SUPERFAMILY 1.75 HMM library and genome assignments server


Clc chloride channel superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Membrane and cell surface proteins and peptides [ 56835] (58)
Fold:   Clc chloride channel [ 81341]
Superfamily:   Clc chloride channel [ 81340]
Families:   Clc chloride channel [ 69912]


Superfamily statistics
Genomes (2,131) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 6,039 24,228 14
Proteins 5,948 24,144 14


Functional annotation
General category Processes_IC
Detailed category Ion metabolism and transport

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) localization 0 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.0002815 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.3619 Least Informative Inherited
Biological Process (BP) regulation of localization 4.891e-12 Moderately Informative Direct
Biological Process (BP) ion transport 5.752e-12 Moderately Informative Direct
Biological Process (BP) system process 5.423e-05 Moderately Informative Direct
Biological Process (BP) homeostatic process 0.05645 Moderately Informative Inherited
Biological Process (BP) regulation of ion transport 0 Informative Direct
Biological Process (BP) transmembrane transport 1.114e-05 Informative Direct
Biological Process (BP) anion transport 0.0002706 Informative Direct
Biological Process (BP) vesicle-mediated transport 1 Informative Inherited
Biological Process (BP) inorganic anion transport 0 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transporter activity 0 Moderately Informative Direct
Molecular Function (MF) anion transmembrane transporter activity 2.478e-14 Informative Direct
Molecular Function (MF) protein domain specific binding 8.839e-08 Highly Informative Direct
Molecular Function (MF) ion gated channel activity 1.917e-05 Highly Informative Direct
Cellular Component (CC) membrane 2.069e-14 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.8463 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1296 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.6447 Least Informative Inherited
Cellular Component (CC) plasma membrane 7.897e-08 Moderately Informative Direct
Cellular Component (CC) organelle membrane 2.535e-05 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.01866 Moderately Informative Inherited
Cellular Component (CC) vesicle 0.001294 Moderately Informative Inherited
Cellular Component (CC) endosome 1.57e-11 Informative Direct
Cellular Component (CC) Golgi apparatus 1.545e-06 Informative Direct
Cellular Component (CC) vacuolar part 3.121e-05 Informative Direct
Cellular Component (CC) integral to membrane 0.0004371 Informative Direct
Cellular Component (CC) sarcolemma 1.801e-10 Highly Informative Direct

Document: GO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.09534Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.1943Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the urinary system0.09344Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cation homeostasis3.262e-06InformativeDirect
Phenotypic Abnormality (PA)Abnormal urinary electrolyte concentration3.637e-06Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of calcium homeostasis2.082e-05Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.1264Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.5534Least InformativeInherited
Mammalian Phenotype (MP)renal/urinary system phenotype0.002162Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal protein level0.01348Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.0393Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.08271Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.1519Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.1877Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology0.002326InformativeInherited
Mammalian Phenotype (MP)abnormal kidney physiology0.2994InformativeInherited
Mammalian Phenotype (MP)abnormal renal protein reabsorption2.813e-07Highly InformativeDirect
Mammalian Phenotype (MP)abnormal photoreceptor inner segment morphology3.006e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal photoreceptor outer segment morphology4.568e-05Highly InformativeDirect
Mammalian Phenotype (MP)retinal degeneration6.589e-05Highly InformativeDirect
Mammalian Phenotype (MP)kyphosis0.0007415Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)electrophysiology variant0InformativeDirect
Worm Phenotype (WP)nervous system physiology variant8.942e-14Highly InformativeDirect

Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)oviduct0InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence 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.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 processTransport0Least InformativeDirect
Biological processIon transport0Moderately InformativeDirect
Biological processAntiport0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentGolgi apparatus4.312e-06Moderately InformativeDirect
Cellular componentCell membrane0.000575Moderately InformativeDirect
DiseaseDisease mutation2.065e-05Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainRepeat0.0009021Least InformativeDirect
DomainCBS domain0Highly InformativeDirect
Molecular functionCalcium0.000875Moderately InformativeDirect
Molecular functionChloride0Highly InformativeDirect
Post-translational modificationIon channel0InformativeDirect
Post-translational modificationVoltage-gated channel2.825e-09Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR014743 SSF81340 Protein matches
Abstract

This entry represents the core domain of the cholide ion channel.


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) · Human Phenotype (HP) · Mouse Phenotype (MP) · 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 Clc chloride channel 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 Clc chloride channel 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) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]