GapMind for Amino acid biosynthesis

 

L-glutamine biosynthesis in Synechococcus elongatus PCC 7942

Best path

glnA

Also see fitness data for the top candidates

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.

7 steps (5 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
glnA glutamine synthetase Synpcc7942_2156 Synpcc7942_0169
Alternative steps:
gatA aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A Synpcc7942_2117
gatB aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B Synpcc7942_0118
gatC aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C Synpcc7942_2322
gatD glutamyl-tRNA(Gln) amidotransferase, subunit D
gatE glutamyl-tRNA(Gln) amidotransferase, subunit E
gltX glutamyl-tRNA(Glx) synthetase Synpcc7942_2393 Synpcc7942_0922

Confidence: high confidence medium confidence low confidence
? – known gap: despite the lack of a good candidate for this step, this organism (or a related organism) performs the pathway

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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