SUPERFAMILY 1.75 HMM library and genome assignments server

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DLC superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   DLC [ 54647]
Superfamily:   DLC [ 54648]
Families:   DLC [ 54649] (2)

Superfamily statistics
Genomes (419) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 1,725 1,378 7
Proteins 1,696 1,369 7

 Functional annotation
General category Processes_IC
Detailed category Cell motility

Document: Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)single-organism cellular process0.001580.0151Least InformativeInherited
Biological Process (BP)cellular component movement1.924e-085.925e-07InformativeDirect
Biological Process (BP)microtubule-based process3.32e-121.297e-12InformativeDirect
Biological Process (BP)microtubule-based movement2.894e-096.884e-08Highly InformativeDirect
Cellular Component (CC)intracellular non-membrane-bounded organelle6.76e-071.343e-05Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.0015020.02637Least InformativeInherited
Cellular Component (CC)protein complex1.749e-070.2415Least InformativeInherited
Cellular Component (CC)cytoskeleton3.574e-130.0001524Moderately InformativeDirect
Cellular Component (CC)microtubule cytoskeleton0.0047210.006739InformativeInherited
Cellular Component (CC)microtubule associated complex00Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) single-organism cellular process 0.0151 Least Informative Inherited
Biological Process (BP) cellular component movement 5.925e-07 Informative Direct
Biological Process (BP) microtubule-based process 1.297e-12 Informative Direct
Biological Process (BP) microtubule-based movement 6.884e-08 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 1.343e-05 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.02637 Least Informative Inherited
Cellular Component (CC) protein complex 0.2415 Least Informative Inherited
Cellular Component (CC) cytoskeleton 0.0001524 Moderately Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.006739 Informative Inherited
Cellular Component (CC) microtubule associated complex 0 Highly Informative Direct

Document: GO annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)sepal0Least InformativeDirect
Plant ANatomical entity (PAN)petal0Least InformativeDirect
Plant ANatomical entity (PAN)androecium0Least InformativeDirect
Plant ANatomical entity (PAN)collective leaf structure0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport3.948e-05Least InformativeDirect
Cellular componentCytoplasm3.413e-10Least InformativeDirect
Cellular componentCytoskeleton0Moderately InformativeDirect
Cellular componentCell projection1.294e-08Moderately InformativeDirect
Cellular componentMicrotubule0InformativeDirect
Cellular componentCilium1.882e-12Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001372 SSF54648 Protein matches
Abstract

Dynein is a multisubunit microtubule-dependent motor enzyme that acts as the force generating protein of eukaryotic cilia and flagella. The cytoplasmic isoform of dynein acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules.

Dynein is composed of a number of ATP-binding large subunits (see ), intermediate size subunits and small subunits. Among the small subunits, there is a family of highly conserved proteins which make up this family [PubMed7744782, PubMed8628263].


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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) ]

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 2 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 DLC 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 2 hidden Markov models representing the DLC 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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · 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.

Please send feedback, comments or questions to superfamily@cs.bris.ac.uk or use the feedback form.

© Copyright 2013 The SUPERFAMILY authors and Julian Gough.