GraphML file for homologues and reconstructed ancestors of arylsulfatases and phosphonate monoester hydrolases (doi:10.18419/darus-817)

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Part 2: Study Description
Part 5: Other Study-Related Materials
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Document Description

Citation

Title:

GraphML file for homologues and reconstructed ancestors of arylsulfatases and phosphonate monoester hydrolases

Identification Number:

doi:10.18419/darus-817

Distributor:

DaRUS

Date of Distribution:

2021-05-03

Version:

1

Bibliographic Citation:

Buchholz, Patrick C. F., 2021, "GraphML file for homologues and reconstructed ancestors of arylsulfatases and phosphonate monoester hydrolases", https://doi.org/10.18419/darus-817, DaRUS, V1

Study Description

Citation

Title:

GraphML file for homologues and reconstructed ancestors of arylsulfatases and phosphonate monoester hydrolases

Identification Number:

doi:10.18419/darus-817

Authoring Entity:

Buchholz, Patrick C. F. (Universität Stuttgart)

Distributor:

DaRUS

Access Authority:

Pleiss, Jürgen

Depositor:

Buchholz, Patrick C. F.

Date of Deposit:

2020-07-01

Study Scope

Keywords:

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

Abstract:

Protein sequence network for homologues of arylsulfatases and phosphonate monoester hydrolases, including reconstructed ancestral sequences from a maximum-likelihood phylogenetic tree.

Notes:

The GraphML attributes for the edges comprise the edge weights (pairwise sequence identity, "weight"). The GraphML attributes for the nodes comprise several annotations, if available: the annotated name ("Annotation"), the source organism ("Organism"), the accessions from the Protein Data Bank ("PDB"), an accession to public sequence databases such as the NCBI GenBank ("Accession"), an annotated name for the sequence ("Name"), and the group it belongs to ("Group"). Reconstructed ancestors are labelled by an integer as "Name" and "reconstructed ancestor" as "Annotation".

Methodology and Processing

Sources Statement

Data Sources:

van Loo B, Schober M, Valkov E, Heberlein M, Bornberg-Bauer E, Faber K, et al. Structural and Mechanistic Analysis of the Choline Sulfatase from Sinorhizobium melliloti: A Class I Sulfatase Specific for an Alkyl Sulfate Ester. J Mol Biol. 2018;430: 1004-1023. <a href="https://doi.org/10.1016/j.jmb.2018.02.010">doi:10.1016/j.jmb.2018.02.010</a>

van Loo B, Bayer CD, Fischer G, Jonas S, Valkov E, Mohamed MF, et al. Balancing Specificity and Promiscuity in Enzyme Evolution: Multidimensional Activity Transitions in the Alkaline Phosphatase Superfamily. J Am Chem Soc. 2019;141: 370-387. <a href="https://doi.org/10.1021/jacs.8b10290">doi:10.1021/jacs.8b10290</a>

Data Access

Notes:

CC0 Waiver

Other Study Description Materials

Related Studies

<a href="https://doi.org/10.18419/darus-1801">https://doi.org/10.18419/darus-1801</a>

Related Publications

Citation

Bibliographic Citation:

Patrick C. F. Buchholz, Bert van Loo, Bernard D. G. Eenink, Erich Bornberg-Bauer, Jürgen Pleiss: "Ancestral sequences of a large promiscuous enzyme family correspond to bridges in sequence space in a network representation" (submitted)

Other Study-Related Materials

Label:

AS_PMH_ancestors.graphml

Text:

GraphML formatted file for an undirected graph (network) containing 238 nodes connected by 28,203 edges.

Notes:

text/xml-graphml