The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:

• the number of sequences which exhibit this architecture
• a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin. This example describes an architecture with one Gla domain, followed by two consecutive EGF domains, and finally a single Trypsin domain
• a link to the page in the Pfam site showing information about the sequence that the graphic describes
• the UniProt description of the protein sequence
• the number of residues in the sequence
• the Pfam graphic itself.

Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.

Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.

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In brackets beside each number is the percentage of the total number of sequence hits for the clan that are represented by this domain. The rightmost column provides a link to the alignments tab for each domain. Finally, the last row in the table provides a link to the HTML representation of the alignment for the seed alignments for all members of this clan.

Please note: the clan alignment can be extremely large and the resulting HTML file is often too large to be rendered by web-browsers. Please consider downloading the alignment (by right-clicking the link) rather than viewing it in your browser.

Relationships between families in a clan are determined by a PRC alignment between family HMMs. Families are deemed to be closely related if their E-value is less than 10^-3 and these relationships are shown with a solid line. Less closely related family pairs, with an E-value of between 10^-3 and 10^-1, are shown with a dashed line.

The E-value for each pair of closely or partially related families is shown next to the line linking the families. Clicking on the E-value will take you to the pairwise HMM-logo for that relationship. You can see the information regarding a Pfam family by clicking on the family box.

This tree shows the occurrence of the domains in this clan across different species. More...

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We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in journal article that accompanies the website.

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