1
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit WP_011884535.1 WP_011881086.1
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit WP_011884536.1 WP_011881085.1
davA 5-aminovaleramidase WP_011884876.1 WP_011875588.1
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase WP_011882174.1 WP_011881987.1
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit WP_011880114.1 WP_011876072.1
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit WP_011880115.1 WP_041494177.1
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM) WP_011885685.1 WP_011876051.1
hisP L-lysine ABC transporter, ATPase component HisP WP_011879720.1 WP_011884020.1
hisQ L-lysine ABC transporter, permease component 2 (HisQ) WP_011876050.1 WP_011885684.1
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase
kamD L-beta-lysine 5,6-aminomutase, alpha subunit
kamE L-beta-lysine 5,6-aminomutase, beta subunit
kce (S)-5-amino-3-oxohexanoate cleavage enzyme WP_011880746.1
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase WP_011880937.1 WP_011880718.1
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) WP_011886286.1
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase WP_011884898.1
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase WP_011885633.1 WP_011880937.1
Slc7a1 L-lysine transporter Slc7a1 WP_011886294.1
ydiJ (R)-2-hydroxyglutarate dehydrogenase WP_011880666.1 WP_011884515.1

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