Visualizing Hydrogenase Sequence Diversity

Sequence similarity networks (SSNs)18 (link) constructed using Cytoscape 4.144 (link) were used to visualize the distribution and diversity of the retrieved hydrogenase sequences. In this analysis, each node represents one of the 3248 hydrogenase sequences in the reference database (Dataset S1). Each edge represents the sequence similarity between them as determined by E-values from all-vs-all BLAST analysis, with all self and duplicate edges removed. Three networks were constructed, namely for the [NiFe]-hydrogenase large subunit sequences (Dataset S2), [FeFe]-hydrogenase catalytic domain sequences (Dataset S3), and [Fe]-hydrogenase sequences (Dataset S4). To control the degree of separation between nodes, logE cutoffs that were incrementally decreased from −5 to −200 until no major changes in clustering was observed. The logE cutoffs used for the final classifications are shown in Fig. 1 and Figure S1.

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Søndergaard D., Pedersen C.N, & Greening C. (2016). HydDB: A web tool for hydrogenase classification and analysis. Scientific Reports, 6, 34212.

Publication 2016

Catalytic domain Fe hydrogenase Hydrogenase Nife hydrogenase Subunit

Corresponding Organization :

Other organizations : Aarhus University, CSIRO Land and Water, Commonwealth Scientific and Industrial Research Organisation

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Variable analysis

independent variables

Log E cutoffs that were incrementally decreased from -5 to -200

dependent variables

Degree of separation between nodes in the sequence similarity networks

control variables

Degree of separation between nodes until no major changes in clustering was observed

controls

No positive or negative controls were explicitly mentioned in the provided information.

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