GapMind for Amino acid biosynthesis

 

L-proline biosynthesis

Analysis of pathway pro in 35 genomes

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

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 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