L-glutamate catabolism in Rhizobium leguminosarum 3841

Best path

braC, braD, braE, braF, braG, gdhA

Rules

Overview: Glutamate is a single transamination reaction from 2-oxoglutarate (alpha-ketoglutarate), which is an intermediate in the TCA cycle. Amino acid transaminases are often non-specific, so glutamate catabolism could be considered trivial. However, many amino acid transaminases are 2-oxoglutarate dependent, so they cannot contribute to glutamate catabolism. And even if the amino group is transfered elsewhere, the ammonium group still needs to be liberated somehow. GapMind represents glutamate degradation using MetaCyc pathways L-glutamate degradation I (glutamate dehydrogenase, link), pathway II via aspartate ammonia-lyase (link), and pathway VI via glutamate mutase (link). Several other MetaCyc pathways are not included in GapMind. Pathway IV (via gamma-aminobutanoate, link) is not thought to occur in prokaryotes. Pathways V (via hydroxyglutarate, link) and XI (reductive Stickland reaction, link) combine glutamate dehydrogenase with reductive pathways; these are omitted because glutamate dehydrogenase alone suffices for catabolism under respiratory conditions. Pathways VII (to butanoate, link) and VIII (to propanoate, link) are similar to pathway VI but also describe the fermentation of the pyruvate. Pathway IX (via 4-aminobutanoate, link) does not yield net consumption of glutamate: the catabolism of 4-aminobutanoate relies on a transamination reaction that converts 2-oxoglutarate to glutamate.

• all:
  • glutamate-transport and gdhA
  • or glutamate-transport and aspA
  • or glutamate-transport, glmS, glmE, mal, fumD and mcl
  • Comment: GdhA is glutamate dehydrogenase (forming 2-oxoglutarate and ammonia). In pathway II, glutamate and oxaloacetate are transaminated to 2-oxoglutarate and aspartate, and the aspartate is cleaved to fumarate and ammonium by aspA. (The transamination reaction is not represented. Both oxaloacetate and fumarate are TCA cycle intermediates.) In pathway VI, the mutase glmSE converts glutamate to (2S,3S)-3-methylaspartate, the lyase mal forms 2-methylfumarate (mesaconate), the hydratase fumD forms (S)-2-methylmalate (citramalate), and a lyase forms acetate and pyruvate.
• glutamate-transport:
  • gltI, gltJ, gltK and gltL
  • or gltL, gluB, gluC and gluD
  • or bztA, bztB, bztC and gltL
  • or braC, braD, braE, braF and braG
  • or gltL and glnP
  • or peb1A, peb1B and gltL
  • or gtrA, gtrB and gtrC
  • or aapJ, aapQ, aapM and aapP
  • or gltS
  • or acaP
  • or gltP
  • or yveA
  • or gltS_Syn
  • or dmeA
  • Comment: Transporters were identified using query: transporter:glutamate:L-glutamate:glu

38 steps (27 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
braC	ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC	RL_RS19315	RL_RS18225
braD	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)	RL_RS19340	RL_RS14695
braE	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)	RL_RS19335	RL_RS14690
braF	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)	RL_RS19330	RL_RS34950
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	RL_RS19325	RL_RS27140
gdhA	glutamate dehydrogenase, NAD-dependent	RL_RS24285
Alternative steps:
aapJ	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ	RL_RS11425
aapM	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM)	RL_RS11415	RL_RS33340
aapP	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP	RL_RS11410	RL_RS30155
aapQ	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)	RL_RS11420	RL_RS27775
acaP	L-glutamate permease AcaP
aspA	L-aspartate ammonia-lyase	RL_RS13950	RL_RS25495
bztA	L-glutamate ABC transporter, substrate-binding component	RL_RS11425
bztB	L-glutamate ABC transporter, permease component 1 (BztB)	RL_RS11420	RL_RS38465
bztC	L-glutamate ABC transporter, permease component 2 (BztC)	RL_RS11415	RL_RS29540
dmeA	L-glutamate transporter DmeA	RL_RS19435
fumD	(S)-2-methylmalate dehydratase (mesaconase)	RL_RS13960
glmE	L-glutamate mutase, E component
glmS	L-glutamate mutase, S component
glnP	L-glutamate ABC transporter, fused permease and substrate-binding components GlnP
gltI	L-glutamate ABC transporter, substrate-binding component (GltI/AatJ)
gltJ	L-glutamate ABC transporter, permease component 1 (gltJ/aatQ)	RL_RS29545	RL_RS23105
gltK	L-glutamate ABC transporter, permease component 1 (gltK/aatM)	RL_RS36580	RL_RS23105
gltL	L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C)	RL_RS23120	RL_RS11410
gltP	L-glutamate:cation symporter GltP/GltT	RL_RS17640	RL_RS34290
gltS	L-glutamate:Na+ symporter GltS
gltS_Syn	L-glutamate:Na+ symporter GltS_Syn
gluB	L-glutamate ABC transporter, substrate-binding component GluB
gluC	L-glutamate ABC transporter, permease component 1 (GluC)	RL_RS29545	RL_RS23105
gluD	L-glutamate ABC transporter, permease component 2 (GluD)	RL_RS36580	RL_RS29540
gtrA	tripartite L-glutamate:Na+ symporter, small membrane component GtrA	RL_RS21350
gtrB	tripartite L-glutamate:Na+ symporter, large membrane component GtrB	RL_RS21355	RL_RS35400
gtrC	tripartite L-glutamate:Na+ symporter, substrate-binding component GtrC	RL_RS33295
mal	methylaspartate ammonia-lyase
mcl	(S)-citramalyl-CoA pyruvate-lyase	RL_RS24195	RL_RS28860
peb1A	L-glutamate ABC transporter, substrate-binding component Peb1A
peb1B	L-glutamate ABC transporter, permease component Peb1B	RL_RS27775	RL_RS22980
yveA	L-glutamate:H+ symporter YveA

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.