GapMind for Amino acid biosynthesis


L-serine biosynthesis

Analysis of pathway ser in 35 genomes

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

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 Apr 09 2024. The underlying query database was built on Apr 09 2024.



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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:

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