GapMind for catabolism of small carbon sources

 

L-glutamate catabolism in Desulfovibrio vulgaris Miyazaki F

Best path

dmeA, aspA

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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
dmeA L-glutamate transporter DmeA DvMF_1542
aspA L-aspartate ammonia-lyase DvMF_0565 DvMF_2075
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ DvMF_3152
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) DvMF_2786
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP DvMF_2788 DvMF_3151
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
acaP L-glutamate permease AcaP
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC DvMF_2607 DvMF_2750
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) DvMF_2608 DvMF_2751
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) DvMF_2609 DvMF_2752
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) DvMF_2610 DvMF_1481
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) DvMF_2611 DvMF_2754
bztA L-glutamate ABC transporter, substrate-binding component DvMF_3152
bztB L-glutamate ABC transporter, permease component 1 (BztB) DvMF_3153
bztC L-glutamate ABC transporter, permease component 2 (BztC) DvMF_2786
fumD* (S)-2-methylmalate dehydratase (mesaconase) DvMF_2461 with DvMF_2462
gdhA glutamate dehydrogenase, NAD-dependent DvMF_1346
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) DvMF_3152 DvMF_2787
gltJ L-glutamate ABC transporter, permease component 1 (gltJ/aatQ) DvMF_3153 DvMF_2786
gltK L-glutamate ABC transporter, permease component 1 (gltK/aatM) DvMF_3154 DvMF_3153
gltL L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) DvMF_2788 DvMF_3151
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) DvMF_1343 DvMF_2686
gluD L-glutamate ABC transporter, permease component 2 (GluD) DvMF_3154 DvMF_2786
gtrA tripartite L-glutamate:Na+ symporter, small membrane component GtrA
gtrB tripartite L-glutamate:Na+ symporter, large membrane component GtrB DvMF_2137
gtrC tripartite L-glutamate:Na+ symporter, substrate-binding component GtrC DvMF_3152
mal methylaspartate ammonia-lyase
mcl (S)-citramalyl-CoA pyruvate-lyase
peb1A L-glutamate ABC transporter, substrate-binding component Peb1A DvMF_3152
peb1B L-glutamate ABC transporter, permease component Peb1B DvMF_2786 DvMF_1919
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 Aug 02 2021. The underlying query database was built on Aug 02 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, 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