GraphML files for protein sequence networks of glycoside hydrolase 19 homologues (doi:10.18419/darus-802)

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GraphML files for protein sequence networks of glycoside hydrolase 19 homologues

doi:10.18419/darus-802

DaRUS

2020-06-01

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Orlando, Marco, 2020, "GraphML files for protein sequence networks of glycoside hydrolase 19 homologues", https://doi.org/10.18419/darus-802, DaRUS, V1

GraphML files for protein sequence networks of glycoside hydrolase 19 homologues

doi:10.18419/darus-802

Orlando, Marco (University of Milano Bicocca)

031B0571A

EXC2075

DaRUS

Pleiss, Jürgen

Buchholz, Patrick C. F.

2020-05-11

https://doi.org/10.18419/darus-802

Medicine, Health and Life Sciences, alignment, network, amino acid sequence, graph, protein sequence

GraphML files for undirected weighted graphs with nodes that represent protein sequences of glycoside hydrolase 19 homologues. Protein sequences were clustered by a threshold of 90% sequence identity to derive representative sequences. Pairwise sequence identity between two sequences was derived from global Needleman-Wunsch alignment. Protein sequence networks were generated with edge weights of pairwise sequence identity, filtered by a predefined threshold. Metadata of the nodes (e.g. annotations) and of the edges (the edge weights) were summarized in GraphML files.

The GraphML attributes for the edges comprise the edge weights (pairwise sequence identity, "weight"). The GraphML attributes for the nodes comprise the identifiers from the GH19ED ("sequence_id", "protein_id", "hfam_id", and "sfam_id" for sequence, protein, homologous family and superfamily identifiers, respectively), the NCBI taxonomy ID ("tax_id"), the annotated (organism) source name ("tax_name"), the taxonomic lineage of the source organism ("lineage", with taxa separated by "<--"), and the length of the amino acid sequence ("sequence_length"). In addition, suggested color names are given for both fill color and border color of each node ("color" and "color_border").

<a href="http://pfam.xfam.org/family/Glyco_hydro_19">http://pfam.xfam.org/family/Glyco_hydro_19</a>

<a href="https://gh19ed.biocatnet.de/">https://gh19ed.biocatnet.de/</a>

Orlando M, Buchholz PCF, Lotti M, Pleiss J (2020) Large-scale exploration of sequences, substrate specificity and evolution in glycoside hydrolase family 19: the GH19 Engineering Database (submitted)

Orlando M, Buchholz PCF, Lotti M, Pleiss J (2020) Large-scale exploration of sequences, substrate specificity and evolution in glycoside hydrolase family 19: the GH19 Engineering Database (submitted)

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CHITs_60_percent_identity_cutoff.graphml

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Protein sequence network for the chitinase domains from the Glycoside Hydrolase 19 Engineering Database. The GraphML file contains representative nodes (clustered by 90% in USEARCH) connected by at least 60% pairwise sequence identity (edge weights derived from Needleman-Wunsch alignments).

text/xml-graphml

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ELYSs_60_percent_identity_cutoff.graphml

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Protein sequence network for the endolysin domains from the Glycoside Hydrolase 19 Engineering Database. The GraphML file contains representative nodes (clustered by 90% in USEARCH) connected by at least 60% pairwise sequence identity (edge weights derived from Needleman-Wunsch alignments).

text/xml-graphml

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GH19_40_percent_identity_cutoff.graphml

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Protein sequence network for representative GH19 domains (corresponding to Pfam’s GH19 profile HMM: PF00182) from the Glycoside Hydrolase 19 Engineering Database. The GraphML file contains representative nodes (clustered by 90% in USEARCH) connected by at least 40% pairwise sequence identity (edge weights derived from Needleman-Wunsch alignments).

text/xml-graphml