GapMind for catabolism of small carbon sources

 

L-glutamate catabolism in Belnapia rosea CPCC 100156

Best path

gltP, 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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gltP L-glutamate:cation symporter GltP/GltT BLR02_RS19285 BLR02_RS06920
gdhA glutamate dehydrogenase, NAD-dependent BLR02_RS22625
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ BLR02_RS24970 BLR02_RS21740
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) BLR02_RS24960
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BLR02_RS24955 BLR02_RS10420
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BLR02_RS24965
acaP L-glutamate permease AcaP
aspA L-aspartate ammonia-lyase BLR02_RS16540
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC BLR02_RS12505
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) BLR02_RS12525 BLR02_RS10285
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) BLR02_RS12520 BLR02_RS10290
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) BLR02_RS12515 BLR02_RS03485
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) BLR02_RS12510 BLR02_RS10300
bztA L-glutamate ABC transporter, substrate-binding component BLR02_RS24970 BLR02_RS08020
bztB L-glutamate ABC transporter, permease component 1 (BztB) BLR02_RS24965
bztC L-glutamate ABC transporter, permease component 2 (BztC) BLR02_RS24960
dmeA L-glutamate transporter DmeA
fumD (S)-2-methylmalate dehydratase (mesaconase) BLR02_RS16515
glmE L-glutamate mutase, E component
glmS L-glutamate mutase, S component BLR02_RS21895
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) BLR02_RS24965 BLR02_RS19475
gltK L-glutamate ABC transporter, permease component 1 (gltK/aatM) BLR02_RS24960 BLR02_RS10410
gltL L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) BLR02_RS24955 BLR02_RS10420
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) BLR02_RS10415 BLR02_RS24965
gluD L-glutamate ABC transporter, permease component 2 (GluD) BLR02_RS19470 BLR02_RS10410
gtrA tripartite L-glutamate:Na+ symporter, small membrane component GtrA BLR02_RS18240
gtrB tripartite L-glutamate:Na+ symporter, large membrane component GtrB BLR02_RS18245 BLR02_RS12990
gtrC tripartite L-glutamate:Na+ symporter, substrate-binding component GtrC
mal methylaspartate ammonia-lyase
mcl (S)-citramalyl-CoA pyruvate-lyase BLR02_RS21200 BLR02_RS05885
peb1A L-glutamate ABC transporter, substrate-binding component Peb1A
peb1B L-glutamate ABC transporter, permease component Peb1B BLR02_RS02405 BLR02_RS10410
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