GapMind for catabolism of small carbon sources

 

L-glutamate catabolism in Magnetospirillum magneticum AMB-1

Best path

braC, braD, braE, braF, braG, 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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC AMB_RS15010
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) AMB_RS09135 AMB_RS08455
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) AMB_RS09130 AMB_RS14460
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) AMB_RS09125 AMB_RS08465
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) AMB_RS09120 AMB_RS10230
gdhA glutamate dehydrogenase, NAD-dependent AMB_RS00165
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM)
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP AMB_RS10565 AMB_RS05625
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
acaP L-glutamate permease AcaP
aspA L-aspartate ammonia-lyase AMB_RS18480
bztA L-glutamate ABC transporter, substrate-binding component
bztB L-glutamate ABC transporter, permease component 1 (BztB)
bztC L-glutamate ABC transporter, permease component 2 (BztC)
dmeA L-glutamate transporter DmeA AMB_RS04225 AMB_RS14120
fumD (S)-2-methylmalate dehydratase (mesaconase) AMB_RS06760
glmE L-glutamate mutase, E component
glmS L-glutamate mutase, S component AMB_RS02225
glnP L-glutamate ABC transporter, fused permease and substrate-binding components GlnP
gltI L-glutamate ABC transporter, substrate-binding component (GltI/AatJ) AMB_RS19155
gltJ L-glutamate ABC transporter, permease component 1 (gltJ/aatQ)
gltK L-glutamate ABC transporter, permease component 1 (gltK/aatM)
gltL L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) AMB_RS10565 AMB_RS06945
gltP L-glutamate:cation symporter GltP/GltT
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)
gluD L-glutamate ABC transporter, permease component 2 (GluD)
gtrA tripartite L-glutamate:Na+ symporter, small membrane component GtrA AMB_RS12995
gtrB tripartite L-glutamate:Na+ symporter, large membrane component GtrB AMB_RS13000
gtrC tripartite L-glutamate:Na+ symporter, substrate-binding component GtrC
mal methylaspartate ammonia-lyase
mcl (S)-citramalyl-CoA pyruvate-lyase AMB_RS20125 AMB_RS19980
peb1A L-glutamate ABC transporter, substrate-binding component Peb1A
peb1B L-glutamate ABC transporter, permease component Peb1B
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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