GapMind for catabolism of small carbon sources

 

Definition of L-glutamate catabolism

As rules and steps, or see full text

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.

Steps

gltI: L-glutamate ABC transporter, substrate-binding component (GltI/AatJ)

gltJ: L-glutamate ABC transporter, permease component 1 (gltJ/aatQ)

gltK: L-glutamate ABC transporter, permease component 1 (gltK/aatM)

gltL: L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C)

gluB: L-glutamate ABC transporter, substrate-binding component GluB

gluC: L-glutamate ABC transporter, permease component 1 (GluC)

gluD: L-glutamate ABC transporter, permease component 2 (GluD)

bztA: L-glutamate ABC transporter, substrate-binding component

bztB: L-glutamate ABC transporter, permease component 1 (BztB)

bztC: L-glutamate ABC transporter, permease component 2 (BztC)

braC: ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC

braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)

braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)

braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)

braG: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)

glnP: L-glutamate ABC transporter, fused permease and substrate-binding components GlnP

peb1A: L-glutamate ABC transporter, substrate-binding component Peb1A

peb1B: L-glutamate ABC transporter, permease component Peb1B

gtrA: tripartite L-glutamate:Na+ symporter, small membrane component GtrA

gtrB: tripartite L-glutamate:Na+ symporter, large membrane component GtrB

gtrC: tripartite L-glutamate:Na+ symporter, substrate-binding component GtrC

aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ

aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)

aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM)

aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP

gltS: L-glutamate:Na+ symporter GltS

acaP: L-glutamate permease AcaP

gltP: L-glutamate:cation symporter GltP/GltT

yveA: L-glutamate:H+ symporter YveA

gltS_Syn: L-glutamate:Na+ symporter GltS_Syn

dmeA: L-glutamate transporter DmeA

gdhA: glutamate dehydrogenase, NAD-dependent

aspA: L-aspartate ammonia-lyase

glmS: L-glutamate mutase, S component

glmE: L-glutamate mutase, E component

mal: methylaspartate ammonia-lyase

fumD: (S)-2-methylmalate dehydratase (mesaconase)

mcl: (S)-citramalyl-CoA pyruvate-lyase

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

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

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:

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. Gaps may be due to:

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, or view the source code.

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