GapMind for catabolism of small carbon sources

 

L-glutamate catabolism in Cupriavidus basilensis 4G11

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) RR42_RS02575 RR42_RS04390
gltJ L-glutamate ABC transporter, permease component 1 (gltJ/aatQ) RR42_RS02580 RR42_RS31740
gltK L-glutamate ABC transporter, permease component 1 (gltK/aatM) RR42_RS02585 RR42_RS04400
gltL L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) RR42_RS02590 RR42_RS31735
gdhA glutamate dehydrogenase, NAD-dependent RR42_RS07270 RR42_RS02570
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) RR42_RS27120 RR42_RS09485
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP RR42_RS16370 RR42_RS02590
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) RR42_RS31740 RR42_RS16450
acaP L-glutamate permease AcaP
aspA L-aspartate ammonia-lyase RR42_RS26135 RR42_RS33090
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC RR42_RS16980 RR42_RS14425
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) RR42_RS14420 RR42_RS16975
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) RR42_RS14415 RR42_RS16970
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) RR42_RS14410 RR42_RS29450
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) RR42_RS14405 RR42_RS16960
bztA L-glutamate ABC transporter, substrate-binding component
bztB L-glutamate ABC transporter, permease component 1 (BztB) RR42_RS02585
bztC L-glutamate ABC transporter, permease component 2 (BztC) RR42_RS04400
dmeA L-glutamate transporter DmeA RR42_RS28180 RR42_RS05960
fumD (S)-2-methylmalate dehydratase (mesaconase) RR42_RS13905 RR42_RS27740
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 RR42_RS26105 RR42_RS01695
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) RR42_RS07810 RR42_RS31740
gluD L-glutamate ABC transporter, permease component 2 (GluD) RR42_RS34310 RR42_RS02580
gtrA tripartite L-glutamate:Na+ symporter, small membrane component GtrA RR42_RS15930
gtrB tripartite L-glutamate:Na+ symporter, large membrane component GtrB RR42_RS15935
gtrC tripartite L-glutamate:Na+ symporter, substrate-binding component GtrC
mal methylaspartate ammonia-lyase
mcl (S)-citramalyl-CoA pyruvate-lyase RR42_RS36610 RR42_RS24325
peb1A L-glutamate ABC transporter, substrate-binding component Peb1A
peb1B L-glutamate ABC transporter, permease component Peb1B RR42_RS04400 RR42_RS09485
yveA L-glutamate:H+ symporter YveA RR42_RS36375

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 Aug 02 2021. The underlying query database was built on Aug 02 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