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Open Access Highly Accessed Research article

Evolutionarily consistent families in SCOP: sequence, structure and function

Ralph B Pethica1*, Michael Levitt2 and Julian Gough1

Author Affiliations

1 Department of Computer Science, University of Bristol, The Merchant Venturers Building, Room 3.16, Woodland Road, Bristol, UK

2 Department of Structural Biology, Stanford University School of Medicine, Stanford, 94305, CA, USA

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BMC Structural Biology 2012, 12:27  doi:10.1186/1472-6807-12-27

Published: 18 October 2012

Additional files

Additional file 1: Table S1.:

An Extended View of the Levels at which All Single Domain Proteins Associated With a Specific GO Term are Found in SCOP. Table shows an extended version of the level in SCOP at which all single domains associated with a particular GO term are found. The different levels shown are designed to illustrate the level at which GO terms fall, independently to the SCOP hierarchy. The distribution of GO terms assigned to domains is broken down into the following categories: · Sub Family: GO terms are found in some, but not all members of a family. · Family Equivalent: Exactly fits a family, i.e. found in all members of a family, but not in other families. · Multi Family: Found in all members of more than one family, but not in all families in the superfamily. · Partial Family: Completes one or more families, is absent from one or more families and is incomplete from exactly one family of a specific superfamily. · Scattered Families: May or may not complete one family, more than one incomplete family, and at least one empty family per superfamily. · Scattered in Superfamily: Present in, but does not complete, all families in a superfamily. · Almost Superfamily: Present in all families, competes some of them. · Superfamily Equivalent: Present for every domain of just one superfamily. · Multi Superfamilies: Present in every domain in more than one superfamily. · Partial Superfamilies: Completes at least one superfamily; partially completes exactly one other superfamily. · Scattered Superfamilies: May or may not complete one superfamily; present but not completing at least one other superfamily.

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Additional file 2: Table S2.:

Statistics for the number of domains used in the phylogenetic analysis. Statistics for domains in raw SCOP 1.73 and after filtering to 95% sequence identity and removal of trivially solvable cases.

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