L-glutamate catabolism in Sinorhizobium medicae WSM419

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 (26 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	SMED_RS11940	SMED_RS02690
braD	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)	SMED_RS11965	SMED_RS26550
braE	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)	SMED_RS11960
braF	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)	SMED_RS11955	SMED_RS26560
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	SMED_RS11950	SMED_RS26555
gdhA	glutamate dehydrogenase, NAD-dependent	SMED_RS15985
Alternative steps:
aapJ	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ	SMED_RS05540	SMED_RS12910
aapM	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM)	SMED_RS05530	SMED_RS31555
aapP	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP	SMED_RS31560	SMED_RS14260
aapQ	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)	SMED_RS31550	SMED_RS10470
acaP	L-glutamate permease AcaP
aspA	L-aspartate ammonia-lyase	SMED_RS07910
bztA	L-glutamate ABC transporter, substrate-binding component	SMED_RS05540	SMED_RS12910
bztB	L-glutamate ABC transporter, permease component 1 (BztB)	SMED_RS31550	SMED_RS14270
bztC	L-glutamate ABC transporter, permease component 2 (BztC)	SMED_RS05530	SMED_RS31555
dmeA	L-glutamate transporter DmeA	SMED_RS26305
fumD	(S)-2-methylmalate dehydratase (mesaconase)
glmE	L-glutamate mutase, E component
glmS	L-glutamate mutase, S component	SMED_RS08865
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)	SMED_RS15570	SMED_RS14270
gltK	L-glutamate ABC transporter, permease component 1 (gltK/aatM)	SMED_RS10475	SMED_RS05530
gltL	L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C)	SMED_RS31560	SMED_RS14260
gltP	L-glutamate:cation symporter GltP/GltT	SMED_RS20915
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)	SMED_RS15745	SMED_RS24825
gluD	L-glutamate ABC transporter, permease component 2 (GluD)	SMED_RS33320	SMED_RS31550
gtrA	tripartite L-glutamate:Na+ symporter, small membrane component GtrA	SMED_RS08555
gtrB	tripartite L-glutamate:Na+ symporter, large membrane component GtrB	SMED_RS08560	SMED_RS19230
gtrC	tripartite L-glutamate:Na+ symporter, substrate-binding component GtrC	SMED_RS22735
mal	methylaspartate ammonia-lyase
mcl	(S)-citramalyl-CoA pyruvate-lyase
peb1A	L-glutamate ABC transporter, substrate-binding component Peb1A
peb1B	L-glutamate ABC transporter, permease component Peb1B	SMED_RS14965	SMED_RS15745
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.