L-glutamate catabolism in Microvirga lotononidis WSM3557

GapMind for catabolism of small carbon sources

L-glutamate catabolism in Microvirga lotononidis WSM3557

Best path

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	MICLODRAFT_RS30935	MICLODRAFT_RS25195
braD	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)	MICLODRAFT_RS30910	MICLODRAFT_RS10115
braE	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)	MICLODRAFT_RS30915	MICLODRAFT_RS24145
braF	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)	MICLODRAFT_RS30920	MICLODRAFT_RS24155
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	MICLODRAFT_RS30925	MICLODRAFT_RS27000
gdhA	glutamate dehydrogenase, NAD-dependent	MICLODRAFT_RS29155	MICLODRAFT_RS11685
Alternative steps:
aapJ	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ	MICLODRAFT_RS26245	MICLODRAFT_RS19560
aapM	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM)	MICLODRAFT_RS19550	MICLODRAFT_RS26255
aapP	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP	MICLODRAFT_RS26260	MICLODRAFT_RS31925
aapQ	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)	MICLODRAFT_RS26250	MICLODRAFT_RS19555
acaP	L-glutamate permease AcaP
aspA	L-aspartate ammonia-lyase	MICLODRAFT_RS22090
bztA	L-glutamate ABC transporter, substrate-binding component	MICLODRAFT_RS26245	MICLODRAFT_RS19560
bztB	L-glutamate ABC transporter, permease component 1 (BztB)	MICLODRAFT_RS26250	MICLODRAFT_RS19555
bztC	L-glutamate ABC transporter, permease component 2 (BztC)	MICLODRAFT_RS26255	MICLODRAFT_RS19550
dmeA	L-glutamate transporter DmeA	MICLODRAFT_RS19135
fumD	(S)-2-methylmalate dehydratase (mesaconase)
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)	MICLODRAFT_RS25060	MICLODRAFT_RS06875
gltK	L-glutamate ABC transporter, permease component 1 (gltK/aatM)	MICLODRAFT_RS25060	MICLODRAFT_RS26255
gltL	L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C)	MICLODRAFT_RS26260	MICLODRAFT_RS31925
gltP	L-glutamate:cation symporter GltP/GltT	MICLODRAFT_RS02570	MICLODRAFT_RS10565
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)	MICLODRAFT_RS11610	MICLODRAFT_RS06135
gluD	L-glutamate ABC transporter, permease component 2 (GluD)	MICLODRAFT_RS25060	MICLODRAFT_RS11610
gtrA	tripartite L-glutamate:Na+ symporter, small membrane component GtrA	MICLODRAFT_RS09855
gtrB	tripartite L-glutamate:Na+ symporter, large membrane component GtrB	MICLODRAFT_RS09850	MICLODRAFT_RS19360
gtrC	tripartite L-glutamate:Na+ symporter, substrate-binding component GtrC	MICLODRAFT_RS06145
mal	methylaspartate ammonia-lyase
mcl	(S)-citramalyl-CoA pyruvate-lyase	MICLODRAFT_RS23165	MICLODRAFT_RS08850
peb1A	L-glutamate ABC transporter, substrate-binding component Peb1A
peb1B	L-glutamate ABC transporter, permease component Peb1B	MICLODRAFT_RS00225	MICLODRAFT_RS06135
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.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources