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Actinomycetales Genome Database

Actinomycetales Genome Database

Coming soon.


Enediyne Genome Neighboorhood Network (GNN)
image

A virtual survey of the GenBank and JGI Genome databases revealed 87 enediyne biosynthetic gene clusters from 78 bacteria strains. An enediyne genome neighborhood network (GNN) was constructed to analyze these gene clusters in a high-throughput manner. Please reference J. D. Rudolf, X. Yan, and B. Shen. (2016J. Ind. Microbiol. Biotechnol. 43, 261-276. Access to the enediyne GNN is available via the following files:

FASTA file containing proteins in the enediyne genome neighborhoods

BLAST result at an E-value of 10

Imported BLAST result at an E-value of 10-8

Imported BLAST result at an E-value of 10-75

Annotation table

Cytoscape session file displaying known enediynes at an E-value of 10-8 (Fig. 3) 

Cytoscape session file displaying known enediynes at an E-value of 10-75 (Fig. 6)

Cytoscape session file displaying 9- vs 10-membered prediction at an E-value of 10-75 (Fig. 7)  

Download links for BLAST+ and Cytoscape

Contact jrudolf@scripps.edu for questions.


P450s in Streptomyces (SNN)

P450 image

We surveyed the current catalytic landscape of P450s within the Streptomyces genus. A sequence similarity network (SNN) was constructed to analyze sequence–function relationships of these remarkable biocatalysts. Please reference J. D. Rudolf, C.-Y. Chang, M. Ma, and B. Shen. (2017Nat. Prod. Rep., in press. Access to the P450 SSN is available via the following files:

FASTA file containing the P450 protein sequences used in the SSN

Cytoscape session file displayed at an E-value of 10-85 (Fig. 5)

Cytoscape session file displayed at an E-value of 10-124 (Fig. 6)

Link to the Enzyme Similarity Tool made available by the Enzyme Function Initiative

Contact jrudolf@scripps.edu for questions