S100 Family: 3.40.50.1980.5.1.1.1

Representative domain: 1m1nB03

Classification Lineage (3.40.50.1980.5.1.1.1)

CATH Code	Level Description	Links
3	Alpha Beta
3.40	3-Layer(aba) Sandwich
3.40.50	Rossmann fold
3.40.50.1980	Nitrogenase molybdenum iron protein domain	Gene3D
3.40.50.1980.5
3.40.50.1980.5.1
3.40.50.1980.5.1.1
3.40.50.1980.5.1.1.1

Summary of Non-Redundant Representatives


-	-	-	-	-	-	-	-	37

Non-Redundant Representatives (37)
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 3.40.50.1980.5.1.1.1 (37)

CATH code	Domain ID	Keywords
3.40.50.1980.5.1.1.1.1	1m1nB03	Nitrogenase molybdenum-iron protein beta chain, Nitrogenase., nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1], Metabolic pathways, Azotobacter vinelandii, Nitrogen metabolism
3.40.50.1980.5.1.1.1.2	1m1nD03	nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1], Nitrogenase., Nitrogenase molybdenum-iron protein beta chain, Nitrogen metabolism, Azotobacter vinelandii, Metabolic pathways
3.40.50.1980.5.1.1.1.3	1m1nF03	Azotobacter vinelandii, Nitrogen metabolism, Metabolic pathways, nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1], Nitrogenase molybdenum-iron protein beta chain, Nitrogenase.
3.40.50.1980.5.1.1.1.4	1m1nH03	Metabolic pathways, Azotobacter vinelandii, Nitrogen metabolism, Nitrogenase molybdenum-iron protein beta chain, Nitrogenase., nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1]
3.40.50.1980.5.1.1.1.5	2minB03	nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1], Nitrogenase molybdenum-iron protein beta chain, Nitrogenase., Azotobacter vinelandii, Nitrogen metabolism, Metabolic pathways
3.40.50.1980.5.1.1.1.6	2minD03	Nitrogenase., Nitrogenase molybdenum-iron protein beta chain, nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1], Metabolic pathways, Nitrogen metabolism, Azotobacter vinelandii
3.40.50.1980.5.1.1.1.7	3minB03	Nitrogen metabolism, Azotobacter vinelandii, Metabolic pathways, nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1], Nitrogenase., Nitrogenase molybdenum-iron protein beta chain
3.40.50.1980.5.1.1.1.8	3minD03	nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1], Nitrogenase., Nitrogenase molybdenum-iron protein beta chain, Nitrogen metabolism, Azotobacter vinelandii, Metabolic pathways
3.40.50.1980.5.1.1.1.9	2afhB04	Metabolic pathways, Nitrogen metabolism, Azotobacter vinelandii, Nitrogenase., Nitrogenase molybdenum-iron protein beta chain, nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1]
3.40.50.1980.5.1.1.1.10	2afhD04	nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1], Nitrogenase., Nitrogenase molybdenum-iron protein beta chain, Nitrogen metabolism, Azotobacter vinelandii, Metabolic pathways
3.40.50.1980.5.1.1.1.11	1g20B03	nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1], Nitrogenase molybdenum-iron protein beta chain, Nitrogenase., Azotobacter vinelandii, Nitrogen metabolism, Metabolic pathways
3.40.50.1980.5.1.1.1.12	1g20D03	Metabolic pathways, Azotobacter vinelandii, Nitrogen metabolism, Nitrogenase molybdenum-iron protein beta chain, Nitrogenase., nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1]
3.40.50.1980.5.1.1.1.13	3k1aB04	Metabolic pathways, Nitrogen metabolism, Azotobacter vinelandii, Nitrogenase., Nitrogenase molybdenum-iron protein beta chain, nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1]
3.40.50.1980.5.1.1.1.14	3k1aD04	nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1], Nitrogenase molybdenum-iron protein beta chain, Nitrogenase., Azotobacter vinelandii, Nitrogen metabolism, Metabolic pathways
3.40.50.1980.5.1.1.1.15	1l5hB03	Metabolic pathways, Nitrogen metabolism, Azotobacter vinelandii, Nitrogenase., Nitrogenase molybdenum-iron protein beta chain, nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1]
3.40.50.1980.5.1.1.1.16	1m34B03	Metabolic pathways, Azotobacter vinelandii, Nitrogen metabolism, Nitrogenase molybdenum-iron protein beta chain, Nitrogenase., nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1]
3.40.50.1980.5.1.1.1.17	1m34D03	Metabolic pathways, Azotobacter vinelandii, Nitrogen metabolism, Nitrogenase molybdenum-iron protein beta chain, Nitrogenase., nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1]
