L-asparagine biosynthesis in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

L-asparagine biosynthesis in Synechococcus elongatus PCC 7942

Best path

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).

all:

to_asn_tRNA
or to_asparagine

to_asn_tRNA: aspS2 and transamidation
transamidation: gatA, gatB and gatC

Comment: Some organisms have gatDE instead of gatABC. GatDE are thought to form glutaminyl-tRNA only, so they are not described here (but TIGRFam suggests that gatD might replace gatB in some archaea). In the step definitions of gatABC, metacyc entries are added separately because they have HTML tags in their descriptions. Also there are no hits for some of the terms -- often, only gatB is annotated as a aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit.

to_asparagine:

asnB
or asnA

6 steps (4 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
aspS2	aspartyl-tRNA(Asp/Asn) synthetase	Synpcc7942_1313	Synpcc7942_2415
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
Alternative steps:
asnA	aspartate--ammonia ligase
asnB	asparagine synthase (glutamine-hydrolysing)

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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the original 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

GapMind for Amino acid biosynthesis