GapMind for Amino acid biosynthesis

 

L-glutamine biosynthesis in Haloechinothrix alba DSM 45207

Best path

glnA

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 CHB84_RS19600 CHB84_RS21510
Alternative steps:
gatA aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A CHB84_RS03180 CHB84_RS16940
gatB aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B CHB84_RS03185
gatC aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C CHB84_RS03175
gatD glutamyl-tRNA(Gln) amidotransferase, subunit D
gatE glutamyl-tRNA(Gln) amidotransferase, subunit E
gltX glutamyl-tRNA(Glx) synthetase CHB84_RS03245

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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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