GapMind for catabolism of small carbon sources

 

L-glutamate catabolism in Pseudomonas fluorescens FW300-N2E2

Best path

gltI, gltJ, gltK, 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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gltI L-glutamate ABC transporter, substrate-binding component (GltI/AatJ) Pf6N2E2_5570
gltJ L-glutamate ABC transporter, permease component 1 (gltJ/aatQ) Pf6N2E2_5569 Pf6N2E2_5568
gltK L-glutamate ABC transporter, permease component 1 (gltK/aatM) Pf6N2E2_5568 Pf6N2E2_5404
gltL L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) Pf6N2E2_5567 Pf6N2E2_5405
gdhA glutamate dehydrogenase, NAD-dependent Pf6N2E2_634
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ Pf6N2E2_5402
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) Pf6N2E2_5404 Pf6N2E2_1799
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Pf6N2E2_5405 Pf6N2E2_5567
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) Pf6N2E2_5403
acaP L-glutamate permease AcaP
aspA L-aspartate ammonia-lyase Pf6N2E2_4085 Pf6N2E2_3276
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC Pf6N2E2_3580 Pf6N2E2_2921
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) Pf6N2E2_3579 Pf6N2E2_2923
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) Pf6N2E2_2924 Pf6N2E2_3578
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) Pf6N2E2_3577 Pf6N2E2_2925
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Pf6N2E2_3576 Pf6N2E2_2926
bztA L-glutamate ABC transporter, substrate-binding component Pf6N2E2_5402
bztB L-glutamate ABC transporter, permease component 1 (BztB) Pf6N2E2_5403
bztC L-glutamate ABC transporter, permease component 2 (BztC) Pf6N2E2_5404 Pf6N2E2_3404
dmeA L-glutamate transporter DmeA Pf6N2E2_455
fumD (S)-2-methylmalate dehydratase (mesaconase) Pf6N2E2_5489
glmE L-glutamate mutase, E component
glmS L-glutamate mutase, S component
glnP L-glutamate ABC transporter, fused permease and substrate-binding components GlnP
gltP L-glutamate:cation symporter GltP/GltT Pf6N2E2_4148 Pf6N2E2_2249
gltS L-glutamate:Na+ symporter GltS Pf6N2E2_4368
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) Pf6N2E2_4456 Pf6N2E2_3920
gluD L-glutamate ABC transporter, permease component 2 (GluD) Pf6N2E2_3404 Pf6N2E2_2051
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 Pf6N2E2_2053
mal methylaspartate ammonia-lyase
mcl (S)-citramalyl-CoA pyruvate-lyase Pf6N2E2_1831
peb1A L-glutamate ABC transporter, substrate-binding component Peb1A
peb1B L-glutamate ABC transporter, permease component Peb1B Pf6N2E2_2051 Pf6N2E2_3920
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