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 (484) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,569 4,382 22
Proteins 2,853 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 0.000000000001145 Least Informative Direct
Biological Process (BP) protein metabolic process 0.00000005506 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0001583 Least Informative Direct
Biological Process (BP) localization 0.0001964 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.6544 Least Informative Inherited
Biological Process (BP) developmental process 0.0212 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 0.001817 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.09848 Least Informative Inherited
Biological Process (BP) cellular localization 0.000003906 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.000005287 Moderately Informative Direct
Biological Process (BP) organelle organization 0.00001823 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.00002505 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.00003021 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.002836 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.5313 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.001127 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 biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) system process 0.01458 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.9226 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.7968 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.5947 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.1696 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.9072 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) regulation of phosphate metabolic process 0.09075 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.6318 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.1245 Moderately Informative Inherited
Biological Process (BP) microtubule-based process 0 Informative Direct
Biological Process (BP) regulation of establishment of protein localization 0.00000000000008236 Informative Direct
Biological Process (BP) organelle localization 0.0000000000005124 Informative Direct
Biological Process (BP) cytoskeleton organization 0.00000000062 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.0000000035 Informative Direct
Biological Process (BP) regulation of organelle organization 0.000003612 Informative Direct
Biological Process (BP) positive regulation of transport 0.00002028 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.0002401 Informative Direct
Biological Process (BP) protein modification by small protein conjugation or removal 0.0002831 Informative Direct
Biological Process (BP) regulation of intracellular transport 0.000959 Informative Direct
Biological Process (BP) protein transport 0.001158 Informative Inherited
Biological Process (BP) cell cycle process 0.001426 Informative Inherited
Biological Process (BP) transmission of nerve impulse 0.003875 Informative Inherited
Biological Process (BP) cell-cell signaling 0.01249 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 0.02187 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.00134 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.02806 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.0397 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.06819 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.2014 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.001808 Informative Inherited
Biological Process (BP) positive regulation of protein modification process 0.001674 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.005996 Informative Inherited
Biological Process (BP) regulation of intracellular protein transport 0.0000000001265 Highly Informative Direct
Biological Process (BP) protein folding 0.000000000286 Highly Informative Direct
Biological Process (BP) microtubule cytoskeleton organization 0.0000000308 Highly Informative Direct
Biological Process (BP) establishment or maintenance of cell polarity 0.0000001544 Highly Informative Direct
Biological Process (BP) negative regulation of sequence-specific DNA binding transcription factor activity 0.0000003284 Highly Informative Direct
Biological Process (BP) establishment of vesicle localization 0.000002272 Highly Informative Direct
Biological Process (BP) regulation of protein complex assembly 0.00001336 Highly Informative Direct
Biological Process (BP) lipoprotein metabolic process 0.0001353 Highly Informative Direct
Biological Process (BP) positive regulation of programmed cell death 0.0008158 Highly Informative Direct
Biological Process (BP) regulation of nucleocytoplasmic transport 0.3189 Highly Informative Inherited
Biological Process (BP) regulation of protein localization to nucleus 0.02436 Highly Informative Inherited
Biological Process (BP) negative regulation of intracellular transport 0.002395 Highly Informative Inherited
Biological Process (BP) negative regulation of protein transport 0.01981 Highly Informative Inherited
Biological Process (BP) negative regulation of cytoskeleton organization 0.002446 Highly Informative Inherited
Biological Process (BP) regulation of microtubule polymerization or depolymerization 0.005316 Highly Informative Inherited
Molecular Function (MF) binding 0.0000001643 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.04607 Least Informative Inherited
Molecular Function (MF) cation binding 0.005051 Moderately Informative Inherited
Molecular Function (MF) cytoskeletal protein binding 0 Informative Direct
Molecular Function (MF) transition metal ion binding 0.0001246 Informative Direct
Molecular Function (MF) peptidase activity 0.0007595 Informative Direct
Molecular Function (MF) lipid binding 0.02051 Informative Inherited
Molecular Function (MF) tubulin binding 0 Highly Informative Direct
Molecular Function (MF) glycolipid binding 0.0000000001316 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 0.00000000002156 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.2048 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 0.5825 Moderately Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0 Informative Direct
Cellular Component (CC) cell leading edge 0.0000004026 Informative Direct
Cellular Component (CC) cell cortex 0.0000143 Informative Direct
Cellular Component (CC) endosome 0.00005351 Informative Direct
Cellular Component (CC) actin cytoskeleton 1 Informative Inherited
Cellular Component (CC) chromosome 1 Informative Inherited
Cellular Component (CC) cytoplasmic microtubule 0 Highly Informative Direct
Cellular Component (CC) centrosome 0.00000000009326 Highly Informative Direct
Cellular Component (CC) midbody 0.0000000007095 Highly Informative Direct
Cellular Component (CC) microtubule associated complex 0.000001124 Highly Informative Direct
Cellular Component (CC) kinetochore 0.000001299 Highly Informative Direct
Cellular Component (CC) spindle 0.000002814 Highly Informative Direct
Cellular Component (CC) trans-Golgi network 0.00001064 Highly Informative Direct
Cellular Component (CC) membrane raft 0.00002323 Highly Informative Direct
Cellular Component (CC) endosomal part 0.000502 Highly Informative Direct
Cellular Component (CC) recycling endosome 0.0006448 Highly Informative Direct
Cellular Component (CC) early endosome 0.002615 Highly Informative Inherited

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 phenotype0.1131Least InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.2626Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal spinal cord morphology0.003452Highly 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 progression0.0006616InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system0Least InformativeDirect
Fly Anatomy (FA)portion of tissue0Moderately 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 pathway0.000000000361InformativeDirect
Biological processUbl conjugation pathway0.00002301InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentCytoskeleton0Moderately InformativeDirect
Cellular componentGolgi apparatus0.00008095Moderately InformativeDirect
Cellular componentMicrotubule0InformativeDirect
DomainRepeat0.0000004194Least InformativeDirect
DomainCoiled coil0.000000000001355Moderately InformativeDirect
DomainLeucine-rich repeat0.0000000002068InformativeDirect
DomainANK repeat0.0000001033InformativeDirect
Post-translational modificationHydrolase0.9371Least InformativeInherited
Post-translational modificationProtease0.002069Moderately InformativeInherited
Post-translational modificationChaperone0InformativeDirect
Post-translational modificationThiol protease0.0000001386InformativeDirect
Post-translational modificationPhosphoprotein0.0000000008391Least 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 Phenotype (FP) · 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 Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]