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XPC-binding domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   XPC-binding domain [ 101237]
Superfamily:   XPC-binding domain [ 101238]
Families:   XPC-binding domain [ 101239] (3)

Superfamily statistics
Genomes (427) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 834 685 5
Proteins 833 684 5

 Functional annotation
General category General
Detailed category Small molecule binding

Document: Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) response to stimulus 2.058e-06 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.3605 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.001146 Least Informative Inherited
Biological Process (BP) cellular response to stress 1.113e-08 Moderately Informative Direct
Biological Process (BP) reproduction 0.002607 Moderately Informative Inherited
Biological Process (BP) response to DNA damage stimulus 0 Informative Direct
Biological Process (BP) sexual reproduction 3.068e-05 Informative Direct
Biological Process (BP) multicellular organismal reproductive process 4.009e-05 Informative Direct
Biological Process (BP) single organism reproductive process 0.001104 Informative Inherited
Biological Process (BP) spermatogenesis 1.762e-07 Highly Informative Direct
Molecular Function (MF) binding 0.1093 Least Informative Inherited
Molecular Function (MF) protein binding 0.08462 Moderately Informative Inherited
Cellular Component (CC) protein complex 0.02831 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.04731 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.08127 Least Informative Inherited
Cellular Component (CC) nuclear part 0.01265 Moderately Informative Inherited

Document: GO annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)shoot apex0Least InformativeDirect
Plant ANatomical entity (PAN)shoot internode0Least InformativeDirect
Plant ANatomical entity (PAN)root0Least InformativeDirect
Plant ANatomical entity (PAN)plant embryo0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)vascular leaf0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)sepal0Least InformativeDirect
Plant ANatomical entity (PAN)petal0Least InformativeDirect
Plant ANatomical entity (PAN)stem0Least InformativeDirect
Plant ANatomical entity (PAN)pedicel0Least InformativeDirect
Plant ANatomical entity (PAN)androecium0Least InformativeDirect
Plant ANatomical entity (PAN)gynoecium0Least InformativeDirect
Plant ANatomical entity (PAN)leaf lamina0Least InformativeDirect
Plant ANatomical entity (PAN)collective leaf structure0Least InformativeDirect
Plant ANatomical entity (PAN)stalk0Least InformativeDirect
Plant ANatomical entity (PAN)phyllome apex0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
Biological processUbl conjugation pathway4.513e-11InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentProteasome6.395e-16Highly InformativeDirect
DomainRepeat0Least InformativeDirect
Post-translational modificationPhosphoprotein4.691e-08Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR015360 SSF101238 Protein matches
Abstract

Members of this entry adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair [PubMed15885096].


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-coverage) · 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 3 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 XPC-binding domain 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 3 hidden Markov models representing the XPC-binding domain 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-coverage) · 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.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.