GapMind for Amino acid biosynthesis

 

L-asparagine biosynthesis in Pedobacter sp. GW460-11-11-14-LB5

Best path

aspS2, gatA, gatB, gatC

Also see fitness data for the top candidates

Rules

Overview: Asparagine biosynthesis in GapMind is based on MetaCyc pathways L-asparagine biosynthesis I (link), II (link), or III (tRNA-dependent) (link). In pathways I or II, aspartate is amidated directly, with glutamine or ammonia as the nitrogen source. In pathway III, aspartate is ligated to tRNA(Asn) and then amidated to Asn-tRNA(Asn).

6 steps (6 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aspS2 aspartyl-tRNA(Asp/Asn) synthetase CA265_RS19975 CA265_RS05115
gatA aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A CA265_RS19010
gatB aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B CA265_RS09170
gatC aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C CA265_RS07480
Alternative steps:
asnA aspartate--ammonia ligase CA265_RS07955
asnB asparagine synthase (glutamine-hydrolysing) CA265_RS07955 CA265_RS01810

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