GapMind for catabolism of small carbon sources

 

L-glutamate catabolism in Pseudomonas fluorescens FW300-N1B4

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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gltI L-glutamate ABC transporter, substrate-binding component (GltI/AatJ) Pf1N1B4_771 Pf1N1B4_2375
gltJ L-glutamate ABC transporter, permease component 1 (gltJ/aatQ) Pf1N1B4_772 Pf1N1B4_773
gltK L-glutamate ABC transporter, permease component 1 (gltK/aatM) Pf1N1B4_773 Pf1N1B4_915
gltL L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) Pf1N1B4_774 Pf1N1B4_914
gdhA glutamate dehydrogenase, NAD-dependent Pf1N1B4_4643
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ Pf1N1B4_917
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) Pf1N1B4_915 Pf1N1B4_4805
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Pf1N1B4_914 Pf1N1B4_774
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) Pf1N1B4_916 Pf1N1B4_772
acaP L-glutamate permease AcaP
aspA L-aspartate ammonia-lyase Pf1N1B4_2025 Pf1N1B4_1088
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC Pf1N1B4_1382 Pf1N1B4_3218
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) Pf1N1B4_1381 Pf1N1B4_3217
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) Pf1N1B4_3216 Pf1N1B4_1380
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) Pf1N1B4_1379 Pf1N1B4_3215
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Pf1N1B4_1378 Pf1N1B4_3214
bztA L-glutamate ABC transporter, substrate-binding component Pf1N1B4_917
bztB L-glutamate ABC transporter, permease component 1 (BztB) Pf1N1B4_916
bztC L-glutamate ABC transporter, permease component 2 (BztC) Pf1N1B4_915
dmeA L-glutamate transporter DmeA Pf1N1B4_5004
fumD (S)-2-methylmalate dehydratase (mesaconase) Pf1N1B4_683
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 Pf1N1B4_1888 Pf1N1B4_3487
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) Pf1N1B4_2211 Pf1N1B4_1694
gluD L-glutamate ABC transporter, permease component 2 (GluD) Pf1N1B4_772 Pf1N1B4_773
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 Pf1N1B4_5645
mal methylaspartate ammonia-lyase
mcl (S)-citramalyl-CoA pyruvate-lyase Pf1N1B4_5615
peb1A L-glutamate ABC transporter, substrate-binding component Peb1A
peb1B L-glutamate ABC transporter, permease component Peb1B Pf1N1B4_5643 Pf1N1B4_1694
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