GapMind for catabolism of small carbon sources

 

L-glutamate catabolism in Pseudomonas fluorescens GW456-L13

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) PfGW456L13_4770 PfGW456L13_1042
gltJ L-glutamate ABC transporter, permease component 1 (gltJ/aatQ) PfGW456L13_4771 PfGW456L13_4772
gltK L-glutamate ABC transporter, permease component 1 (gltK/aatM) PfGW456L13_4772 PfGW456L13_1700
gltL L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) PfGW456L13_4773 PfGW456L13_1701
gdhA glutamate dehydrogenase, NAD-dependent PfGW456L13_3298 PfGW456L13_1455
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ PfGW456L13_1698
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) PfGW456L13_1700 PfGW456L13_4772
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP PfGW456L13_1701 PfGW456L13_4773
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) PfGW456L13_1699
acaP L-glutamate permease AcaP
aspA L-aspartate ammonia-lyase PfGW456L13_742 PfGW456L13_5022
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC PfGW456L13_124 PfGW456L13_4606
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) PfGW456L13_123 PfGW456L13_4608
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) PfGW456L13_4609 PfGW456L13_122
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) PfGW456L13_121 PfGW456L13_4610
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) PfGW456L13_120 PfGW456L13_4611
bztA L-glutamate ABC transporter, substrate-binding component PfGW456L13_1698
bztB L-glutamate ABC transporter, permease component 1 (BztB) PfGW456L13_1699
bztC L-glutamate ABC transporter, permease component 2 (BztC) PfGW456L13_1700 PfGW456L13_3607
dmeA L-glutamate transporter DmeA PfGW456L13_2934
fumD (S)-2-methylmalate dehydratase (mesaconase) PfGW456L13_1808
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 PfGW456L13_578 PfGW456L13_2016
gltS L-glutamate:Na+ symporter GltS PfGW456L13_786
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) PfGW456L13_877 PfGW456L13_445
gluD L-glutamate ABC transporter, permease component 2 (GluD) PfGW456L13_4772 PfGW456L13_4771
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
mal methylaspartate ammonia-lyase
mcl (S)-citramalyl-CoA pyruvate-lyase
peb1A L-glutamate ABC transporter, substrate-binding component Peb1A PfGW456L13_444
peb1B L-glutamate ABC transporter, permease component Peb1B PfGW456L13_445 PfGW456L13_877
yveA L-glutamate:H+ symporter YveA PfGW456L13_3582

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