SUPERFAMILY 1.73 HMM library and genome assignments server

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Rudiment single hybrid motif superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (165)
Fold:   Barrel-sandwich hybrid [ 51229] (4)
  sandwich of half-barrel shaped beta-sheets
Superfamily:   Rudiment single hybrid motif [ 51246] (2)
Families:   BC C-terminal domain-like [ 51247] (5)
  probable rudiment form of the biotinyl-carrier domain
  Cytochrome f, small domain [ 51256]

 Superfamily statistics
Genomes (1,175) UniProt 15.0 PDB chains (SCOP 1.73)
Domains 5,509 6,194 22
Proteins 5,506 6,191 22

 Functional annotation
General category Processes_IC
Detailed category Transport

Function annotation of SCOP domain superfamilies
InterPro annotation
Cross references IPR011054 SSF51246 Protein matches
Abstract

The rudiment single hybrid motif has a beta-barrel sandwich hybrid motif, consisting of a sandwich of half-barrel shaped beta-sheets. This motif is found in the small domain of cytochrome f [PubMed10423236], as well as in the C-terminal domain of the biotin carboxylase subunit of acetyl-CoA carboxylase [PubMed10821865], and its family members, such as glycinamide ribonucleotide synthetase C-terminal domain [PubMed9843369], N5-carboxyaminoimidazole ribonucleotide synthetase PurK C-terminal domain [PubMed10569930], and glycinamide ribonucleotide transformylase PurT C-terminal domain [PubMed11953435].


InterPro database
PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.

Alignments of sequences to 11 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Rudiment single hybrid motif domain.

Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 11 hidden Markov models representing the Rudiment single hybrid motif superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2001-2010 The Medical Research Council and the SUPERFAMILY authors; Derek Wilson, Martin Madera and Julian Gough.