GapMind for catabolism of small carbon sources

 

L-glutamate catabolism in Williamsia sterculiae CPCC 203464

Best path

gltL, gluB, gluC, gluD, 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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gltL L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) BW971_RS05930 BW971_RS16645
gluB L-glutamate ABC transporter, substrate-binding component GluB BW971_RS05925
gluC L-glutamate ABC transporter, permease component 1 (GluC) BW971_RS05920 BW971_RS15735
gluD L-glutamate ABC transporter, permease component 2 (GluD) BW971_RS05915 BW971_RS15735
gdhA glutamate dehydrogenase, NAD-dependent BW971_RS14270
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) BW971_RS15735
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BW971_RS05930 BW971_RS17350
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
acaP L-glutamate permease AcaP
aspA L-aspartate ammonia-lyase BW971_RS04330
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC BW971_RS17400
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) BW971_RS17395
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) BW971_RS17390
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) BW971_RS17385 BW971_RS06860
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) BW971_RS17380 BW971_RS12845
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) BW971_RS05915
dmeA L-glutamate transporter DmeA
fumD (S)-2-methylmalate dehydratase (mesaconase)
glmE L-glutamate mutase, E component
glmS L-glutamate mutase, S component BW971_RS07195
glnP L-glutamate ABC transporter, fused permease and substrate-binding components GlnP BW971_RS15735
gltI L-glutamate ABC transporter, substrate-binding component (GltI/AatJ)
gltJ L-glutamate ABC transporter, permease component 1 (gltJ/aatQ) BW971_RS15735 BW971_RS05920
gltK L-glutamate ABC transporter, permease component 1 (gltK/aatM) BW971_RS16650 BW971_RS05915
gltP L-glutamate:cation symporter GltP/GltT BW971_RS19650 BW971_RS12205
gltS L-glutamate:Na+ symporter GltS
gltS_Syn L-glutamate:Na+ symporter GltS_Syn
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 BW971_RS04845 BW971_RS03260
peb1A L-glutamate ABC transporter, substrate-binding component Peb1A
peb1B L-glutamate ABC transporter, permease component Peb1B BW971_RS16650 BW971_RS17355
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.

Links

Downloads

Related tools

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