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 (440) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 3,393 2,940 22
Proteins 2,701 2,327 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 6.16e-09 Least Informative Direct
Biological Process (BP) protein metabolic process 8.916e-09 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 1.176e-05 Least Informative Direct
Biological Process (BP) developmental process 0.000362 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.985 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.2545 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.06344 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) localization 0.06942 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.1246 Least Informative Inherited
Biological Process (BP) macromolecule localization 3.618e-07 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 3.263e-06 Moderately Informative Direct
Biological Process (BP) organelle organization 1.993e-05 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.0005712 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.0009125 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.04129 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.00313 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.58 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.009197 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.1465 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.1496 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 0.9671 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) system process 0.07919 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.8942 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.5631 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.5547 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.6855 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.8809 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 0.8521 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.1776 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.6802 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.8738 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.2952 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.4398 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.0824 Moderately Informative Inherited
Biological Process (BP) microtubule-based process 0 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 5.093e-09 Informative Direct
Biological Process (BP) regulation of protein localization 8.085e-09 Informative Direct
Biological Process (BP) cytoskeleton organization 1.312e-07 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.0001505 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.0002034 Informative Direct
Biological Process (BP) protein modification by small protein conjugation or removal 0.0002305 Informative Direct
Biological Process (BP) cell cycle process 0.0006289 Informative Direct
Biological Process (BP) protein transport 0.0008805 Informative Direct
Biological Process (BP) positive regulation of phosphorus metabolic process 0.0009982 Informative Direct
Biological Process (BP) regulation of intracellular transport 0.03282 Informative Inherited
Biological Process (BP) synaptic transmission 0.00532 Informative Inherited
Biological Process (BP) positive regulation of transport 0.003524 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.0103 Informative Inherited
Biological Process (BP) regulation of apoptotic process 0.02449 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 0.01467 Informative Inherited
Biological Process (BP) negative regulation of molecular function 0.002996 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.0243 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.02469 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.009788 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.01053 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.02991 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.1334 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.003147 Informative Inherited
Biological Process (BP) positive regulation of protein metabolic process 0.004274 Informative Inherited
Biological Process (BP) protein folding 1.74e-10 Highly Informative Direct
Biological Process (BP) establishment or maintenance of cell polarity 9.001e-09 Highly Informative Direct
Biological Process (BP) organelle localization 4.193e-08 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular transport 1.037e-07 Highly Informative Direct
Biological Process (BP) negative regulation of sequence-specific DNA binding transcription factor activity 2.289e-07 Highly Informative Direct
Biological Process (BP) lipid homeostasis 2.386e-07 Highly Informative Direct
Biological Process (BP) stress-activated protein kinase signaling cascade 4.386e-07 Highly Informative Direct
Biological Process (BP) negative regulation of protein transport 1.081e-06 Highly Informative Direct
Biological Process (BP) regulation of nucleocytoplasmic transport 3.068e-06 Highly Informative Direct
Biological Process (BP) microtubule cytoskeleton organization 4.584e-06 Highly Informative Direct
Biological Process (BP) regulation of intracellular protein transport 5.837e-06 Highly Informative Direct
Biological Process (BP) protein complex localization 3.763e-05 Highly Informative Direct
Biological Process (BP) regulation of protein complex assembly 7.24e-05 Highly Informative Direct
Biological Process (BP) positive regulation of apoptotic process 0.0001083 Highly Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 0.0001104 Highly Informative Direct
Biological Process (BP) lipoprotein metabolic process 0.0001414 Highly Informative Direct
Biological Process (BP) negative regulation of cytoskeleton organization 0.0009497 Highly Informative Direct
Biological Process (BP) regulation of protein localization to nucleus 0.00433 Highly Informative Inherited
Biological Process (BP) regulation of microtubule polymerization or depolymerization 0.009094 Highly Informative Inherited
Biological Process (BP) negative regulation of signal transduction 0.008182 Highly Informative Inherited
Biological Process (BP) aging 0.001095 Highly Informative Inherited
Molecular Function (MF) binding 1.296e-07 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.01525 Least Informative Inherited
Molecular Function (MF) protein binding 3.4e-05 Moderately Informative Direct
Molecular Function (MF) cation binding 0.003665 Moderately Informative Inherited
Molecular Function (MF) cytoskeletal protein binding 0 Informative Direct
Molecular Function (MF) peptidase activity 4.308e-05 Informative Direct
Molecular Function (MF) transition metal ion binding 9.335e-05 Informative Direct
Molecular Function (MF) lipid binding 0.01322 Informative Inherited
Molecular Function (MF) tubulin binding 0 Highly Informative Direct
Molecular Function (MF) glycolipid binding 8.198e-11 Highly Informative Direct
Molecular Function (MF) zinc ion binding 1.649e-06 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 7.213e-14 Least Informative Direct
Cellular Component (CC) protein complex 7.719e-12 Least Informative Direct
Cellular Component (CC) intracellular organelle part 2.58e-08 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.01044 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 0.3273 Moderately Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0 Informative Direct
Cellular Component (CC) cell leading edge 1.703e-07 Informative Direct
Cellular Component (CC) endosome 7.626e-06 Informative Direct
Cellular Component (CC) cell cortex 1.087e-05 Informative Direct
Cellular Component (CC) actin cytoskeleton 1 Informative Inherited
Cellular Component (CC) chromosome 0.7502 Informative Inherited
Cellular Component (CC) cytoplasmic microtubule 0 Highly Informative Direct
Cellular Component (CC) midbody 3.73e-09 Highly Informative Direct
Cellular Component (CC) spindle 2.518e-08 Highly Informative Direct
Cellular Component (CC) kinetochore 1.196e-07 Highly Informative Direct
Cellular Component (CC) microtubule associated complex 2.013e-07 Highly Informative Direct
Cellular Component (CC) trans-Golgi network 5.716e-06 Highly Informative Direct
Cellular Component (CC) membrane raft 1.08e-05 Highly Informative Direct
Cellular Component (CC) endosomal part 0.0001161 Highly Informative Direct
Cellular Component (CC) recycling endosome 0.0002912 Highly Informative Direct
Cellular Component (CC) microtubule organizing center 0.1226 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

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 progression0.0006809InformativeDirect
Yeast Phenotype (YP)subcellular morphology0.1931InformativeInherited
Yeast Phenotype (YP)nuclear morphology2.598e-07Highly InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)behavior defective0.001911Moderately InformativeInherited
Fly Phenotype (FP)locomotor behavior defective0.0001957InformativeDirect

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

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)male genitalia0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)sensory 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 pathway2.608e-10InformativeDirect
Biological processUbl conjugation pathway1.675e-05InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentCytoskeleton0Moderately InformativeDirect
Cellular componentGolgi apparatus5.655e-05Moderately InformativeDirect
Cellular componentMicrotubule0InformativeDirect
DomainRepeat3.156e-06Least InformativeDirect
DomainCoiled coil1.794e-12Moderately InformativeDirect
DomainLeucine-rich repeat4.985e-09InformativeDirect
DomainANK repeat1.406e-07InformativeDirect
Post-translational modificationHydrolase0.8877Least InformativeInherited
Post-translational modificationProtease0.001597Moderately InformativeInherited
Post-translational modificationChaperone4.371e-15InformativeDirect
Post-translational modificationThiol protease1.008e-07InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]