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 (587) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 5,023 4,723 4
Proteins 4,923 4,623 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 4.467e-10 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 2.748e-05 Least Informative Direct
Biological Process (BP) developmental process 7.885e-05 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.002421 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.3718 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.1927 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.7812 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.9382 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.8094 Least Informative Inherited
Biological Process (BP) regulation of localization 2.118e-05 Moderately Informative Direct
Biological Process (BP) cellular localization 0.0001064 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.000137 Moderately Informative Direct
Biological Process (BP) organelle organization 0.000158 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0001803 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.0003276 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.2471 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.724 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.07525 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.08741 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.005009 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.8078 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.1329 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.5544 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.2956 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.02316 Moderately Informative Inherited
Biological Process (BP) reproduction 0.2466 Moderately Informative Inherited
Biological Process (BP) immune system process 0.1402 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.08519 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.1584 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.1019 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.04115 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.0318 Moderately Informative Inherited
Biological Process (BP) organ development 0.001322 Moderately Informative Inherited
Biological Process (BP) tissue development 0.313 Moderately Informative Inherited
Biological Process (BP) vesicle-mediated transport 2.079e-07 Informative Direct
Biological Process (BP) organ morphogenesis 7.151e-07 Informative Direct
Biological Process (BP) cell projection organization 2.218e-06 Informative Direct
Biological Process (BP) embryonic organ development 4.205e-06 Informative Direct
Biological Process (BP) embryo development ending in birth or egg hatching 2.687e-05 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 0.0001057 Informative Direct
Biological Process (BP) embryonic morphogenesis 0.0002944 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.0004669 Informative Direct
Biological Process (BP) negative regulation of signaling 0.0006737 Informative Direct
Biological Process (BP) negative regulation of cell communication 0.0008415 Informative Direct
Biological Process (BP) regulation of system process 0.6201 Informative Inherited
Biological Process (BP) regulation of secretion 0.0424 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.01014 Informative Inherited
Biological Process (BP) regulation of intracellular transport 0.1871 Informative Inherited
Biological Process (BP) sensory organ development 0.1545 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.1194 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.3523 Informative Inherited
Biological Process (BP) regulation of cell development 0.8904 Informative Inherited
Biological Process (BP) cardiovascular system development 0.5777 Informative Inherited
Biological Process (BP) protein complex assembly 0.2804 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.001666 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.002535 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.002008 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.1159 Informative Inherited
Biological Process (BP) cell activation 0.1499 Informative Inherited
Biological Process (BP) hematopoietic or lymphoid organ development 0.3891 Informative Inherited
Biological Process (BP) generation of neurons 0.07402 Informative Inherited
Biological Process (BP) central nervous system development 0.1188 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.008263 Informative Inherited
Biological Process (BP) muscle structure development 0.228 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.206 Informative Inherited
Biological Process (BP) organelle localization 0.2158 Informative Inherited
Biological Process (BP) membrane organization 0.0024 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.07469 Informative Inherited
Biological Process (BP) positive regulation of transport 0.04833 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.0422 Informative Inherited
Biological Process (BP) epithelium development 0.8608 Informative Inherited
Biological Process (BP) regulation of vesicle-mediated transport 4.58e-09 Highly Informative Direct
Biological Process (BP) tube formation 1.295e-08 Highly Informative Direct
Biological Process (BP) artery morphogenesis 2.578e-08 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 1.141e-07 Highly Informative Direct
Biological Process (BP) regulation of organ morphogenesis 4.154e-07 Highly Informative Direct
Biological Process (BP) vesicle organization 4.11e-06 Highly Informative Direct
Biological Process (BP) protein glycosylation 4.396e-06 Highly Informative Direct
Biological Process (BP) post-translational protein modification 1.601e-05 Highly Informative Direct
Biological Process (BP) epidermal cell differentiation 4.649e-05 Highly Informative Direct
Biological Process (BP) regulation of cellular response to growth factor stimulus 8.497e-05 Highly Informative Direct
