GapMind for Amino acid biosynthesis

 

L-glutamine biosynthesis in Pseudomonas fluorescens FW300-N2E2

Best path

gltX, glnA, gatA, gatB, gatC

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
gltX glutamyl-tRNA(Glx) synthetase Pf6N2E2_153 Pf6N2E2_53
glnA glutamine synthetase Pf6N2E2_3821 Pf6N2E2_4511
gatA aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A Pf6N2E2_3289 Pf6N2E2_3403
gatB aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B Pf6N2E2_3290
gatC aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C Pf6N2E2_3288
Alternative steps:
gatD glutamyl-tRNA(Gln) amidotransferase, subunit D
gatE glutamyl-tRNA(Gln) amidotransferase, subunit E

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 (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