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 (496) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,753 4,382 22
Proteins 2,973 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 Least Informative Direct
Biological Process (BP) protein metabolic process 0.000000007796 Least Informative Direct
Biological Process (BP) localization 0.00000002028 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.00003292 Least Informative Direct
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) developmental process 0.00776 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.03431 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 0.6027 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.369 Least Informative Inherited
Biological Process (BP) single-organism organelle organization 0.000000001127 Moderately Informative Direct
Biological Process (BP) cellular localization 0.00000001748 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.000002986 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.00008502 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.01007 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.01889 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.5533 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.4965 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.196 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.5886 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.04791 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.014 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.9316 Moderately Informative Inherited
Biological Process (BP) regulation of phosphorus metabolic process 0.1412 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.1904 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.924 Moderately Informative Inherited
Biological Process (BP) microtubule-based process 0 Informative Direct
Biological Process (BP) regulation of protein localization 0.000000000002521 Informative Direct
Biological Process (BP) single-organism cellular localization 0.00000000001057 Informative Direct
Biological Process (BP) cytoskeleton organization 0.0000000002467 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.00000001317 Informative Direct
Biological Process (BP) organelle localization 0.00000003877 Informative Direct
Biological Process (BP) regulation of organelle organization 0.00001778 Informative Direct
Biological Process (BP) positive regulation of transport 0.00001808 Informative Direct
Biological Process (BP) protein transport 0.00006129 Informative Direct
Biological Process (BP) protein modification by small protein conjugation or removal 0.0001096 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.0004055 Informative Direct
Biological Process (BP) positive regulation of cell death 0.000447 Informative Direct
Biological Process (BP) cell cycle process 0.0005549 Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 0.0008328 Informative Direct
Biological Process (BP) regulation of intracellular transport 0.0009564 Informative Direct
Biological Process (BP) negative regulation of signaling 0.04673 Informative Inherited
Biological Process (BP) single-organism membrane organization 0.002009 Informative Inherited
Biological Process (BP) synaptic transmission 0.001732 Informative Inherited
Biological Process (BP) single-organism intracellular transport 0.05694 Informative Inherited
Biological Process (BP) regulation of apoptotic process 0.02824 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.08941 Informative Inherited
Biological Process (BP) negative regulation of transport 0.001472 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.06863 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.003028 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.2649 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.005949 Informative Inherited
Biological Process (BP) positive regulation of cellular protein metabolic process 0.008025 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.02909 Informative Inherited
Biological Process (BP) protein folding 0.000000000473 Highly Informative Direct
Biological Process (BP) plasma membrane organization 0.000000007256 Highly Informative Direct
Biological Process (BP) establishment or maintenance of cell polarity 0.00000004506 Highly Informative Direct
Biological Process (BP) negative regulation of sequence-specific DNA binding transcription factor activity 0.0000009064 Highly Informative Direct
Biological Process (BP) regulation of protein complex assembly 0.00002299 Highly Informative Direct
Biological Process (BP) lipoprotein metabolic process 0.000152 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular signal transduction 0.0004133 Highly Informative Direct
Biological Process (BP) regulation of endocytosis 0.005106 Highly Informative Inherited
Biological Process (BP) protein localization to membrane 0.2889 Highly Informative Inherited
Biological Process (BP) regulation of nucleocytoplasmic transport 0.2657 Highly Informative Inherited
Biological Process (BP) regulation of protein localization to nucleus 0.0183 Highly Informative Inherited
Biological Process (BP) regulation of peptide transport 0.0134 Highly Informative Inherited
Biological Process (BP) negative regulation of intracellular transport 0.003293 Highly Informative Inherited
Biological Process (BP) negative regulation of protein transport 0.01845 Highly Informative Inherited
Biological Process (BP) regulation of protein targeting 1 Highly Informative Inherited
Biological Process (BP) negative regulation of cytoskeleton organization 0.00194 Highly Informative Inherited
Biological Process (BP) regulation of microtubule polymerization or depolymerization 0.003862 Highly Informative Inherited
Molecular Function (MF) binding 0.00000006225 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.03776 Least Informative Inherited
Molecular Function (MF) cation binding 0.005006 Moderately Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.2177 Moderately Informative Inherited
Molecular Function (MF) protein complex binding 0 Informative Direct
Molecular Function (MF) cytoskeletal protein binding 0 Informative Direct
Molecular Function (MF) zinc ion binding 0.000002133 Informative Direct
Molecular Function (MF) peptidase activity 0.000786 Informative Direct
Molecular Function (MF) lipid binding 0.02026 Informative Inherited
Molecular Function (MF) tubulin binding 0 Highly Informative Direct
Molecular Function (MF) glycolipid binding 0.0000000001144 Highly Informative Direct
Cellular Component (CC) protein complex 0 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.00000000004106 Least Informative Direct
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1589 Least Informative Inherited
Cellular Component (CC) cytoskeleton 0 Moderately Informative Direct
Cellular Component (CC) membrane region 0.03135 Moderately Informative Inherited
Cellular Component (CC) bounding membrane of organelle 0.05834 Moderately Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0 Informative Direct
Cellular Component (CC) cell leading edge 0.0000003163 Informative Direct
Cellular Component (CC) cell cortex 0.00001231 Informative Direct
Cellular Component (CC) endosome 0.00004729 Informative Direct
Cellular Component (CC) actin cytoskeleton 1 Informative Inherited
Cellular Component (CC) Golgi apparatus 0.05426 Informative Inherited
Cellular Component (CC) chromosome 0.9749 Informative Inherited
Cellular Component (CC) midbody 0.0000000006916 Highly Informative Direct
Cellular Component (CC) chromosome, centromeric region 0.000000003286 Highly Informative Direct
Cellular Component (CC) microtubule associated complex 0.00000323 Highly Informative Direct
Cellular Component (CC) trans-Golgi network 0.000008843 Highly Informative Direct
Cellular Component (CC) spindle 0.00005167 Highly Informative Direct
Cellular Component (CC) endosomal part 0.0004444 Highly Informative Direct
Cellular Component (CC) microtubule organizing center 0.002508 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 phenotype0.1147Least 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 ]