Also see fitness data for the top candidates
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.
Or see definitions of steps
| Step | Description | Best candidate | 2nd candidate |
|---|---|---|---|
| dmeA | L-glutamate transporter DmeA | DvMF_1542 | |
| aspA | L-aspartate ammonia-lyase | DvMF_0565 | DvMF_2075 |
| Alternative steps: | |||
| aapJ | ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ | DvMF_3152 | |
| aapM | ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | DvMF_2786 | |
| aapP | ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | DvMF_2788 | DvMF_3151 |
| aapQ | ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | ||
| acaP | L-glutamate permease AcaP | ||
| braC | ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC | DvMF_2607 | DvMF_2750 |
| braD | ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | DvMF_2608 | DvMF_2751 |
| braE | ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | DvMF_2609 | DvMF_2752 |
| braF | ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) | DvMF_2610 | DvMF_1481 |
| braG | ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) | DvMF_2611 | DvMF_2754 |
| bztA | L-glutamate ABC transporter, substrate-binding component | DvMF_3152 | |
| bztB | L-glutamate ABC transporter, permease component 1 (BztB) | DvMF_3153 | |
| bztC | L-glutamate ABC transporter, permease component 2 (BztC) | DvMF_2786 | |
| fumD* | (S)-2-methylmalate dehydratase (mesaconase) | DvMF_2461 with DvMF_2462 | |
| gdhA | glutamate dehydrogenase, NAD-dependent | DvMF_1346 | |
| 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) | DvMF_3152 | DvMF_2787 |
| gltJ | L-glutamate ABC transporter, permease component 1 (gltJ/aatQ) | DvMF_3153 | DvMF_2786 |
| gltK | L-glutamate ABC transporter, permease component 1 (gltK/aatM) | DvMF_3154 | DvMF_3153 |
| gltL | L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) | DvMF_2788 | DvMF_3151 |
| gltP | L-glutamate:cation symporter GltP/GltT | ||
| 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) | DvMF_1343 | DvMF_2686 |
| gluD | L-glutamate ABC transporter, permease component 2 (GluD) | DvMF_3154 | DvMF_2786 |
| gtrA | tripartite L-glutamate:Na+ symporter, small membrane component GtrA | ||
| gtrB | tripartite L-glutamate:Na+ symporter, large membrane component GtrB | DvMF_2137 | |
| gtrC | tripartite L-glutamate:Na+ symporter, substrate-binding component GtrC | DvMF_3152 | |
| mal | methylaspartate ammonia-lyase | ||
| mcl | (S)-citramalyl-CoA pyruvate-lyase | ||
| peb1A | L-glutamate ABC transporter, substrate-binding component Peb1A | DvMF_3152 | |
| peb1B | L-glutamate ABC transporter, permease component Peb1B | DvMF_2786 | DvMF_1919 |
| 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 17 2021. The underlying query database was built on Sep 17 2021.
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:
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