GapMind for catabolism of small carbon sources

 

L-glutamate catabolism in Desulfovibrio vulgaris Hildenborough

Best path

dmeA, aspA

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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
dmeA L-glutamate transporter DmeA DVU0406 DVU2887
aspA L-aspartate ammonia-lyase DVU1871 DVU1766
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ DVU2342
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) DVU0967 DVU0751
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP DVU0753 DVU2343
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) DVU2341
acaP L-glutamate permease AcaP
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC DVU0547 DVU0712
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) DVU0548 DVU0713
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) DVU0549 DVU0714
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) DVU0550 DVU0715
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) DVU0551 DVU0716
bztA L-glutamate ABC transporter, substrate-binding component
bztB L-glutamate ABC transporter, permease component 1 (BztB) DVU0751 DVU0676
bztC L-glutamate ABC transporter, permease component 2 (BztC) DVU0751
fumD* (S)-2-methylmalate dehydratase (mesaconase) DVU3264 with DVU3265
gdhA glutamate dehydrogenase, NAD-dependent DVU0964
glmE L-glutamate mutase, E component
glmS L-glutamate mutase, S component DVU1585
glnP L-glutamate ABC transporter, fused permease and substrate-binding components GlnP
gltI L-glutamate ABC transporter, substrate-binding component (GltI/AatJ) DVU2342 DVU0752
gltJ L-glutamate ABC transporter, permease component 1 (gltJ/aatQ) DVU2341 DVU0751
gltK L-glutamate ABC transporter, permease component 1 (gltK/aatM) DVU0967 DVU2340
gltL L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) DVU0753 DVU2343
gltP L-glutamate:cation symporter GltP/GltT
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) DVU0967 DVU0674
gluD L-glutamate ABC transporter, permease component 2 (GluD) DVU2340 DVU0967
gtrA tripartite L-glutamate:Na+ symporter, small membrane component GtrA
gtrB tripartite L-glutamate:Na+ symporter, large membrane component GtrB DVU2823
gtrC tripartite L-glutamate:Na+ symporter, substrate-binding component GtrC
mal methylaspartate ammonia-lyase
mcl (S)-citramalyl-CoA pyruvate-lyase
peb1A L-glutamate ABC transporter, substrate-binding component Peb1A DVU2342
peb1B L-glutamate ABC transporter, permease component Peb1B DVU0751 DVU2341
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