GapMind for catabolism of small carbon sources

 

L-glutamate catabolism in Ruegeria conchae TW15

Best path

bztA, bztB, bztC, 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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bztA L-glutamate ABC transporter, substrate-binding component G7G_RS0100225
bztB L-glutamate ABC transporter, permease component 1 (BztB) G7G_RS0100230
bztC L-glutamate ABC transporter, permease component 2 (BztC) G7G_RS0100235
gltL L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) G7G_RS0100240 G7G_RS0111050
gdhA glutamate dehydrogenase, NAD-dependent G7G_RS0113625
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ G7G_RS0100225
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) G7G_RS0100235
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP G7G_RS0100240 G7G_RS0111050
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) G7G_RS0100230
acaP L-glutamate permease AcaP
aspA L-aspartate ammonia-lyase G7G_RS0106895
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) G7G_RS0101020 G7G_RS0107140
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) G7G_RS0118395 G7G_RS0116930
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) G7G_RS0118410 G7G_RS0107130
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) G7G_RS0115355 G7G_RS0107125
dmeA L-glutamate transporter DmeA
fumD (S)-2-methylmalate dehydratase (mesaconase)
glmE L-glutamate mutase, E component
glmS L-glutamate mutase, S component
glnP L-glutamate ABC transporter, fused permease and substrate-binding components GlnP
gltI L-glutamate ABC transporter, substrate-binding component (GltI/AatJ)
gltJ L-glutamate ABC transporter, permease component 1 (gltJ/aatQ) G7G_RS0111520 G7G_RS0111055
gltK L-glutamate ABC transporter, permease component 1 (gltK/aatM) G7G_RS0111055 G7G_RS0100235
gltP L-glutamate:cation symporter GltP/GltT
gltS L-glutamate:Na+ symporter GltS G7G_RS0105395
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) G7G_RS0111520 G7G_RS0101320
gluD L-glutamate ABC transporter, permease component 2 (GluD) G7G_RS0100235
gtrA tripartite L-glutamate:Na+ symporter, small membrane component GtrA
gtrB tripartite L-glutamate:Na+ symporter, large membrane component GtrB G7G_RS0111790 G7G_RS0104905
gtrC tripartite L-glutamate:Na+ symporter, substrate-binding component GtrC
mal methylaspartate ammonia-lyase
mcl (S)-citramalyl-CoA pyruvate-lyase G7G_RS0121500 G7G_RS0102045
peb1A L-glutamate ABC transporter, substrate-binding component Peb1A
peb1B L-glutamate ABC transporter, permease component Peb1B G7G_RS0111530 G7G_RS0111520
yveA L-glutamate:H+ symporter YveA G7G_RS0106595

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