SUPERFAMILY 1.75 HMM library and genome assignments server


beta-sandwich domain of Sec23/24 superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Common fold of diphtheria toxin/transcription factors/cytochrome f [ 49379] (10)
Superfamily:   beta-sandwich domain of Sec23/24 [ 81995]
Families:   beta-sandwich domain of Sec23/24 [ 81996] (2)


Superfamily statistics
Genomes (638) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,408 7,084 4
Proteins 5,295 6,950 4


Functional annotation
General category Other
Detailed category Unknown function

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) localization 2.778e-12 Least Informative Direct
Biological Process (BP) developmental process 1.002e-06 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 2.163e-06 Least Informative Direct
Biological Process (BP) multicellular organismal process 4.825e-05 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.1044 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.9784 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.9319 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.16 Least Informative Inherited
Biological Process (BP) cellular localization 2.447e-05 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 5.184e-05 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.0001543 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0003276 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.0003864 Moderately Informative Direct
Biological Process (BP) organelle organization 0.0009132 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.3601 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.8913 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.7253 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.2387 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.01471 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.847 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.1771 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.9928 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.4888 Moderately Informative Inherited
Biological Process (BP) immune system process 0.2362 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.3085 Moderately Informative Inherited
Biological Process (BP) reproduction 0.1669 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.2019 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.2163 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.06419 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.05204 Moderately Informative Inherited
Biological Process (BP) organ development 0.00611 Moderately Informative Inherited
Biological Process (BP) tissue development 0.769 Moderately Informative Inherited
Biological Process (BP) vesicle-mediated transport 2.878e-08 Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 5.729e-08 Informative Direct
Biological Process (BP) cell projection organization 1.102e-07 Informative Direct
Biological Process (BP) organ morphogenesis 5.659e-06 Informative Direct
Biological Process (BP) embryonic organ development 1.099e-05 Informative Direct
Biological Process (BP) cellular component morphogenesis 3.614e-05 Informative Direct
Biological Process (BP) cellular membrane organization 7.723e-05 Informative Direct
Biological Process (BP) regulation of anatomical structure size 9.745e-05 Informative Direct
Biological Process (BP) embryo development ending in birth or egg hatching 0.0002403 Informative Direct
Biological Process (BP) positive regulation of developmental process 0.0003042 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 0.000323 Informative Direct
Biological Process (BP) negative regulation of signaling 0.0004935 Informative Direct
Biological Process (BP) negative regulation of cell communication 0.0005278 Informative Direct
Biological Process (BP) regulation of system process 0.5698 Informative Inherited
Biological Process (BP) regulation of secretion 0.02938 Informative Inherited
Biological Process (BP) negative regulation of transport 0.0261 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.07425 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.1247 Informative Inherited
Biological Process (BP) regulation of intracellular transport 0.3574 Informative Inherited
Biological Process (BP) tube development 0.00169 Informative Inherited
Biological Process (BP) sensory organ development 0.2048 Informative Inherited
Biological Process (BP) cardiovascular system development 0.6746 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.002315 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.006467 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.002431 Informative Inherited
Biological Process (BP) leukocyte activation 0.0724 Informative Inherited
Biological Process (BP) hematopoietic or lymphoid organ development 0.6768 Informative Inherited
Biological Process (BP) generation of neurons 0.1616 Informative Inherited
Biological Process (BP) central nervous system development 0.3523 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.005368 Informative Inherited
Biological Process (BP) muscle structure development 0.2733 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.4125 Informative Inherited
Biological Process (BP) sexual reproduction 0.04458 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.06136 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 0.2486 Informative Inherited
Biological Process (BP) single organism reproductive process 0.2672 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.3589 Informative Inherited
Biological Process (BP) organelle localization 0.2089 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.03261 Informative Inherited
Biological Process (BP) positive regulation of transport 0.01129 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.1435 Informative Inherited
Biological Process (BP) epithelium development 0.8616 Informative Inherited
Biological Process (BP) locomotion 0.01059 Informative Inherited
Biological Process (BP) cellular component movement 0.01345 Informative Inherited
Biological Process (BP) localization of cell 1 Informative Inherited
Biological Process (BP) Golgi vesicle transport 1.073e-08 Highly Informative Direct
Biological Process (BP) artery morphogenesis 3.483e-08 Highly Informative Direct
Biological Process (BP) respiratory system development 1.636e-07 Highly Informative Direct
Biological Process (BP) regulation of organ morphogenesis 1.267e-06 Highly Informative Direct
Biological Process (BP) protein glycosylation 2.33e-06 Highly Informative Direct
Biological Process (BP) vesicle organization 6.995e-06 Highly Informative Direct
Biological Process (BP) post-translational protein modification 1.028e-05 Highly Informative Direct
Biological Process (BP) establishment or maintenance of cell polarity 1.917e-05 Highly Informative Direct
Biological Process (BP) epidermal cell differentiation 5.406e-05 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0.0001023 Highly Informative Direct
Biological Process (BP) regulation of synaptic transmission 0.0001412 Highly Informative Direct
Biological Process (BP) connective tissue development 0.0001416 Highly Informative Direct
Biological Process (BP) regulation of cellular response to growth factor stimulus 0.0002106 Highly Informative Direct
Biological Process (BP) embryonic organ morphogenesis 0.0003199 Highly Informative Direct
Biological Process (BP) post-embryonic development 0.0004549 Highly Informative Direct
Biological Process (BP) T cell differentiation 0.0005807 Highly Informative Direct
