GapMind for Amino acid biosynthesis

 

L-glutamine biosynthesis

Analysis of pathway gln in 35 genomes

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

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.

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 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