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
- Ignore hits to P81643 when looking for 'other' hits (Glutamine synthetase 2 isozyme; Chloroplast GS2; Glutamate--ammonia ligase; EC 6.3.1.2)
- Ignore hits to P85087 when looking for 'other' hits (Glutamine synthetase; Glutamate--ammonia ligase; EC 6.3.1.2)
- Predicted: UniProt sequence A5N4G9: SubName: Full=GlnA {ECO:0000313|EMBL:EDK32200.1}; EC=6.3.1.2 {ECO:0000313|EMBL:EDK32200.1};
- Predicted: UniProt sequence A5N4G9: SubName: Full=GlnA {ECO:0000313|EMBL:EDK32200.1}; EC=6.3.1.2 {ECO:0000313|EMBL:EDK32200.1};
- 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. link_2156-MONOMER is annotated with the same reaction, but was not originally given this EC number. In SwissProt, P81643 and P85087 are annotated with this activity but they are very short, so are ignored. CKL_RS00630 (A5N4G9) from Clostridium kluyveri is distantly related to characterized glutamine synthetases, but the active site residues and transition state binding residues are conserved (see alignment to 2whiA), so it is probably the missing glnA.
- Total: 2 HMMs and 84 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};
- Ignore hits to P00962 when looking for 'other' hits (glutamine-tRNA ligase (EC 6.1.1.18); glutamate-tRNAGln ligase (EC 6.1.1.24). glutaminyl-tRNA synthetase; EC 6.1.1.18. Glutamine--tRNA ligase; Glutaminyl-tRNA synthetase; GlnRS; EC 6.1.1.18. glutamine—tRNA ligase (EC 6.1.1.18). glutamine—tRNA ligase (EC 6.1.1.18))
- Curated sequence Q8DLI5: Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17
- 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). E. coli glutamine-tRNA ligase (P00962) is misannotated in BRENDA as the non-discriminating ligase. Q8DLI5 is a non-discriminating glutamyl-tRNA synthetase (PMID:16876193) but is not given this EC number in SwissProt.
- Total: 6 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