L-lysine catabolism in Rhizobium freirei PRF 81

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	RHSP_RS03670	RHSP_RS00535
hisM	L-lysine ABC transporter, permease component 1 (HisM)	RHSP_RS03680	RHSP_RS22960
hisQ	L-lysine ABC transporter, permease component 2 (HisQ)	RHSP_RS03675	RHSP_RS22965
hisP	L-lysine ABC transporter, ATPase component HisP	RHSP_RS08130	RHSP_RS00540
lysDH	L-lysine 6-dehydrogenase	RHSP_RS09400
amaB	L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd)	RHSP_RS09385	RHSP_RS26425
lysN	2-aminoadipate transaminase	RHSP_RS09390	RHSP_RS11085
hglS	D-2-hydroxyglutarate synthase	RHSP_RS09380
ydiJ	(R)-2-hydroxyglutarate dehydrogenase	RHSP_RS09395	RHSP_RS04905
Alternative steps:
alr	lysine racemase	RHSP_RS20500
amaA	L-pipecolate oxidase	RHSP_RS18170	RHSP_RS26430
amaD	D-lysine oxidase	RHSP_RS04250	RHSP_RS16255
atoB	acetyl-CoA C-acetyltransferase	RHSP_RS28350	RHSP_RS31340
bcd	butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit	RHSP_RS25890	RHSP_RS19445
bgtB	L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA	lysine decarboxylase	RHSP_RS13425	RHSP_RS27255
ctfA	butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit	RHSP_RS31330
ctfB	butanoyl-CoA:acetoacetate CoA-transferase, beta subunit	RHSP_RS31335
davA	5-aminovaleramidase	RHSP_RS00580	RHSP_RS14170
davB	L-lysine 2-monooxygenase
davD	glutarate semialdehyde dehydrogenase	RHSP_RS06225	RHSP_RS23545
davT	5-aminovalerate aminotransferase	RHSP_RS29535	RHSP_RS18005
dpkA	1-piperideine-2-carboxylate reductase	RHSP_RS05430	RHSP_RS26420
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	RHSP_RS02715	RHSP_RS30920
etfA	butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit	RHSP_RS26745	RHSP_RS07120
etfB	butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit	RHSP_RS26750	RHSP_RS32195
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	RHSP_RS12325	RHSP_RS06890
gcdG	succinyl-CoA:glutarate CoA-transferase	RHSP_RS10450	RHSP_RS31460
gcdH	glutaryl-CoA dehydrogenase	RHSP_RS12310	RHSP_RS31465
glaH	glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kal	3-aminobutyryl-CoA deaminase
kamA	L-lysine 2,3-aminomutase	RHSP_RS28195	RHSP_RS31215
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	RHSP_RS07720	RHSP_RS06675
kdd	3,5-diaminohexanoate dehydrogenase
lat	L-lysine 6-aminotransferase	RHSP_RS29535	RHSP_RS18005
lhgD	L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
LHT	L-lysine transporter
lysL	L-lysine transporter LysL
lysP	L-lysine:H+ symporter LysP	RHSP_RS26460
patA	cadaverine aminotransferase	RHSP_RS30730	RHSP_RS29535
patD	5-aminopentanal dehydrogenase	RHSP_RS13620	RHSP_RS16250
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.