GapMind for catabolism of small carbon sources

 

L-glutamate catabolism in Pseudomonas putida KT2440

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) PP_1071
gltJ L-glutamate ABC transporter, permease component 1 (gltJ/aatQ) PP_1070 PP_5023
gltK L-glutamate ABC transporter, permease component 1 (gltK/aatM) PP_1069 PP_4749
gltL L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) PP_1068 PP_1300
gdhA glutamate dehydrogenase, NAD-dependent PP_2080 PP_0675
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ PP_1297
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) PP_1299 PP_1069
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP PP_1300 PP_3597
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) PP_1298 PP_5023
acaP L-glutamate permease AcaP
aspA L-aspartate ammonia-lyase PP_5338 PP_1755
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC PP_4867 PP_1141
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) PP_1140 PP_4866
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) PP_1139 PP_4865
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) PP_4864 PP_1138
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) PP_4863 PP_1137
bztA L-glutamate ABC transporter, substrate-binding component PP_1297
bztB L-glutamate ABC transporter, permease component 1 (BztB) PP_1298 PP_1070
bztC L-glutamate ABC transporter, permease component 2 (BztC) PP_1299 PP_1069
dmeA L-glutamate transporter DmeA
fumD (S)-2-methylmalate dehydratase (mesaconase) PP_0897
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 PP_0137 PP_1188
gltS L-glutamate:Na+ symporter GltS PP_0996
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) PP_5023 PP_4427
gluD L-glutamate ABC transporter, permease component 2 (GluD) PP_5023 PP_0280
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 PP_0227
peb1B L-glutamate ABC transporter, permease component Peb1B PP_0226 PP_1070
yveA L-glutamate:H+ symporter YveA PP_1259

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, 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