Biological Process (BP) embryonic organ morphogenesis 9.802e-05 Highly Informative Direct
Biological Process (BP) connective tissue development 0.0001269 Highly Informative Direct
Biological Process (BP) establishment or maintenance of cell polarity 0.0002179 Highly Informative Direct
Biological Process (BP) post-embryonic development 0.0003364 Highly Informative Direct
Biological Process (BP) regulation of synaptic transmission 0.0004039 Highly Informative Direct
Biological Process (BP) T cell differentiation 0.0004542 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0.0004717 Highly Informative Direct
Biological Process (BP) regulation of protein complex assembly 0.0005054 Highly Informative Direct
Biological Process (BP) neural tube development 0.0006 Highly Informative Direct
Biological Process (BP) response to osmotic stress 0.0009596 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.09015 Highly Informative Inherited
Biological Process (BP) negative regulation of secretion 0.1009 Highly Informative Inherited
Biological Process (BP) lung development 0.002555 Highly Informative Inherited
Biological Process (BP) skeletal system development 0.007771 Highly Informative Inherited
Biological Process (BP) epithelial cell development 0.04583 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.04661 Highly Informative Inherited
Biological Process (BP) negative regulation of cell differentiation 0.05059 Highly Informative Inherited
Biological Process (BP) neuron projection development 0.6307 Highly Informative Inherited
Biological Process (BP) cell part morphogenesis 0.6908 Highly Informative Inherited
Biological Process (BP) establishment of vesicle localization 0.04275 Highly Informative Inherited
Biological Process (BP) positive regulation of cell differentiation 0.09096 Highly Informative Inherited
Biological Process (BP) limb morphogenesis 0.1781 Highly Informative Inherited
Biological Process (BP) regulation of cell adhesion 0.006947 Highly Informative Inherited
Biological Process (BP) muscle organ development 0.1329 Highly Informative Inherited
Biological Process (BP) positive regulation of secretion 0.006569 Highly Informative Inherited
Biological Process (BP) heart morphogenesis 0.1915 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.05188 Highly Informative Inherited
Biological Process (BP) antigen processing and presentation 0.001272 Highly Informative Inherited
Biological Process (BP) inner ear development 0.001576 Highly Informative Inherited
Biological Process (BP) ossification 0.005061 Highly Informative Inherited
Biological Process (BP) cell fate commitment 0.001118 Highly Informative Inherited
Biological Process (BP) morphogenesis of embryonic epithelium 0.006851 Highly Informative Inherited
Biological Process (BP) epithelial tube morphogenesis 1 Highly Informative Inherited
Molecular Function (MF) binding 0.1151 Least Informative Inherited
Molecular Function (MF) transcription factor binding 0.001596 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 0.01012 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.05747 Least Informative Inherited
Cellular Component (CC) protein complex 0.02717 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.03662 Least Informative Inherited
Cellular Component (CC) membrane 0.2144 Least Informative Inherited
Cellular Component (CC) vesicle 1.513e-13 Moderately Informative Direct
Cellular Component (CC) endomembrane system 1.415e-11 Moderately Informative Direct
Cellular Component (CC) organelle membrane 9.988e-08 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.9648 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.01179 Moderately Informative Inherited
Cellular Component (CC) coated vesicle 6.905e-10 Informative Direct
Cellular Component (CC) nucleoplasm part 0.0008721 Informative Direct
Cellular Component (CC) Golgi apparatus 0.01973 Informative Inherited
Cellular Component (CC) transport vesicle 0 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 1.027e-08 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 2.724e-05 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)Protein-serine/threonine kinases1.415e-09Moderately InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details) Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details) 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 mortality0.01667Least InformativeInherited
Fly Phenotype (FP)lethal - all die before end of P-stage0.02722Moderately InformativeInherited

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
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 structure0.03191Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.6897Moderately 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 groups0.000104Least InformativeDirect
Enzyme Commission (EC)Hydrolases0.3533Least InformativeInherited
Enzyme Commission (EC)Protein-serine/threonine kinases1.743e-10Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.009055Moderately 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 regulation9.642e-05Moderately InformativeDirect
Biological processER-Golgi transport0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentNucleus2.224e-05Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
DomainCoiled coil9.621e-15Moderately InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMetal-binding5.314e-07Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationDevelopmental protein2.1e-10Moderately InformativeDirect
Post-translational modificationKinase0.05704Moderately InformativeInherited
Post-translational modificationSerine/threonine-protein kinase6.144e-07InformativeDirect
Post-translational modificationPhosphoprotein3.4e-06Least InformativeDirect
Post-translational modificationAcetylation0.0001567Least InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · 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) ]

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) · 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) · Internal database links ]