GapMind for catabolism of small carbon sources

 

L-glutamate catabolism in Pseudomonas benzenivorans DSM 8628

Best path

gltI, gltJ, gltK, gltL, gdhA

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) BLS63_RS18555
gltJ L-glutamate ABC transporter, permease component 1 (gltJ/aatQ) BLS63_RS18550 BLS63_RS18545
gltK L-glutamate ABC transporter, permease component 1 (gltK/aatM) BLS63_RS18545 BLS63_RS08610
gltL L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) BLS63_RS18540 BLS63_RS08615
gdhA glutamate dehydrogenase, NAD-dependent BLS63_RS12860
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ BLS63_RS08600
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) BLS63_RS08610 BLS63_RS18545
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BLS63_RS08615 BLS63_RS23600
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BLS63_RS08605 BLS63_RS11280
acaP L-glutamate permease AcaP
aspA L-aspartate ammonia-lyase BLS63_RS18500 BLS63_RS12400
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC BLS63_RS23775 BLS63_RS09655
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) BLS63_RS23780 BLS63_RS09650
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) BLS63_RS09645 BLS63_RS23785
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) BLS63_RS09640 BLS63_RS23790
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) BLS63_RS23795 BLS63_RS09635
bztA L-glutamate ABC transporter, substrate-binding component BLS63_RS08600
bztB L-glutamate ABC transporter, permease component 1 (BztB) BLS63_RS08605
bztC L-glutamate ABC transporter, permease component 2 (BztC) BLS63_RS08610 BLS63_RS18545
dmeA L-glutamate transporter DmeA BLS63_RS22925
fumD (S)-2-methylmalate dehydratase (mesaconase) BLS63_RS19955
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 BLS63_RS18495 BLS63_RS07270
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) BLS63_RS11280 BLS63_RS18550
gluD L-glutamate ABC transporter, permease component 2 (GluD) BLS63_RS01120 BLS63_RS24445
gtrA tripartite L-glutamate:Na+ symporter, small membrane component GtrA BLS63_RS18725
gtrB tripartite L-glutamate:Na+ symporter, large membrane component GtrB BLS63_RS18720 BLS63_RS23880
gtrC tripartite L-glutamate:Na+ symporter, substrate-binding component GtrC
mal methylaspartate ammonia-lyase
mcl (S)-citramalyl-CoA pyruvate-lyase BLS63_RS17685
peb1A L-glutamate ABC transporter, substrate-binding component Peb1A
peb1B L-glutamate ABC transporter, permease component Peb1B BLS63_RS18550
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 24 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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