SUPERFAMILY 1.75 HMM library and genome assignments server

Intermediate filament protein, coiled coil region superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Coiled coil proteins [ 57942] (7)
Fold:   Parallel coiled-coil [ 57943] (34)
Superfamily:   Intermediate filament protein, coiled coil region [ 64593]
Families:   Intermediate filament protein, coiled coil region [ 64594] (2)


Superfamily statistics
Genomes (154) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 10,352 11,520 4
Proteins 5,375 6,065 4


Functional annotation
General category Other
Detailed category Unknown function

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) developmental process 0.00000000000004938 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.000000000003016 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.000001211 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000018 Least Informative Direct
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) organelle organization 0 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.000000001421 Moderately Informative Direct
Biological Process (BP) tissue development 0.000000007372 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.0008956 Moderately Informative Direct
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) organ development 0.08923 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.9007 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.6617 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.2287 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.07986 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.00595 Moderately Informative Inherited
Biological Process (BP) nervous system development 1 Moderately Informative Inherited
Biological Process (BP) cytoskeleton organization 0 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.000195 Informative Direct
Biological Process (BP) regulation of nervous system development 0.0002651 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.0249 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.06122 Informative Inherited
Biological Process (BP) epithelium development 0.6467 Informative Inherited
Biological Process (BP) sensory organ development 0.009312 Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.04149 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.1258 Informative Inherited
Biological Process (BP) central nervous system development 0.222 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.1055 Informative Inherited
Biological Process (BP) organ morphogenesis 1 Informative Inherited
Biological Process (BP) regulation of anatomical structure size 0.02497 Informative Inherited
Biological Process (BP) regulation of cell development 0.001611 Informative Inherited
Biological Process (BP) generation of neurons 0.002627 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 1 Informative Inherited
Biological Process (BP) embryonic organ development 0.3488 Informative Inherited
Biological Process (BP) microtubule-based process 0.002835 Informative Inherited
Biological Process (BP) cellular component movement 0.9368 Informative Inherited
Biological Process (BP) cellular membrane organization 0.3945 Informative Inherited
Biological Process (BP) regulation of neuron projection development 0.000000002196 Highly Informative Direct
Biological Process (BP) cytoskeleton-dependent intracellular transport 0.00003568 Highly Informative Direct
Biological Process (BP) regulation of protein complex disassembly 0.000129 Highly Informative Direct
Biological Process (BP) glial cell differentiation 0.0001515 Highly Informative Direct
Biological Process (BP) regulation of neural precursor cell proliferation 0.0007305 Highly Informative Direct
Biological Process (BP) positive regulation of organelle organization 0.02272 Highly Informative Inherited
Biological Process (BP) epidermal cell differentiation 1 Highly Informative Inherited
Biological Process (BP) regulation of cell morphogenesis involved in differentiation 0.242 Highly Informative Inherited
Biological Process (BP) hair follicle development 0.09103 Highly Informative Inherited
Biological Process (BP) microtubule-based movement 0.001795 Highly Informative Inherited
Biological Process (BP) nucleus organization 0.01441 Highly Informative Inherited
Molecular Function (MF) binding 0.3319 Least Informative Inherited
Molecular Function (MF) structural molecule activity 0 Moderately Informative Direct
Molecular Function (MF) protein complex binding 0.0000995 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0 Least Informative Direct
Cellular Component (CC) protein complex 0 Least Informative Direct
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0 Moderately Informative Direct
Cellular Component (CC) vesicle 0.000000002441 Moderately Informative Direct
Cellular Component (CC) cell projection 0.000006085 Moderately Informative Direct
Cellular Component (CC) plasma membrane 1 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) nuclear part 1 Moderately Informative Inherited
Cellular Component (CC) endomembrane system 0.00804 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 0.125 Moderately Informative Inherited
Cellular Component (CC) extracellular membrane-bounded organelle 0 Informative Direct
Cellular Component (CC) nuclear envelope 0.000000002582 Informative Direct
Cellular Component (CC) neuron projection 0.00001039 Informative Direct
Cellular Component (CC) contractile fiber part 0.0001652 Informative Direct
Cellular Component (CC) intermediate filament cytoskeleton 0 Highly Informative Direct
Cellular Component (CC) sarcolemma 0.000002795 Highly Informative Direct

Document: GO annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0.4172Least InformativeInherited
Disease Ontology (DO)cell type cancer0.04083Moderately InformativeInherited
Disease Ontology (DO)genetic disease0.1444Moderately InformativeInherited
Disease Ontology (DO)skin disease0.6465Moderately InformativeInherited
Disease Ontology (DO)lung carcinoma0.03912InformativeInherited
Disease Ontology (DO)autosomal dominant disease0.06412InformativeInherited
Disease Ontology (DO)pulmonary large cell neuroendocrine carcinoma0.000000002516Highly InformativeDirect
Disease Ontology (DO)neuroendocrine carcinoma0.0000001723Highly InformativeDirect
Disease Ontology (DO)keratosis0.07976Highly InformativeInherited

