GapMind for catabolism of small carbon sources

 

L-glutamate catabolism in Verminephrobacter eiseniae EF01-2

Best path

gltI, gltJ, gltK, gltL, 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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gltI L-glutamate ABC transporter, substrate-binding component (GltI/AatJ) VEIS_RS22945 VEIS_RS05960
gltJ L-glutamate ABC transporter, permease component 1 (gltJ/aatQ) VEIS_RS05955 VEIS_RS10530
gltK L-glutamate ABC transporter, permease component 1 (gltK/aatM) VEIS_RS05950 VEIS_RS17265
gltL L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) VEIS_RS03530 VEIS_RS05945
gdhA glutamate dehydrogenase, NAD-dependent VEIS_RS08285
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) VEIS_RS16205 VEIS_RS17265
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP VEIS_RS16195 VEIS_RS03530
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) VEIS_RS07805
acaP L-glutamate permease AcaP
aspA L-aspartate ammonia-lyase VEIS_RS15645 VEIS_RS22245
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC VEIS_RS09140 VEIS_RS23840
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) VEIS_RS09145 VEIS_RS14585
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) VEIS_RS09150 VEIS_RS14580
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) VEIS_RS09155 VEIS_RS01440
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) VEIS_RS09160 VEIS_RS01435
bztA L-glutamate ABC transporter, substrate-binding component VEIS_RS16405
bztB L-glutamate ABC transporter, permease component 1 (BztB) VEIS_RS05955
bztC L-glutamate ABC transporter, permease component 2 (BztC)
dmeA L-glutamate transporter DmeA
fumD (S)-2-methylmalate dehydratase (mesaconase) VEIS_RS15640
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 VEIS_RS08985 VEIS_RS01530
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) VEIS_RS16875 VEIS_RS14660
gluD L-glutamate ABC transporter, permease component 2 (GluD) VEIS_RS07805 VEIS_RS14660
gtrA tripartite L-glutamate:Na+ symporter, small membrane component GtrA VEIS_RS14040
gtrB tripartite L-glutamate:Na+ symporter, large membrane component GtrB VEIS_RS14035 VEIS_RS11465
gtrC tripartite L-glutamate:Na+ symporter, substrate-binding component GtrC VEIS_RS16405
mal methylaspartate ammonia-lyase
mcl (S)-citramalyl-CoA pyruvate-lyase VEIS_RS23265 VEIS_RS07705
peb1A L-glutamate ABC transporter, substrate-binding component Peb1A
peb1B L-glutamate ABC transporter, permease component Peb1B VEIS_RS14660 VEIS_RS10530
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