GapMind for Amino acid biosynthesis


glycine biosynthesis

Analysis of pathway gly in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 glyA
Azospirillum brasilense Sp245 glyA
Bacteroides thetaiotaomicron VPI-5482 glyA
Burkholderia phytofirmans PsJN glyA
Caulobacter crescentus NA1000 glyA
Cupriavidus basilensis 4G11 glyA
Dechlorosoma suillum PS glyA
Desulfovibrio vulgaris Hildenborough glyA
Desulfovibrio vulgaris Miyazaki F glyA
Dinoroseobacter shibae DFL-12 glyA
Dyella japonica UNC79MFTsu3.2 glyA
Echinicola vietnamensis KMM 6221, DSM 17526 glyA
Escherichia coli BW25113 glyA
Herbaspirillum seropedicae SmR1 glyA
Klebsiella michiganensis M5al glyA
Magnetospirillum magneticum AMB-1 glyA
Marinobacter adhaerens HP15 glyA
Paraburkholderia bryophila 376MFSha3.1 glyA
Pedobacter sp. GW460-11-11-14-LB5 glyA
Phaeobacter inhibens BS107 glyA
Pseudomonas fluorescens FW300-N1B4 glyA
Pseudomonas fluorescens FW300-N2C3 glyA
Pseudomonas fluorescens FW300-N2E2 glyA
Pseudomonas fluorescens FW300-N2E3 glyA
Pseudomonas fluorescens GW456-L13 glyA
Pseudomonas putida KT2440 glyA
Pseudomonas simiae WCS417 glyA
Pseudomonas stutzeri RCH2 glyA
Shewanella amazonensis SB2B glyA
Shewanella loihica PV-4 aceA, agx1
Shewanella oneidensis MR-1 glyA
Shewanella sp. ANA-3 glyA
Sinorhizobium meliloti 1021 glyA
Sphingomonas koreensis DSMZ 15582 glyA
Synechococcus elongatus PCC 7942 glyA

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.



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:

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