GapMind for catabolism of small carbon sources

 

L-glutamate catabolism in Paraburkholderia bryophila 376MFSha3.1

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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gltI L-glutamate ABC transporter, substrate-binding component (GltI/AatJ) H281DRAFT_04270 H281DRAFT_02625
gltJ L-glutamate ABC transporter, permease component 1 (gltJ/aatQ) H281DRAFT_04269 H281DRAFT_03349
gltK L-glutamate ABC transporter, permease component 1 (gltK/aatM) H281DRAFT_04268 H281DRAFT_02563
gltL L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) H281DRAFT_04267 H281DRAFT_02565
gdhA glutamate dehydrogenase, NAD-dependent H281DRAFT_03183 H281DRAFT_04271
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) H281DRAFT_05402 H281DRAFT_04268
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP H281DRAFT_04267 H281DRAFT_02565
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) H281DRAFT_03349 H281DRAFT_04269
acaP L-glutamate permease AcaP
aspA L-aspartate ammonia-lyase H281DRAFT_04314 H281DRAFT_00025
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC H281DRAFT_02405 H281DRAFT_01194
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) H281DRAFT_04062 H281DRAFT_02378
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) H281DRAFT_04061 H281DRAFT_05513
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) H281DRAFT_04060 H281DRAFT_02383
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) H281DRAFT_04059 H281DRAFT_02384
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) H281DRAFT_04268
dmeA L-glutamate transporter DmeA
fumD (S)-2-methylmalate dehydratase (mesaconase) H281DRAFT_04956
glmE L-glutamate mutase, E component
glmS L-glutamate mutase, S component H281DRAFT_02110
glnP L-glutamate ABC transporter, fused permease and substrate-binding components GlnP
gltP L-glutamate:cation symporter GltP/GltT H281DRAFT_01718 H281DRAFT_01363
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) H281DRAFT_02572 H281DRAFT_05871
gluD L-glutamate ABC transporter, permease component 2 (GluD) H281DRAFT_03349 H281DRAFT_05299
gtrA tripartite L-glutamate:Na+ symporter, small membrane component GtrA
gtrB tripartite L-glutamate:Na+ symporter, large membrane component GtrB
gtrC tripartite L-glutamate:Na+ symporter, substrate-binding component GtrC
mal methylaspartate ammonia-lyase
mcl (S)-citramalyl-CoA pyruvate-lyase H281DRAFT_02940 H281DRAFT_05549
peb1A L-glutamate ABC transporter, substrate-binding component Peb1A
peb1B L-glutamate ABC transporter, permease component Peb1B H281DRAFT_05872 H281DRAFT_00741
yveA L-glutamate:H+ symporter YveA H281DRAFT_05687

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.

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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