Definition of L-glutamine biosynthesis
As rules and steps, or see full text
Rules
Overview: Glutamine biosynthesis in GapMind is based on MetaCyc pathways L-glutamine biosynthesis I from glutamine (link) or glutaminyl-tRNA(Gln) biosynthesis via transamidation (link). Both of these pathways require glutamate. The biosynthesis of glutamate is not represented in GapMind, as glutamate can be formed by transamination of alpha-ketoglutarate, an interemdiate in the TCA cycle.
- all:
- to_glutamine
- or to_gln_tRNA
- to_gln_tRNA: gltX, glnA and transamidation
- Comment: In the transamidation pathway, glutamate is ligated to tRNA, but free glutamine is still required, because amidotransferase uses a glutaminase subunit to obtain ammonia.
- to_glutamine: glnA
- transamidation:
- gatA, gatB and gatC
- or gatD and gatE
- Comment: Two types of glutamyl-tRNA amidotransferases are known, GatABC or GatDE. GatABC are generally thought to act on both glutamyl-tRNA and aspartyl-tRNA, while GatDE is thought to act only on glutamyl-tRNA.
Steps
glnA: glutamine synthetase
- Curated proteins or TIGRFams with EC 6.3.1.2
- Ignore hits to items matching EC 5.4.4.3 when looking for 'other' hits
- Curated sequence SYNPCC7942_2156-MONOMER: glutamine synthetase, type I
- Comment: A protein from Cupriavidus necator is reported to be a 3-hydroxylaminophenol mutase (see Swiss-Prot 3HAPM_CUPNJ), involved in 3-nitrophenol degradation. That is the only glutamine synthetase-like protein in the proteome of Cupriavidus necator (strain JMP 134 / LMG 1197) [see proteome UP000002697] and is 96% identical to the essential protein RR42_RS12995 from Cupriavidus basilensis 4G11. It is probably a glutamine synthetase. SYNPCC7942_2156-MONOMER is annotated with the same reaction, but was not originally given this EC number.
- Total: 2 HMMs and 78 characterized proteins
gltX: glutamyl-tRNA(Glx) synthetase
- Curated proteins or TIGRFams with EC 6.1.1.24
- UniProt sequence A0A0H3C8P5_CAUVN: RecName: Full=Glutamate--tRNA ligase {ECO:0000256|HAMAP-Rule:MF_00022}; EC=6.1.1.17 {ECO:0000256|HAMAP-Rule:MF_00022}; AltName: Full=Glutamyl-tRNA synthetase {ECO:0000256|HAMAP-Rule:MF_00022}; Short=GluRS {ECO:0000256|HAMAP-Rule:MF_00022};
- Comment: Glutamyl-tRNA(Glu/Gln) is usually formed by a nondescriminating glutamyl-tRNA synthetase. CCNA_01982 (A0A0H3C8P5_CAUVN) from Caulobacter crescentus is the sole glutamyl-tRNA synthetase, there is no glutaminyl-tRNA synthetase, and gatABC are present, so we annotated it as non-discriminating. In contrast, as of March 2019, unirule UR000075658 labeled it as EC 6.1.1.17 (the discriminating kind).
- Total: 4 characterized proteins
gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A
gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
gatC: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C
gatD: glutamyl-tRNA(Gln) amidotransferase, subunit D
gatE: glutamyl-tRNA(Gln) amidotransferase, subunit E
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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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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