GapMind for catabolism of small carbon sources

 

L-glutamate catabolism in Dinoroseobacter shibae DFL-12

Best path

bztA, bztB, bztC, gltL, 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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bztA L-glutamate ABC transporter, substrate-binding component Dshi_0318
bztB L-glutamate ABC transporter, permease component 1 (BztB) Dshi_0319
bztC L-glutamate ABC transporter, permease component 2 (BztC) Dshi_0320
gltL L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) Dshi_0321 Dshi_2221
gdhA glutamate dehydrogenase, NAD-dependent Dshi_3841
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ Dshi_0318
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) Dshi_0320
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Dshi_0321 Dshi_2221
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) Dshi_0319
acaP L-glutamate permease AcaP
aspA L-aspartate ammonia-lyase Dshi_2334
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) Dshi_3725 Dshi_0861
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) Dshi_0379
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) Dshi_0375 Dshi_3727
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Dshi_0381 Dshi_1400
dmeA L-glutamate transporter DmeA Dshi_3287
fumD (S)-2-methylmalate dehydratase (mesaconase) Dshi_1426
glmE L-glutamate mutase, E component
glmS L-glutamate mutase, S component Dshi_1073
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) Dshi_0319
gltK L-glutamate ABC transporter, permease component 1 (gltK/aatM) Dshi_0320 Dshi_0319
gltP L-glutamate:cation symporter GltP/GltT
gltS L-glutamate:Na+ symporter GltS Dshi_1261
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)
gluD L-glutamate ABC transporter, permease component 2 (GluD)
gtrA tripartite L-glutamate:Na+ symporter, small membrane component GtrA Dshi_1970
gtrB tripartite L-glutamate:Na+ symporter, large membrane component GtrB Dshi_1970 Dshi_3395
gtrC tripartite L-glutamate:Na+ symporter, substrate-binding component GtrC
mal methylaspartate ammonia-lyase
mcl (S)-citramalyl-CoA pyruvate-lyase Dshi_3050 Dshi_2490
peb1A L-glutamate ABC transporter, substrate-binding component Peb1A
peb1B L-glutamate ABC transporter, permease component Peb1B
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