L-lysine catabolism in Pseudomonas taeanensis MS-3

Best path

argT, hisM, hisQ, hisP, lysDH, amaB, lysN, hglS, ydiJ

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.

• all:
  • lysine-transport, cadA, patA, patD and 5-aminovalerate-degradation
  • or lysine-transport, davB, davA and 5-aminovalerate-degradation
  • or lysine-transport, alr, amaD, dpkA, amaA, amaB and L-2-aminoadipate-degradation
  • or lysine-transport, lat, amaB and L-2-aminoadipate-degradation
  • or lysine-transport, lysDH, amaB and L-2-aminoadipate-degradation
  • or lysine-transport, kamA, kamD, kamE, kdd, kce, kal, bcd, etfA, etfB, ctfA, ctfB and atoB
  • Comment: In pathway I, lysine is decarboxylated by cadA to cadaverine (1,5-diaminopentane), transaminated to 5-aminopentanal by patA, and oxidized to 5-aminovalerate by patD. In pathway IV, the monooxygenase/decarboxylase davB forms 5-aminopentanamide, which is hydrolyzed to 5-aminovalerate (5-aminopentanoate). In pathway V, the racemase alr forms D-lysine, which is oxidized to 6-amino-2-oxo-hexanoate, spontaneously decarboxylates to 1-piperideine-2-carboxylate, a reductase forms L-pipecolate, an oxidase forms 1-piperideine-6-carboxylate, and a dehydrogenase forms L-2-aminoadipate. In pathway VI, lysine 6-aminotransferase (lat) forms (S)-2-amino-6-oxohexanoate, which spontaenously dehydrates to 1-piperideine 6-carboxylate, and a dehydrogenase forms L-2-aminoadipate In pathway VIII, L-lysine 6-dehydrogenase (lysDH) forms (S)-2-amino-6-oxohexanoate, which spontaenously dehydrates to 1-piperideine 6-carboxylate, and a dehydrogenase forms L-2-aminoadipate. In the fermentative pathway, lysine 2,3-aminomutase (kamA) forms L-beta-lysine, another aminomutase forms (3S,5S)-3,5-diaminohexanoate, a dehydrogenase (deaminating) forms (S)-5-amino-3-oxohexanoate, a cleavage enzyme (thiolase) uses acetyl-CoA to form (S)-3-aminobutanoyl-CoA and acetoacetate, a deaminase forms crotonyl-CoA, a dehydrogenase forms butanoyl-CoA, a CoA-transferase converts the butanoyl-CoA and acetoacetate to butanoate (a waste product) and acetoacetyl-CoA, and a C-acetyltransferase (atoB) splits acetyl-CoA to two acetyl-CoA.
• L-2-aminoadipate-degradation: lysN, hglS and ydiJ
  • Comment: L-2-aminoadipate is an intermediate in L-lysine degradation pathways V and VI (link, link). A transaminase forms 2-oxoadipate, a oxygenase/decarboxylase (D-2-hydroxyglutarate synthase) forms (R)-2-hydroxyglutarate, and a dehydrogenase forms 2-oxoglutarate, which is an intermediate in the TCA cycle.
• 5-aminovalerate-degradation: davT, davD and glutarate-degradation
  • Comment: 5-aminovalerate is an intermediate in L-lysine degradation (link, link). It is transaminated to glutarate semialdehyde and oxidized to glutarate. (A fermentative pathway via 5-hydroxyvalerate has also been reported, but does not seem to be fully linked to sequence; see pathway 5 of PMID:11759672.)
• glutarate-degradation:
  • glaH and lhgD
  • or gcdG and glutaryl-CoA-degradation
  • Comment: Glutarate is an intermediate in L-lysine degradation. As part of MetaCyc pathway L-lysine degradation I (link), gluratate is hydroxylated to L-2-hydroxyglutarate (also known as (S)-2-hydroxyglutarate) by a 2-oxoglutarate-dependent oxidase. This reaction releases succinate (a TCA cycle intermediate) and CO2. A dehydrogenase then oxidizes to L-2-hydroxyglutarate to regenerate 2-oxoglutarate. Alternatively, as part of pathway IV (link), glutarate can be activated to glutaryl-CoA by a CoA-transferase. Glutaryl-CoA degradation (link) involves glutaryl-CoA dehydrogenase (decarboxylating) to crotonyl-CoA (trans-but-2-enoyl-CoA), hydration to (S)-hydroxybutanoyl-CoA, oxidization to acetoacetyl-CoA, and cleavage by a C-acetyltransferase to two acetyl-CoA.
• glutaryl-CoA-degradation: gcdH, ech, fadB and atoB
  • Comment: In MetaCyc pathway glutaryl-CoA degradation (link), glutaryl-CoA is oxidized to (E)-glutaconyl-CoA and oxidatively decarboxylated to crotonyl-CoA (both by the same enzyme), hydrated to 3-hydroxybutanoyl-CoA, oxidized to acetoacetyl-CoA, and cleaved to two acetyl-CoA.
• lysine-transport:
  • lysP
  • or LHT
  • or Slc7a1
  • or lysL
  • or argT, hisM, hisQ and hisP
  • or bgtB and hisP
  • Comment: Transporters were identified using query: transporter:lysine:L-lysine:lys:L-lys

