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MOBscan: Automated Annotation of MOB Relaxases

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Horizontal Gene Transfer

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2075))

Abstract

Relaxase-based plasmid classification has become popular in the past 10 years. Nevertheless, it is not obvious how to assign a query protein to a relaxase MOB family. Automated protein annotation is commonly used to classify them into families, gathering evolutionarily related proteins that likely perform the same function, while circumventing the problem of different naming conventions. Here, we implement an automated method, MOBscan, to identify relaxases and classify them into any of the nine MOB families. MOBscan is a web tool that carries out a HMMER search against a curated database of MOB profile Hidden Markov models. It is freely available at https://castillo.dicom.unican.es/mobscan/.

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Acknowledgments

This work was financed by the Spanish Ministry of Economy and Competitiveness (BFU2017-86378-P and RTC-2015-3184-1). We thank E.P.C. Rocha and the members of his team for a long-standing and fruitful collaboration. M. Pilar Garcillán-Barcia and Santiago Redondo-Salvo contributed equally to this work.

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Author notes

  1. M. Pilar Garcillán-Barcia and Santiago Redondo-Salvo contributed equally to this work.

Authors and Affiliations

  1. Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas, Santander, Cantabria, Spain

    M. Pilar Garcillán-Barcia & Santiago Redondo-Salvo

  2. Departamento de Ingeniería de Comunicaciones, Universidad de Cantabria, Santander, Cantabria, Spain

    Luis Vielva

  3. Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC, Santander, Cantabria, Spain

    Fernando de la Cruz

Authors
  1. M. Pilar Garcillán-Barcia
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  2. Santiago Redondo-Salvo
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  3. Luis Vielva
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  4. Fernando de la Cruz
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Corresponding authors

Correspondence to M. Pilar Garcillán-Barcia or Fernando de la Cruz .

Editor information

Editors and Affiliations

  1. Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC, Santander, Cantabria, Spain

    Fernando de la Cruz

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Garcillán-Barcia, M.P., Redondo-Salvo, S., Vielva, L., de la Cruz, F. (2020). MOBscan: Automated Annotation of MOB Relaxases. In: de la Cruz, F. (eds) Horizontal Gene Transfer. Methods in Molecular Biology, vol 2075. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9877-7_21

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  • DOI: https://doi.org/10.1007/978-1-4939-9877-7_21

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9876-0

  • Online ISBN: 978-1-4939-9877-7

  • eBook Packages: Springer Protocols

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