GapMind for catabolism of small carbon sources

 

L-glutamate catabolism in Pseudomonas simiae WCS417

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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gltI L-glutamate ABC transporter, substrate-binding component (GltI/AatJ) PS417_05560 PS417_26550
gltJ L-glutamate ABC transporter, permease component 1 (gltJ/aatQ) PS417_05555 PS417_01810
gltK L-glutamate ABC transporter, permease component 1 (gltK/aatM) PS417_05550 PS417_04910
gltL L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) PS417_05545 PS417_04915
gdhA glutamate dehydrogenase, NAD-dependent PS417_15075 PS417_24260
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ PS417_23345 PS417_04900
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) PS417_04910 PS417_01810
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP PS417_04915 PS417_26115
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) PS417_04905
acaP L-glutamate permease AcaP
aspA L-aspartate ammonia-lyase PS417_28130 PS417_04305
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC PS417_02655 PS417_06615
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) PS417_02660 PS417_06610
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) PS417_06605 PS417_02665
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) PS417_02670 PS417_06600
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) PS417_02675 PS417_06595
bztA L-glutamate ABC transporter, substrate-binding component PS417_23345 PS417_04900
bztB L-glutamate ABC transporter, permease component 1 (BztB) PS417_04905
bztC L-glutamate ABC transporter, permease component 2 (BztC) PS417_04910
dmeA L-glutamate transporter DmeA PS417_14010
fumD (S)-2-methylmalate dehydratase (mesaconase) PS417_22635
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 PS417_00470 PS417_19030
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) PS417_01810 PS417_18125
gluD L-glutamate ABC transporter, permease component 2 (GluD) PS417_01810 PS417_05555
gtrA tripartite L-glutamate:Na+ symporter, small membrane component GtrA
gtrB tripartite L-glutamate:Na+ symporter, large membrane component GtrB PS417_14900
gtrC tripartite L-glutamate:Na+ symporter, substrate-binding component GtrC PS417_12095
mal methylaspartate ammonia-lyase
mcl (S)-citramalyl-CoA pyruvate-lyase PS417_14915
peb1A L-glutamate ABC transporter, substrate-binding component Peb1A
peb1B L-glutamate ABC transporter, permease component Peb1B PS417_12105 PS417_01100
yveA L-glutamate:H+ symporter YveA PS417_14300

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