44 steps (33 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
argT	L-lysine ABC transporter, substrate-binding component ArgT	TMS3_RS04805	TMS3_RS12735
hisM	L-lysine ABC transporter, permease component 1 (HisM)	TMS3_RS04795	TMS3_RS12725
hisQ	L-lysine ABC transporter, permease component 2 (HisQ)	TMS3_RS04800	TMS3_RS12730
hisP	L-lysine ABC transporter, ATPase component HisP	TMS3_RS04810	TMS3_RS12740
lysDH	L-lysine 6-dehydrogenase	TMS3_RS12710
amaB	L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd)	TMS3_RS12820	TMS3_RS02055
lysN	2-aminoadipate transaminase	TMS3_RS12810	TMS3_RS22180
hglS	D-2-hydroxyglutarate synthase	TMS3_RS12800
ydiJ	(R)-2-hydroxyglutarate dehydrogenase	TMS3_RS01750	TMS3_RS19250
Alternative steps:
alr	lysine racemase	TMS3_RS00035	TMS3_RS05880
amaA	L-pipecolate oxidase	TMS3_RS07885	TMS3_RS16830
amaD	D-lysine oxidase	TMS3_RS01605
atoB	acetyl-CoA C-acetyltransferase	TMS3_RS07820	TMS3_RS15420
bcd	butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit	TMS3_RS15300	TMS3_RS15395
bgtB	L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA	lysine decarboxylase	TMS3_RS12705	TMS3_RS07880
ctfA	butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit	TMS3_RS15430
ctfB	butanoyl-CoA:acetoacetate CoA-transferase, beta subunit	TMS3_RS15425
davA	5-aminovaleramidase	TMS3_RS13415	TMS3_RS09705
davB	L-lysine 2-monooxygenase
davD	glutarate semialdehyde dehydrogenase	TMS3_RS02055	TMS3_RS10945
davT	5-aminovalerate aminotransferase	TMS3_RS12810	TMS3_RS11185
dpkA	1-piperideine-2-carboxylate reductase	TMS3_RS08405	TMS3_RS01630
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	TMS3_RS14965	TMS3_RS21560
etfA	butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit	TMS3_RS08875	TMS3_RS21890
etfB	butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit	TMS3_RS08870	TMS3_RS21885
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	TMS3_RS21560	TMS3_RS22410
gcdG	succinyl-CoA:glutarate CoA-transferase	TMS3_RS02090	TMS3_RS09880
gcdH	glutaryl-CoA dehydrogenase	TMS3_RS02095	TMS3_RS15395
glaH	glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)	TMS3_RS10930
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	TMS3_RS00610
kdd	3,5-diaminohexanoate dehydrogenase
lat	L-lysine 6-aminotransferase	TMS3_RS08980	TMS3_RS12810
lhgD	L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)	TMS3_RS10935
LHT	L-lysine transporter
lysL	L-lysine transporter LysL
lysP	L-lysine:H+ symporter LysP
patA	cadaverine aminotransferase	TMS3_RS11185	TMS3_RS03905
patD	5-aminopentanal dehydrogenase	TMS3_RS09905	TMS3_RS00885
Slc7a1	L-lysine transporter Slc7a1

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.