SUPERFAMILY 1.75 HMM library and genome assignments server

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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 0.00000000000006398 Least Informative Direct
Biological Process (BP) protein metabolic process 0.000000005849 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.00003162 Least Informative Direct
Biological Process (BP) localization 0.00006106 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.3512 Least Informative Inherited
Biological Process (BP) developmental process 0.004191 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 0.001384 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.0492 Least Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.000005156 Moderately Informative Direct
Biological Process (BP) cellular localization 0.000006041 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.00001009 Moderately Informative Direct
Biological Process (BP) organelle organization 0.00002853 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.00004545 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.001983 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.5186 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.001154 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 0.01771 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.524 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.9141 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.8767 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.5801 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.1309 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.9314 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) regulation of phosphate metabolic process 0.08412 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.6464 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.1163 Moderately Informative Inherited
Biological Process (BP) microtubule-based process 0 Informative Direct
Biological Process (BP) organelle localization 0.0000000000004937 Informative Direct
Biological Process (BP) regulation of protein localization 0.000000000001844 Informative Direct
Biological Process (BP) cytoskeleton organization 0.0000000006449 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.000000005979 Informative Direct
Biological Process (BP) regulation of organelle organization 0.000006419 Informative Direct
Biological Process (BP) positive regulation of transport 0.00002067 Informative Direct
Biological Process (BP) protein modification by small protein conjugation or removal 0.0001091 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.0002483 Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 0.0006334 Informative Direct
Biological Process (BP) protein transport 0.0009619 Informative Direct
Biological Process (BP) cell cycle process 0.001537 Informative Inherited
Biological Process (BP) synaptic transmission 0.001459 Informative Inherited
Biological Process (BP) negative regulation of transport 0.001478 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 0.02201 Informative Inherited
Biological Process (BP) regulation of intracellular transport 0.001004 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.001795 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.03957 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.05821 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.07373 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.2596 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.001797 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.005625 Informative Inherited
Biological Process (BP) positive regulation of protein metabolic process 0.006911 Informative Inherited
Biological Process (BP) regulation of intracellular protein transport 0.00000000009933 Highly Informative Direct
Biological Process (BP) protein folding 0.0000000005063 Highly Informative Direct
Biological Process (BP) establishment or maintenance of cell polarity 0.0000001794 Highly Informative Direct
Biological Process (BP) negative regulation of sequence-specific DNA binding transcription factor activity 0.0000002707 Highly Informative Direct
Biological Process (BP) regulation of protein complex assembly 0.00001446 Highly Informative Direct
Biological Process (BP) lipoprotein metabolic process 0.0001658 Highly Informative Direct
Biological Process (BP) positive regulation of programmed cell death 0.0008323 Highly Informative Direct
Biological Process (BP) regulation of nucleocytoplasmic transport 0.285 Highly Informative Inherited
Biological Process (BP) regulation of protein localization to nucleus 0.02045 Highly Informative Inherited
Biological Process (BP) negative regulation of intracellular transport 0.002297 Highly Informative Inherited
Biological Process (BP) negative regulation of protein transport 0.01891 Highly Informative Inherited
Biological Process (BP) negative regulation of cytoskeleton organization 0.002171 Highly Informative Inherited
Biological Process (BP) regulation of microtubule polymerization or depolymerization 0.004614 Highly Informative Inherited
Molecular Function (MF) binding 0.00000004701 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.03735 Least Informative Inherited
Molecular Function (MF) cation binding 0.004952 Moderately Informative Inherited
Molecular Function (MF) cytoskeletal protein binding 0 Informative Direct
Molecular Function (MF) zinc ion binding 0.000002046 Informative Direct
Molecular Function (MF) peptidase activity 0.0007633 Informative Direct
Molecular Function (MF) lipid binding 0.0203 Informative Inherited
Molecular Function (MF) tubulin binding 0 Highly Informative Direct
Molecular Function (MF) glycolipid binding 0.0000000001133 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 0.00000000006731 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.1415 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 0.5274 Moderately Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0 Informative Direct
Cellular Component (CC) cell leading edge 0.0000003231 Informative Direct
Cellular Component (CC) cell cortex 0.00001258 Informative Direct
Cellular Component (CC) endosome 0.00004041 Informative Direct
Cellular Component (CC) actin cytoskeleton 1 Informative Inherited
Cellular Component (CC) chromosome 1 Informative Inherited
Cellular Component (CC) centrosome 0.0000000003204 Highly Informative Direct
Cellular Component (CC) midbody 0.0000000005516 Highly Informative Direct
Cellular Component (CC) microtubule associated complex 0.0000007276 Highly Informative Direct
Cellular Component (CC) kinetochore 0.0000009376 Highly Informative Direct
Cellular Component (CC) spindle 0.000001901 Highly Informative Direct
Cellular Component (CC) trans-Golgi network 0.000008609 Highly Informative Direct
Cellular Component (CC) endosomal part 0.0004144 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 phenotype0.1147Least InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.2679Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal spinal cord morphology0.003532Highly 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 progression0.0006608InformativeDirect

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 pathway0.0000000003563InformativeDirect
Biological processUbl conjugation pathway0.00002287InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentCytoskeleton0Moderately InformativeDirect
Cellular componentGolgi apparatus0.00008214Moderately InformativeDirect
Cellular componentMicrotubule0InformativeDirect
DomainRepeat0.0000004246Least InformativeDirect
DomainCoiled coil0.000000000001383Moderately InformativeDirect
DomainLeucine-rich repeat0.0000000001998InformativeDirect
DomainANK repeat0.0000001008InformativeDirect
Post-translational modificationHydrolase0.941Least InformativeInherited
Post-translational modificationProtease0.002057Moderately InformativeInherited
Post-translational modificationChaperone0InformativeDirect
Post-translational modificationThiol protease0.0000001385InformativeDirect
Post-translational modificationPhosphoprotein0.0000000008439Least 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 ]