GapMind for catabolism of small carbon sources

 

Definition of L-lysine catabolism

As rules and steps, or see full text

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.

Steps

lysP: L-lysine:H+ symporter LysP

LHT: L-lysine transporter

Slc7a1: L-lysine transporter Slc7a1

lysL: L-lysine transporter LysL

argT: L-lysine ABC transporter, substrate-binding component ArgT

hisM: L-lysine ABC transporter, permease component 1 (HisM)

hisQ: L-lysine ABC transporter, permease component 2 (HisQ)

hisP: L-lysine ABC transporter, ATPase component HisP

bgtB: L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)

atoB: acetyl-CoA C-acetyltransferase

gcdH: glutaryl-CoA dehydrogenase

ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase

fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase

glaH: glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)

lhgD: L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)

gcdG: succinyl-CoA:glutarate CoA-transferase

davT: 5-aminovalerate aminotransferase

davD: glutarate semialdehyde dehydrogenase

lysN: 2-aminoadipate transaminase

hglS: D-2-hydroxyglutarate synthase

ydiJ: (R)-2-hydroxyglutarate dehydrogenase

cadA: lysine decarboxylase

patA: cadaverine aminotransferase

patD: 5-aminopentanal dehydrogenase

davB: L-lysine 2-monooxygenase

davA: 5-aminovaleramidase

alr: lysine racemase

amaD: D-lysine oxidase

dpkA: 1-piperideine-2-carboxylate reductase

amaA: L-pipecolate oxidase

amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd)

lat: L-lysine 6-aminotransferase

lysDH: L-lysine 6-dehydrogenase

kamA: L-lysine 2,3-aminomutase

kamD: L-beta-lysine 5,6-aminomutase, alpha subunit

kamE: L-beta-lysine 5,6-aminomutase, beta subunit

kdd: 3,5-diaminohexanoate dehydrogenase

kce: (S)-5-amino-3-oxohexanoate cleavage enzyme

kal: 3-aminobutyryl-CoA deaminase

bcd: butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit

etfA: butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit

etfB: butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit

ctfA: butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit

ctfB: butanoyl-CoA:acetoacetate CoA-transferase, beta subunit

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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