S100 Family: 1.25.40.120.1.1.1.1

Representative domain: 2h6fA00

Classification Lineage (1.25.40.120.1.1.1.1)

CATH Code	Level Description	Links
1	Mainly Alpha
1.25	Alpha Horseshoe
1.25.40	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
1.25.40.120		Gene3D
1.25.40.120.1
1.25.40.120.1.1
1.25.40.120.1.1.1
1.25.40.120.1.1.1.1

Summary of Non-Redundant Representatives


-	-	-	-	-	-	-	-	14

Non-Redundant Representatives (14)
Functional Families
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What is a Non-Redundant Representative?

CATH is a tree-like organisation of nodes that begins with the class node (i.e. the first branch-point of the tree) and ends with the domain nodes (i.e. the leaves of the tree). Each node below the class have a parent that they belong to, e.g. the parent of the H level (Homologous superfamily) is the T (Topology). Additionally, each node above the domains have child nodes that belong to them, e.g. the child nodes of a given H (Homologous superfamily) level are the S35 families (domains clustered at > 35% sequence identity).

S100 Count Entries in S100 Family 1.25.40.120.1.1.1.1 (14)

CATH code	Domain ID	Keywords
1.25.40.120.1.1.1.1.1	2h6fA00	microtubule binding, Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha, Homo sapiens, transforming growth factor beta receptor signaling pathway, microtubule associated complex, positive regulation of deacetylase activity, Protein farnesyltransferase., alpha-tubulin binding, protein farnesyltransferase activity, Protein geranylgeranyltransferase type I., positive regulation of tubulin deacetylation
1.25.40.120.1.1.1.1.2	1tn6A00	Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha, microtubule binding, transforming growth factor beta receptor signaling pathway, Homo sapiens, positive regulation of deacetylase activity, microtubule associated complex, positive regulation of tubulin deacetylation, Protein geranylgeranyltransferase type I., alpha-tubulin binding, protein farnesyltransferase activity, Protein farnesyltransferase.
1.25.40.120.1.1.1.1.3	2h6hA00	transforming growth factor beta receptor signaling pathway, Homo sapiens, Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha, microtubule binding, positive regulation of tubulin deacetylation, Protein geranylgeranyltransferase type I., protein farnesyltransferase activity, alpha-tubulin binding, Protein farnesyltransferase., positive regulation of deacetylase activity, microtubule associated complex
1.25.40.120.1.1.1.1.4	2iejA00	positive regulation of tubulin deacetylation, protein farnesyltransferase activity, alpha-tubulin binding, Protein geranylgeranyltransferase type I., Protein farnesyltransferase., microtubule associated complex, positive regulation of deacetylase activity, transforming growth factor beta receptor signaling pathway, Homo sapiens, Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha, microtubule binding
1.25.40.120.1.1.1.1.5	3e37A00	microtubule associated complex, positive regulation of deacetylase activity, protein farnesyltransferase activity, alpha-tubulin binding, Protein geranylgeranyltransferase type I., positive regulation of tubulin deacetylation, Protein farnesyltransferase., Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha, microtubule binding, Homo sapiens, transforming growth factor beta receptor signaling pathway
1.25.40.120.1.1.1.1.6	1ld8A00	Protein farnesyltransferase., alpha-tubulin binding, protein farnesyltransferase activity, Protein geranylgeranyltransferase type I., positive regulation of tubulin deacetylation, microtubule associated complex, positive regulation of deacetylase activity, Homo sapiens, transforming growth factor beta receptor signaling pathway, microtubule binding, Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
1.25.40.120.1.1.1.1.7	2h6gA00	positive regulation of tubulin deacetylation, protein farnesyltransferase activity, alpha-tubulin binding, Protein geranylgeranyltransferase type I., Protein farnesyltransferase., microtubule associated complex, positive regulation of deacetylase activity, transforming growth factor beta receptor signaling pathway, Homo sapiens, Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha, microtubule binding
1.25.40.120.1.1.1.1.8	1s63A00	Homo sapiens, transforming growth factor beta receptor signaling pathway, Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha, microtubule binding, alpha-tubulin binding, protein farnesyltransferase activity, Protein geranylgeranyltransferase type I., positive regulation of tubulin deacetylation, Protein farnesyltransferase., microtubule associated complex, positive regulation of deacetylase activity
1.25.40.120.1.1.1.1.9	1ld7A00	microtubule binding, Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha, transforming growth factor beta receptor signaling pathway, Homo sapiens, positive regulation of deacetylase activity, microtubule associated complex, Protein farnesyltransferase., positive regulation of tubulin deacetylation, Protein geranylgeranyltransferase type I., alpha-tubulin binding, protein farnesyltransferase activity
1.25.40.120.1.1.1.1.10	1mzcA00	microtubule associated complex, positive regulation of deacetylase activity, Protein farnesyltransferase., positive regulation of tubulin deacetylation, alpha-tubulin binding, protein farnesyltransferase activity, Protein geranylgeranyltransferase type I., microtubule binding, Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha, transforming growth factor beta receptor signaling pathway, Homo sapiens
1.25.40.120.1.1.1.1.11	1sa4A00	Protein farnesyltransferase., positive regulation of tubulin deacetylation, Protein geranylgeranyltransferase type I., protein farnesyltransferase activity, alpha-tubulin binding, positive regulation of deacetylase activity, microtubule associated complex, transforming growth factor beta receptor signaling pathway, Homo sapiens, microtubule binding, Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
1.25.40.120.1.1.1.1.12	1jcqA00	transforming growth factor beta receptor signaling pathway, Homo sapiens, Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha, microtubule binding, positive regulation of tubulin deacetylation, alpha-tubulin binding, protein farnesyltransferase activity, Protein geranylgeranyltransferase type I., Protein farnesyltransferase., microtubule associated complex, positive regulation of deacetylase activity
1.25.40.120.1.1.1.1.13	2f0yA00	microtubule associated complex, positive regulation of deacetylase activity, positive regulation of tubulin deacetylation, protein farnesyltransferase activity, alpha-tubulin binding, Protein geranylgeranyltransferase type I., Protein farnesyltransferase., Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha, microtubule binding, transforming growth factor beta receptor signaling pathway, Homo sapiens
1.25.40.120.1.1.1.1.14	2h6iA00	positive regulation of deacetylase activity, microtubule associated complex, Protein farnesyltransferase., positive regulation of tubulin deacetylation, Protein geranylgeranyltransferase type I., protein farnesyltransferase activity, alpha-tubulin binding, microtubule binding, Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha, transforming growth factor beta receptor signaling pathway, Homo sapiens