Biological Process (BP) regulation of cell division 0.0006642 Highly Informative Direct
Biological Process (BP) post-embryonic organ development 0.0008922 Highly Informative Direct
Biological Process (BP) antigen processing and presentation 0.0009312 Highly Informative Direct
Biological Process (BP) regulation of protein complex assembly 0.0009484 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.1702 Highly Informative Inherited
Biological Process (BP) negative regulation of secretion 0.1177 Highly Informative Inherited
Biological Process (BP) regulation of exocytosis 0.03367 Highly Informative Inherited
Biological Process (BP) respiratory tube development 0.006002 Highly Informative Inherited
Biological Process (BP) epithelial cell development 0.07424 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.009887 Highly Informative Inherited
Biological Process (BP) neuron projection development 0.354 Highly Informative Inherited
Biological Process (BP) cell part morphogenesis 0.542 Highly Informative Inherited
Biological Process (BP) regulation of cell adhesion 0.01637 Highly Informative Inherited
Biological Process (BP) limb morphogenesis 0.2583 Highly Informative Inherited
Biological Process (BP) muscle organ development 0.1258 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.006915 Highly Informative Inherited
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0.03048 Highly Informative Inherited
Biological Process (BP) heart morphogenesis 0.2837 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.1174 Highly Informative Inherited
Biological Process (BP) ear development 0.01456 Highly Informative Inherited
Biological Process (BP) skeletal system development 0.028 Highly Informative Inherited
Biological Process (BP) ossification 0.01248 Highly Informative Inherited
Biological Process (BP) cell fate commitment 0.001574 Highly Informative Inherited
Biological Process (BP) neural tube development 0.001502 Highly Informative Inherited
Biological Process (BP) morphogenesis of embryonic epithelium 0.006326 Highly Informative Inherited
Biological Process (BP) epithelial tube formation 0.03427 Highly Informative Inherited
Molecular Function (MF) binding 0.08566 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.01741 Moderately Informative Inherited
Molecular Function (MF) receptor binding 0.08882 Informative Inherited
Molecular Function (MF) DNA binding 0.08827 Informative Inherited
Molecular Function (MF) transcription factor binding 0.002512 Highly Informative Inherited
Molecular Function (MF) transcription factor binding transcription factor activity 0.00766 Highly Informative Inherited
Molecular Function (MF) transcription regulatory region DNA binding 0.00427 Highly Informative Inherited
Cellular Component (CC) protein complex 0.02008 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.05146 Least Informative Inherited
Cellular Component (CC) membrane 0.5334 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.005755 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.01717 Least Informative Inherited
Cellular Component (CC) vesicle 4.695e-12 Moderately Informative Direct
Cellular Component (CC) endomembrane system 1.64e-11 Moderately Informative Direct
Cellular Component (CC) organelle membrane 1.24e-07 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum 0.002077 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.8792 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) coated vesicle 1.598e-10 Informative Direct
Cellular Component (CC) nucleoplasm part 3.331e-05 Informative Direct
Cellular Component (CC) Golgi apparatus 0.04671 Informative Inherited
Cellular Component (CC) transport vesicle 0 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 5.769e-08 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 1.993e-05 Highly Informative Direct
Cellular Component (CC) receptor complex 0.0244 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)Protein-serine/threonine kinases1.415e-09Moderately InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details) Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.1655Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of movement0.08234InformativeInherited
Phenotypic Abnormality (PA)Involuntary movements0.0009842Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)growth/size/body phenotype0.4097Least InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.004687Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.01092Least InformativeInherited
Worm Phenotype (WP)cell organization biogenesis variant7.425e-05Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant7.938e-05Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.0002493Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.00121Moderately InformativeInherited
Worm Phenotype (WP)germline nuclear positioning variant6.218e-07InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant3.777e-06InformativeDirect
Worm Phenotype (WP)germ cell compartment size variant1.995e-07Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0.1834Least InformativeInherited
Fly Phenotype (FP)lethal - all die before end of P-stage0.01044Moderately InformativeInherited
Fly Phenotype (FP)cell shape defective0.0001439Highly InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

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XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0Least InformativeDirect
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)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)intestine0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ovary0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)embryonic structure0.03465Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.6949Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro0InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0.01921Least InformativeInherited
Plant ANatomical entity (PAN)cotyledon0.0009963Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups7.723e-05Least InformativeDirect
Enzyme Commission (EC)Hydrolases0.3491Least InformativeInherited
Enzyme Commission (EC)Protein-serine/threonine kinases1.735e-10Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.008794Moderately InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processProtein transport0Moderately InformativeDirect
Biological processTranscription regulation0.0001341Moderately InformativeDirect
Biological processER-Golgi transport0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentNucleus2.475e-05Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
DomainCoiled coil1.138e-14Moderately InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMetal-binding1.254e-06Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationDevelopmental protein1.996e-10Moderately InformativeDirect
Post-translational modificationKinase0.05757Moderately InformativeInherited
Post-translational modificationSerine/threonine-protein kinase6.103e-07InformativeDirect
Post-translational modificationPhosphoprotein3.752e-06Least InformativeDirect
Post-translational modificationAcetylation0.0001595Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details) Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 2 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 beta-sandwich domain of Sec23/24 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 2 hidden Markov models representing the beta-sandwich domain of Sec23/24 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) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]