GapMind for catabolism of small carbon sources

 

L-glutamate catabolism in Sinorhizobium meliloti 1021

Best path

braC, braD, braE, braF, braG, gdhA

Also see fitness data for the top candidates

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.

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 SMc01946 SMc00078
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) SMc01951 SMc02359
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) SMc01950
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) SMc01949 SMc02357
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) SMc01948 SMc02358
gdhA glutamate dehydrogenase, NAD-dependent SMc04085 SMa0228
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ SMc02118 SMc00676
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) SMc02120 SMc03865
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP SMc02121 SMc03135
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) SMc02119 SMc03865
acaP L-glutamate permease AcaP
aspA L-aspartate ammonia-lyase SMc00149
bztA L-glutamate ABC transporter, substrate-binding component SMc02118 SMc00676
bztB L-glutamate ABC transporter, permease component 1 (BztB) SMc02119 SMc03133
bztC L-glutamate ABC transporter, permease component 2 (BztC) SMc02120 SMc00139
dmeA L-glutamate transporter DmeA SMa1945
fumD (S)-2-methylmalate dehydratase (mesaconase)
glmE L-glutamate mutase, E component
glmS L-glutamate mutase, S component SMc04331
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) SMc03865 SMa0079
gltK L-glutamate ABC transporter, permease component 1 (gltK/aatM) SMc03133 SMc02120
gltL L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) SMc02121 SMc03135
gltP L-glutamate:cation symporter GltP/GltT SM_b20611
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) SMa0081 SM_b20975
gluD L-glutamate ABC transporter, permease component 2 (GluD) SMa2197 SMc02119
gtrA tripartite L-glutamate:Na+ symporter, small membrane component GtrA SMc04248
gtrB tripartite L-glutamate:Na+ symporter, large membrane component GtrB SMc04249 SM_b20297
gtrC tripartite L-glutamate:Na+ symporter, substrate-binding component GtrC SM_b21135
mal methylaspartate ammonia-lyase
mcl (S)-citramalyl-CoA pyruvate-lyase SMc03793
peb1A L-glutamate ABC transporter, substrate-binding component Peb1A
peb1B L-glutamate ABC transporter, permease component Peb1B SMc03893 SM_b21136
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 17 2021. The underlying query database was built on Sep 17 2021.

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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, the preprint on GapMind for carbon sources, 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