GapMind for catabolism of small carbon sources

 

L-glutamate catabolism in Rhizobium subbaraonis JC85

Best path

braC, braD, braE, braF, braG, 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
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC CRO48_RS14965 CRO48_RS23625
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) CRO48_RS14940 CRO48_RS25805
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) CRO48_RS14945 CRO48_RS25800
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) CRO48_RS14950 CRO48_RS30045
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) CRO48_RS14955 CRO48_RS25750
gdhA glutamate dehydrogenase, NAD-dependent CRO48_RS07675
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ CRO48_RS09120 CRO48_RS31205
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) CRO48_RS09110 CRO48_RS31215
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP CRO48_RS09105 CRO48_RS31220
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) CRO48_RS09115 CRO48_RS31210
acaP L-glutamate permease AcaP
aspA L-aspartate ammonia-lyase CRO48_RS08885
bztA L-glutamate ABC transporter, substrate-binding component CRO48_RS09120 CRO48_RS31205
bztB L-glutamate ABC transporter, permease component 1 (BztB) CRO48_RS09115 CRO48_RS08835
bztC L-glutamate ABC transporter, permease component 2 (BztC) CRO48_RS09110 CRO48_RS31215
dmeA L-glutamate transporter DmeA
fumD (S)-2-methylmalate dehydratase (mesaconase)
glmE L-glutamate mutase, E component
glmS L-glutamate mutase, S component
glnP L-glutamate ABC transporter, fused permease and substrate-binding components GlnP
gltI L-glutamate ABC transporter, substrate-binding component (GltI/AatJ)
gltJ L-glutamate ABC transporter, permease component 1 (gltJ/aatQ) CRO48_RS25585 CRO48_RS17465
gltK L-glutamate ABC transporter, permease component 1 (gltK/aatM) CRO48_RS25585 CRO48_RS09110
gltL L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) CRO48_RS09105 CRO48_RS31220
gltP L-glutamate:cation symporter GltP/GltT CRO48_RS04065
gltS L-glutamate:Na+ symporter GltS CRO48_RS05720 CRO48_RS28875
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) CRO48_RS09110 CRO48_RS31210
gluD L-glutamate ABC transporter, permease component 2 (GluD) CRO48_RS25585 CRO48_RS02790
gtrA tripartite L-glutamate:Na+ symporter, small membrane component GtrA CRO48_RS10950
gtrB tripartite L-glutamate:Na+ symporter, large membrane component GtrB CRO48_RS10945 CRO48_RS24270
gtrC tripartite L-glutamate:Na+ symporter, substrate-binding component GtrC
mal methylaspartate ammonia-lyase
mcl (S)-citramalyl-CoA pyruvate-lyase CRO48_RS07585
peb1A L-glutamate ABC transporter, substrate-binding component Peb1A
peb1B L-glutamate ABC transporter, permease component Peb1B CRO48_RS03175 CRO48_RS24225
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