SUPERFAMILY 1.75 HMM library and genome assignments server


Cap-Gly domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   SH3-like barrel [ 50036] (21)
Superfamily:   Cap-Gly domain [ 74924]
Families:   Cap-Gly domain [ 74925] (10)


Superfamily statistics
Genomes (495) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,739 4,382 22
Proteins 2,961 3,441 22


Functional annotation
General category Processes_IC
Detailed category 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) cellular component organization or biogenesis 5.255e-14 Least Informative Direct
Biological Process (BP) protein metabolic process 5.477e-09 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 3.091e-05 Least Informative Direct
Biological Process (BP) localization 5.62e-05 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.3497 Least Informative Inherited
Biological Process (BP) developmental process 0.004169 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.00134 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.04649 Least Informative Inherited
Biological Process (BP) regulation of cellular component organization 4.888e-06 Moderately Informative Direct
Biological Process (BP) cellular localization 5.865e-06 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 9.515e-06 Moderately Informative Direct
Biological Process (BP) organelle organization 2.847e-05 Moderately Informative Direct
Biological Process (BP) regulation of localization 4.35e-05 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.001894 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.5286 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.001212 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) system process 0.01727 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.6993 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.9211 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.8642 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.5741 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.1235 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.9316 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) regulation of phosphate metabolic process 0.08281 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.6394 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.113 Moderately Informative Inherited
Biological Process (BP) microtubule-based process 0 Informative Direct
Biological Process (BP) regulation of establishment of protein localization 7.655e-14 Informative Direct
Biological Process (BP) organelle localization 5.186e-13 Informative Direct
Biological Process (BP) cytoskeleton organization 6.782e-10 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 5.902e-09 Informative Direct
Biological Process (BP) regulation of organelle organization 6.41e-06 Informative Direct
Biological Process (BP) positive regulation of transport 2.036e-05 Informative Direct
Biological Process (BP) protein modification by small protein conjugation or removal 0.0001087 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.0002457 Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 0.0006084 Informative Direct
Biological Process (BP) protein transport 0.0009642 Informative Direct
Biological Process (BP) cell cycle process 0.001554 Informative Inherited
Biological Process (BP) synaptic transmission 0.00143 Informative Inherited
Biological Process (BP) negative regulation of transport 0.001443 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 0.02094 Informative Inherited
Biological Process (BP) regulation of intracellular transport 0.001081 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.001746 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.03799 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.05621 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.07204 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.2591 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.001682 Informative Inherited
Biological Process (BP) positive regulation of protein modification process 0.001513 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.005318 Informative Inherited
Biological Process (BP) regulation of intracellular protein transport 9.91e-11 Highly Informative Direct
Biological Process (BP) protein folding 5.271e-10 Highly Informative Direct
Biological Process (BP) establishment or maintenance of cell polarity 1.767e-07 Highly Informative Direct
Biological Process (BP) negative regulation of sequence-specific DNA binding transcription factor activity 2.682e-07 Highly Informative Direct
Biological Process (BP) regulation of protein complex assembly 1.454e-05 Highly Informative Direct
Biological Process (BP) lipoprotein metabolic process 0.0001694 Highly Informative Direct
Biological Process (BP) positive regulation of programmed cell death 0.0008294 Highly Informative Direct
Biological Process (BP) regulation of nucleocytoplasmic transport 0.2933 Highly Informative Inherited
Biological Process (BP) regulation of protein localization to nucleus 0.02187 Highly Informative Inherited
Biological Process (BP) negative regulation of intracellular transport 0.00228 Highly Informative Inherited
Biological Process (BP) negative regulation of protein transport 0.01897 Highly Informative Inherited
Biological Process (BP) negative regulation of cytoskeleton organization 0.002284 Highly Informative Inherited
Biological Process (BP) regulation of microtubule polymerization or depolymerization 0.004719 Highly Informative Inherited
Molecular Function (MF) binding 4.146e-08 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.03747 Least Informative Inherited
Molecular Function (MF) cation binding 0.004883 Moderately Informative Inherited
Molecular Function (MF) cytoskeletal protein binding 0 Informative Direct
Molecular Function (MF) zinc ion binding 2.043e-06 Informative Direct
Molecular Function (MF) peptidase activity 0.0007348 Informative Direct
Molecular Function (MF) lipid binding 0.02005 Informative Inherited
Molecular Function (MF) tubulin binding 0 Highly Informative Direct
Molecular Function (MF) glycolipid binding 1.142e-10 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) protein complex 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 6.857e-11 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.1396 Least Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoskeleton 0 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0.5268 Moderately Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0 Informative Direct
Cellular Component (CC) cell leading edge 3.274e-07 Informative Direct
Cellular Component (CC) cell cortex 1.215e-05 Informative Direct
Cellular Component (CC) endosome 4.028e-05 Informative Direct
Cellular Component (CC) actin cytoskeleton 1 Informative Inherited
Cellular Component (CC) chromosome 1 Informative Inherited
Cellular Component (CC) centrosome 3.216e-10 Highly Informative Direct
Cellular Component (CC) midbody 5.582e-10 Highly Informative Direct
Cellular Component (CC) microtubule associated complex 7.83e-07 Highly Informative Direct
Cellular Component (CC) kinetochore 9.393e-07 Highly Informative Direct
Cellular Component (CC) spindle 1.885e-06 Highly Informative Direct
Cellular Component (CC) trans-Golgi network 8.42e-06 Highly Informative Direct
Cellular Component (CC) membrane raft 1.931e-05 Highly Informative Direct
Cellular Component (CC) endosomal part 0.0004245 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Omega peptidases0Moderately InformativeDirect

Document: EC annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.1124Least InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.2644Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal spinal cord morphology0.003405Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect
Yeast Phenotype (YP)morphology0Moderately InformativeDirect
Yeast Phenotype (YP)cell cycle progression0.0006617InformativeDirect

Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system0Least InformativeDirect

Document: FA 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)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)visual system0Moderately InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Moderately InformativeDirect
Enzyme Commission (EC)Omega peptidases0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processWnt signaling pathway3.583e-10InformativeDirect
Biological processUbl conjugation pathway2.281e-05InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentCytoskeleton0Moderately InformativeDirect
Cellular componentGolgi apparatus8.047e-05Moderately InformativeDirect
Cellular componentMicrotubule0InformativeDirect
DomainRepeat4.134e-07Least InformativeDirect
DomainCoiled coil1.34e-12Moderately InformativeDirect
DomainLeucine-rich repeat2.039e-10InformativeDirect
DomainANK repeat1.021e-07InformativeDirect
Post-translational modificationHydrolase0.937Least InformativeInherited
Post-translational modificationProtease0.002063Moderately InformativeInherited
Post-translational modificationChaperone0InformativeDirect
Post-translational modificationThiol protease1.381e-07InformativeDirect
Post-translational modificationPhosphoprotein8.208e-10Least InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · 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 16 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 Cap-Gly 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 16 hidden Markov models representing the Cap-Gly 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 · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]