The information on Functional Families (FunFams) is currently being updated and will be released by the end of March 2012. The pages will include the following features:

Multiple alignments for each functional family
Representative structure for each functional with known catalytic and interface residues highlighted, along with conserved residues predicted by scorecons
Detailed functional information on diversity and conservation within Functional families
Multi-domain architectures

In the meantime, please find a summary of information on the FunFams and protein networks within this superfamily on the Gene3D pages:

http://gene3d.biochem.ucl.ac.uk/superfamily/?accession=1.25.40.120.1.1.1.1

What is a Non-Redundant Representative?

Why can't I have a multiple structural alignment of the whole superfamily?

The simple answer is that some of the larger superfamilies in CATH comprise relatives which are very structurally diverse, having different secondary structure embellishments. Attempting to provide a global alignment of all domains in the superfamily would result in poor quality alignments. As a result, structural alignments in CATH are generated by first clustering together the structures that have at least some recognisable structural similarity using a normalised RMSD score (SIMAX = RMSDxNumber of residues in the largest domain/number of aligned residues) less than a given cutoff.

What is an Close Structural Cluster?

A Close Structural Cluster describes a cluster of two or more CATH domains that have been grouped together due to their close structural similarity (SIMAX score < 5Å where SIMAX = RMSD x Number of residues in the larger domain/number of aligned residues).

What is a Distant Structural Cluster?

A Distant Structural Cluster describes a cluster of two or CATH domains that have been grouped together with a more relaxed structural similarity threshold to investigate more distant evolutionary similarities (SIMAX score < 5Å where SIMAX = RMSD x Number of residues in the larger domain/number of aligned residues).

What is a Structural Neighbour?

The term "structural neighbour" is used here to describe two CATH domains that share a degree of structural similarity. The SSAP algorithm is used to calculate this similarity and works by generating a structure-based pairwise alignment of the two domains then scoring this alignment using a RMSD score which has been normalised by the length of the larger domain divided by the number of aligned residues (SIMAX).

S100 Family: 1.25.40.120.1.1.1.1

Classification Lineage (1.25.40.120.1.1.1.1)

Summary of Non-Redundant Representatives

What is a Non-Redundant Representative?

S100 Count Entries in S100 Family 1.25.40.120.1.1.1.1 (14)

What is a Non-Redundant Representative?

Why can't I have a multiple structural alignment of the whole superfamily?

What is an Close Structural Cluster?

What is a Distant Structural Cluster?

What is a Structural Neighbour?

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