3.40.50.1980.5.1.1.1.18	1m34J03	nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1], Nitrogenase., Nitrogenase molybdenum-iron protein beta chain, Nitrogen metabolism, Azotobacter vinelandii, Metabolic pathways
3.40.50.1980.5.1.1.1.19	1m34L03	nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1], Nitrogenase molybdenum-iron protein beta chain, Nitrogenase., Azotobacter vinelandii, Nitrogen metabolism, Metabolic pathways
3.40.50.1980.5.1.1.1.20	2afkB04	Nitrogenase., Nitrogenase molybdenum-iron protein beta chain, nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1], Metabolic pathways, Nitrogen metabolism, Azotobacter vinelandii
3.40.50.1980.5.1.1.1.21	2afkD04	Metabolic pathways, Nitrogen metabolism, Azotobacter vinelandii, Nitrogenase., Nitrogenase molybdenum-iron protein beta chain, nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1]
3.40.50.1980.5.1.1.1.22	1fp4B03	Nitrogenase molybdenum-iron protein beta chain, Nitrogenase., nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1], Metabolic pathways, Azotobacter vinelandii, Nitrogen metabolism
3.40.50.1980.5.1.1.1.23	1fp4D03	Metabolic pathways, Azotobacter vinelandii, Nitrogen metabolism, Nitrogenase molybdenum-iron protein beta chain, Nitrogenase., nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1]
3.40.50.1980.5.1.1.1.24	1g21B03	nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1], Nitrogenase molybdenum-iron protein beta chain, Nitrogenase., Azotobacter vinelandii, Nitrogen metabolism, Metabolic pathways
3.40.50.1980.5.1.1.1.25	1g21D03	Metabolic pathways, Azotobacter vinelandii, Nitrogen metabolism, Nitrogenase molybdenum-iron protein beta chain, Nitrogenase., nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1]
3.40.50.1980.5.1.1.1.26	1n2cB03	nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1], Nitrogenase., Nitrogenase molybdenum-iron protein beta chain, Nitrogen metabolism, Azotobacter vinelandii, Metabolic pathways
3.40.50.1980.5.1.1.1.27	1n2cD03	Metabolic pathways, Nitrogen metabolism, Azotobacter vinelandii, Nitrogenase., Nitrogenase molybdenum-iron protein beta chain, nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1]
3.40.50.1980.5.1.1.1.28	2afiB04	Nitrogenase., Nitrogenase molybdenum-iron protein beta chain, nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1], Metabolic pathways, Nitrogen metabolism, Azotobacter vinelandii
3.40.50.1980.5.1.1.1.29	2afiD04	Azotobacter vinelandii, Nitrogen metabolism, Metabolic pathways, nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1], Nitrogenase molybdenum-iron protein beta chain, Nitrogenase.
3.40.50.1980.5.1.1.1.30	2afiJ04	Metabolic pathways, Nitrogen metabolism, Azotobacter vinelandii, Nitrogenase., Nitrogenase molybdenum-iron protein beta chain, nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1]
3.40.50.1980.5.1.1.1.31	2afiL04	Nitrogen metabolism, Azotobacter vinelandii, Metabolic pathways, nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1], Nitrogenase., Nitrogenase molybdenum-iron protein beta chain
3.40.50.1980.5.1.1.1.32	1m1yB04	nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1], Nitrogenase molybdenum-iron protein beta chain, Nitrogenase., Azotobacter vinelandii, Nitrogen metabolism, Metabolic pathways
3.40.50.1980.5.1.1.1.33	1m1yD04	nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1], Nitrogenase., Nitrogenase molybdenum-iron protein beta chain, Nitrogen metabolism, Azotobacter vinelandii, Metabolic pathways
3.40.50.1980.5.1.1.1.34	1m1yJ04	Metabolic pathways, Azotobacter vinelandii, Nitrogen metabolism, Nitrogenase molybdenum-iron protein beta chain, Nitrogenase., nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1]
3.40.50.1980.5.1.1.1.35	1m1yL04	Metabolic pathways, Nitrogen metabolism, Azotobacter vinelandii, Nitrogenase., Nitrogenase molybdenum-iron protein beta chain, nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1]
3.40.50.1980.5.1.1.1.36	1minB03
3.40.50.1980.5.1.1.1.37	1minD03

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=3.40.50.1980.5.1.1.1

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: 3.40.50.1980.5.1.1.1

Classification Lineage (3.40.50.1980.5.1.1.1)

Summary of Non-Redundant Representatives

What is a Non-Redundant Representative?

S100 Count Entries in S100 Family 3.40.50.1980.5.1.1.1 (37)

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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