GapMind for Amino acid biosynthesis

 

L-histidine biosynthesis

Analysis of pathway his in 35 genomes

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

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