GapMind for catabolism of small carbon sources

 

L-glutamate catabolism in Paraburkholderia phymatum STM815

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) BPHY_RS13055 BPHY_RS23805
gltJ L-glutamate ABC transporter, permease component 1 (gltJ/aatQ) BPHY_RS13050 BPHY_RS35860
gltK L-glutamate ABC transporter, permease component 1 (gltK/aatM) BPHY_RS13045 BPHY_RS05855
gltL L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) BPHY_RS13040 BPHY_RS27405
gdhA glutamate dehydrogenase, NAD-dependent BPHY_RS23255 BPHY_RS13060
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ BPHY_RS29405
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) BPHY_RS13045 BPHY_RS27410
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BPHY_RS13040 BPHY_RS27405
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BPHY_RS13050 BPHY_RS25820
acaP L-glutamate permease AcaP
aspA L-aspartate ammonia-lyase BPHY_RS28240 BPHY_RS04010
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC BPHY_RS15375 BPHY_RS02950
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) BPHY_RS02955 BPHY_RS11455
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) BPHY_RS02960
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) BPHY_RS02965 BPHY_RS15490
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) BPHY_RS02970 BPHY_RS15485
bztA L-glutamate ABC transporter, substrate-binding component BPHY_RS29405
bztB L-glutamate ABC transporter, permease component 1 (BztB) BPHY_RS13045 BPHY_RS13050
bztC L-glutamate ABC transporter, permease component 2 (BztC) BPHY_RS13045
dmeA L-glutamate transporter DmeA
fumD (S)-2-methylmalate dehydratase (mesaconase) BPHY_RS09875
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 BPHY_RS31785 BPHY_RS28230
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) BPHY_RS12035 BPHY_RS33250
gluD L-glutamate ABC transporter, permease component 2 (GluD) BPHY_RS13045 BPHY_RS33255
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 BPHY_RS24785 BPHY_RS29615
peb1A L-glutamate ABC transporter, substrate-binding component Peb1A
peb1B L-glutamate ABC transporter, permease component Peb1B BPHY_RS33255 BPHY_RS27410
yveA L-glutamate:H+ symporter YveA BPHY_RS28885 BPHY_RS13860

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 Apr 09 2024. 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