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Mode of Inheritance (MI)Autosomal dominant inheritance0Least InformativeDirect
Mode of Inheritance (MI)Heterogeneous0.00000817Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of head and neck0.1208Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.5205Least InformativeInherited
Phenotypic Abnormality (PA)Generalized abnormality of skin0.00302Moderately InformativeInherited
Phenotypic Abnormality (PA)Neoplasm0.01633Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the hand0.03052Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the mouth0.3144Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal respiratory system morphology0.3695Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the globe0.9587Moderately InformativeInherited
Phenotypic Abnormality (PA)Regional abnormality of skin0.0009994InformativeDirect
Phenotypic Abnormality (PA)Abnormality of skin morphology0.007676InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the oral cavity0.03483InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper respiratory tract0.07825InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the hair0.4574InformativeInherited
Phenotypic Abnormality (PA)Neoplasm by anatomical site0.5497InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cornea0.8119InformativeInherited
Phenotypic Abnormality (PA)Palmoplantar hyperkeratosis0.000000000001017Highly InformativeDirect
Phenotypic Abnormality (PA)Oral leukoplakia0.0000005146Highly InformativeDirect
Phenotypic Abnormality (PA)Alopecia0.000000975Highly InformativeDirect
Phenotypic Abnormality (PA)Corneal dystrophy0.00000172Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal blistering of the skin0.000005714Highly InformativeDirect
Phenotypic Abnormality (PA)Natal tooth0.00005413Highly InformativeDirect
Phenotypic Abnormality (PA)Neoplasm of the skin0.0002336Highly InformativeDirect
Phenotypic Abnormality (PA)Laryngomalacia0.0004411Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the nail0.0007459Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of hair growth rate0.0009059Highly InformativeDirect
Phenotypic Abnormality (PA)Ichthyosis0.05675Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)growth/size/body phenotype0.07664Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.789Least InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.0000006609Moderately InformativeDirect
Mammalian Phenotype (MP)digestive/alimentary phenotype0.05117Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.1003Moderately InformativeInherited
Mammalian Phenotype (MP)tumorigenesis0.4988Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.7573Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.9138Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial morphology1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal epidermal layer morphology0.001594InformativeInherited
Mammalian Phenotype (MP)abnormal telencephalon morphology0.4039InformativeInherited
Mammalian Phenotype (MP)abnormal facial morphology0.4494InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.7314InformativeInherited
Mammalian Phenotype (MP)abnormal skin appearance0.8633InformativeInherited
Mammalian Phenotype (MP)hyperkeratosis0.0000008582Highly InformativeDirect
Mammalian Phenotype (MP)abnormal tongue morphology0.00001802Highly InformativeDirect
Mammalian Phenotype (MP)abnormal esophagus morphology0.0001126Highly InformativeDirect
Mammalian Phenotype (MP)abnormal sebaceous gland morphology0.0003126Highly InformativeDirect
Mammalian Phenotype (MP)blistering0.000783Highly InformativeDirect
Mammalian Phenotype (MP)abnormal spinal nerve morphology0.0009679Highly InformativeDirect
Mammalian Phenotype (MP)increased integument system tumor incidence0.03295Highly InformativeInherited
Mammalian Phenotype (MP)abnormal epidermis stratum spinosum morphology0.5007Highly InformativeInherited
Mammalian Phenotype (MP)abnormal skin condition0.7062Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.0008925Least InformativeDirect
Worm Phenotype (WP)larval development variant0.5014Least InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.00003939Moderately InformativeDirect
Worm Phenotype (WP)locomotion variant0.004215Moderately InformativeInherited
Worm Phenotype (WP)organ system development variant0.01311Moderately InformativeInherited
Worm Phenotype (WP)body width variant0.000003603InformativeDirect
Worm Phenotype (WP)activity level variant0.01864InformativeInherited
Worm Phenotype (WP)paralyzed0.00001155Highly InformativeDirect
Worm Phenotype (WP)muscle system development variant0.00001855Highly InformativeDirect
Worm Phenotype (WP)molt variant0.0002046Highly InformativeDirect

Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0.01477Least InformativeInherited
Xenopus ANatomical entity (XAN)portion of tissue0.2612Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.463Least InformativeInherited
Xenopus ANatomical entity (XAN)cell1Least InformativeInherited
Xenopus ANatomical entity (XAN)multi-tissue structure0.007361Moderately InformativeInherited
Xenopus ANatomical entity (XAN)surface structure0.03Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.2608Moderately InformativeInherited
Xenopus ANatomical entity (XAN)spinal cord0.00001064InformativeDirect
Xenopus ANatomical entity (XAN)hindbrain0.0002255InformativeDirect
Xenopus ANatomical entity (XAN)skin0.4271InformativeInherited
Xenopus ANatomical entity (XAN)epidermis0.000006363Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial nerve0.000007086Highly InformativeDirect
Xenopus ANatomical entity (XAN)gustatory system0.00001775Highly InformativeDirect
Xenopus ANatomical entity (XAN)neuron0.00004765Highly InformativeDirect
Xenopus ANatomical entity (XAN)ganglion0.0004611Highly InformativeDirect

Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processNeurogenesis0.0000001002InformativeDirect
Coding sequence diversityPolymorphism0.00003566Moderately InformativeDirect
DiseaseDisease mutation0.00000000001937Least InformativeDirect
DiseasePalmoplantar keratoderma0.00000000001119Highly InformativeDirect
DiseaseEctodermal dysplasia0.00000001372Highly InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
Post-translational modificationMuscle protein0.0000000008306Highly InformativeDirect
Post-translational modificationEye lens protein0.0000001338Highly InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationAcetylation0.0000000000002817Least InformativeDirect
Post-translational modificationMethylation0.0000001039Moderately InformativeDirect
Post-translational modificationPrenylation0InformativeDirect
Post-translational modificationADP-ribosylation0.0000005165InformativeDirect
Post-translational modificationCitrullination0Highly InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · 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 4 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 Intermediate filament protein, coiled coil region 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 4 hidden Markov models representing the Intermediate filament protein, coiled coil region 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 · Functional annotation · Gene Ontology (high-coverage) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · Internal database links ]