Figure 2

Outliers, the 1.20.58.60, 3.30.300.20, and 3.30.450.20 superfamilies. (a) The 1.20.58.60 (Cytoskeleton) superfamily; In the table to the right, for each database domain related to the query 1cunA1, we show the number of errors encountered before the domain is retrieved. Both the SEGF and LFF methods retrieve all seven related domains before the 300th error. (In this case, any domain in a fold group other than 1.20.58 is counted as an error.) In contrast, the SSEF method retrieves only 1cunA2, 1hciA4, and 1quuA1. The structure of the query domain 1cunA1 and two related domains are shown on the left, colored according to secondary structure assignments and also schematically represented by diagrams adjacent to the structures. The secondary structure assignment was computed using the DSSP (Dictionary of Protein Secondary Structure) program [25]. (b) The 3.30.300.20 (Rna Binding Protein) superfamily; Given the 1fjgC1 Domain as a query, the SSEF method retrieves all nine related domains before the 300th error. On the other hand, the SEGF and LFF method retrieve only five related domains. The ranking of the related domains is summarized in the table to the right. The structure of the query domain 1fjgC1 and two related domains are shown on the left, colored according to secondary structure assignments and also schematically represented by diagrams adjacent to the structures. (c) The 3.30.450.20 (Signaling Protein) superfamily, an example where the LFF method performs worse than the other two methods; Given the 1bywA0 domain as a query, the SSEF method retrieves all seven related domains, while the SEGF method retrieves six related domains before the 300th error. On the other hand, the LFF method retrieves only three related domains. The ranking of the related domains is summarized in the table to the right. The structure of the query domain 1bywA0 and two related domains are shown on the left, colored according to secondary structure assignments and also schematically represented by diagrams adjacent to the structures. The protein structures were rendered using PyMOL [26].