GapMind for Amino acid biosynthesis


L-asparagine biosynthesis

Analysis of pathway asn in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 aspS2, gatA, gatB, gatC
Azospirillum brasilense Sp245 aspS2, gatA, gatB, gatC
Bacteroides thetaiotaomicron VPI-5482 asnB
Burkholderia phytofirmans PsJN aspS2, gatA, gatB, gatC
Caulobacter crescentus NA1000 aspS2, gatA, gatB, gatC
Cupriavidus basilensis 4G11 aspS2, gatA, gatB, gatC
Dechlorosoma suillum PS aspS2, gatA, gatB, gatC
Desulfovibrio vulgaris Hildenborough aspS2, gatA, gatB, gatC
Desulfovibrio vulgaris Miyazaki F aspS2, gatA, gatB, gatC
Dinoroseobacter shibae DFL-12 aspS2, gatA, gatB, gatC
Dyella japonica UNC79MFTsu3.2 asnB
Echinicola vietnamensis KMM 6221, DSM 17526 asnB
Escherichia coli BW25113 asnB
Herbaspirillum seropedicae SmR1 aspS2, gatA, gatB, gatC
Klebsiella michiganensis M5al asnB
Magnetospirillum magneticum AMB-1 aspS2, gatA, gatB, gatC
Marinobacter adhaerens HP15 aspS2, gatA, gatB, gatC
Paraburkholderia bryophila 376MFSha3.1 aspS2, gatA, gatB, gatC
Pedobacter sp. GW460-11-11-14-LB5 aspS2, gatA, gatB, gatC
Phaeobacter inhibens BS107 aspS2, gatA, gatB, gatC
Pseudomonas fluorescens FW300-N1B4 aspS2, gatA, gatB, gatC
Pseudomonas fluorescens FW300-N2C3 aspS2, gatA, gatB, gatC
Pseudomonas fluorescens FW300-N2E2 aspS2, gatA, gatB, gatC
Pseudomonas fluorescens FW300-N2E3 aspS2, gatA, gatB, gatC
Pseudomonas fluorescens GW456-L13 aspS2, gatA, gatB, gatC
Pseudomonas putida KT2440 aspS2, gatA, gatB, gatC
Pseudomonas simiae WCS417 aspS2, gatA, gatB, gatC
Pseudomonas stutzeri RCH2 aspS2, gatA, gatB, gatC
Shewanella amazonensis SB2B asnB
Shewanella loihica PV-4 asnB
Shewanella oneidensis MR-1 asnB
Shewanella sp. ANA-3 asnB
Sinorhizobium meliloti 1021 aspS2, gatA, gatB, gatC
Sphingomonas koreensis DSMZ 15582 aspS2, gatA, gatB, gatC
Synechococcus elongatus PCC 7942 aspS2, gatA, gatB, gatC

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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