SUPERFAMILY 1.75 HMM library and genome assignments server


Sema domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   7-bladed beta-propeller [ 50964] (14)
Superfamily:   Sema domain [ 101912]
Families:   Sema domain [ 101913] (3)


Superfamily statistics
Genomes (137) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,378 3,801 3
Proteins 3,231 3,756 3


Functional annotation
General category Processes_EC
Detailed category Cell adhesion

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)developmental process7.756e-070Least InformativeDirect
Biological Process (BP)multicellular organismal process2.389e-060Least InformativeDirect
Biological Process (BP)single-organism cellular process4.471e-063.722e-15Least InformativeDirect
Biological Process (BP)regulation of cellular process0.00020880Least InformativeDirect
Biological Process (BP)response to stimulus0.00078020Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.0067830Least InformativeInherited
Biological Process (BP)localization0.0012560.0007363Least InformativeInherited
Biological Process (BP)cell differentiation4.958e-090Moderately InformativeDirect
Biological Process (BP)regulation of developmental process0.00031751.012e-08Moderately InformativeDirect
Biological Process (BP)anatomical structure morphogenesis0.059544.981e-13Moderately InformativeInherited
Biological Process (BP)single-organism developmental process0.0044430Moderately InformativeInherited
Biological Process (BP)tissue development0.0014390.3602Moderately InformativeInherited
Biological Process (BP)regulation of multicellular organismal process0.0010540Moderately InformativeInherited
Biological Process (BP)nervous system development0.0091510Moderately InformativeInherited
Biological Process (BP)regulation of cellular component organization0.0050686.663e-09Moderately InformativeInherited
Biological Process (BP)signal transduction0.05530Moderately InformativeInherited
Biological Process (BP)locomotion9.072e-100InformativeDirect
Biological Process (BP)regulation of anatomical structure morphogenesis3.978e-080InformativeDirect
Biological Process (BP)generation of neurons1.28e-070InformativeDirect
Biological Process (BP)regulation of cell development7.37e-070InformativeDirect
Biological Process (BP)cellular component movement4.201e-060InformativeDirect
Biological Process (BP)localization of cell0.00020950InformativeDirect
Biological Process (BP)cell projection organization0.0005360InformativeDirect
Biological Process (BP)epithelium development0.35580.2254InformativeInherited
Biological Process (BP)cellular component morphogenesis0.0038070InformativeInherited
Biological Process (BP)regulation of nervous system development0.023561.071e-06InformativeInherited
Biological Process (BP)tissue morphogenesis0.0011450.003077InformativeInherited
Biological Process (BP)regulation of cell morphogenesis involved in differentiation1.919e-082.587e-13Highly InformativeDirect
Biological Process (BP)regulation of neuron projection development3.008e-083.234e-06Highly InformativeDirect
Biological Process (BP)axon development9.156e-082.94e-09Highly InformativeDirect
Biological Process (BP)cell morphogenesis involved in neuron differentiation9.993e-080Highly InformativeDirect
Biological Process (BP)cell projection morphogenesis3.418e-070Highly InformativeDirect
Biological Process (BP)chemotaxis5.918e-070Highly InformativeDirect
Molecular Function (MF)binding0.01361.036e-09Least InformativeInherited
Molecular Function (MF)receptor binding0.00046650InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) developmental process 0 Least Informative Direct
Biological Process (BP) multicellular organismal process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 3.722e-15 Least Informative Direct
Biological Process (BP) regulation of cellular process 0 Least Informative Direct
Biological Process (BP) response to stimulus 0 Least Informative Direct
Biological Process (BP) localization 0.0007363 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0 Least Informative Direct
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) cell differentiation 0 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 1.012e-08 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 6.663e-09 Moderately Informative Direct
Biological Process (BP) nervous system development 0 Moderately Informative Direct
Biological Process (BP) regulation of localization 0 Moderately Informative Direct
Biological Process (BP) signal transduction 0 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 4.981e-13 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 1.502e-12 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 8.94e-07 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 6.339e-05 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.0001639 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.003135 Moderately Informative Inherited
Biological Process (BP) tissue development 0.3602 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.7861 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.9012 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) homeostatic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.3468 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) locomotion 0 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 0 Informative Direct
Biological Process (BP) generation of neurons 0 Informative Direct
Biological Process (BP) regulation of cell development 0 Informative Direct
Biological Process (BP) cellular component movement 0 Informative Direct
Biological Process (BP) localization of cell 0 Informative Direct
Biological Process (BP) cell projection organization 0 Informative Direct
Biological Process (BP) cellular component morphogenesis 0 Informative Direct
Biological Process (BP) regulation of nervous system development 1.071e-06 Informative Direct
Biological Process (BP) regulation of cellular component movement 0 Informative Direct
Biological Process (BP) regulation of locomotion 0 Informative Direct
Biological Process (BP) regulation of response to external stimulus 0 Informative Direct
Biological Process (BP) regulation of anatomical structure size 1.512e-11 Informative Direct
Biological Process (BP) regulation of nucleoside metabolic process 1.976e-06 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 3.837e-06 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 1.177e-05 Informative Direct
Biological Process (BP) single-organism behavior 1.344e-05 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 5.426e-05 Informative Direct
Biological Process (BP) regulation of growth 5.941e-05 Informative Direct
Biological Process (BP) central nervous system development 7.496e-05 Informative Direct
Biological Process (BP) regulation of cellular catabolic process 9.814e-05 Informative Direct
Biological Process (BP) organelle localization 0.0004638 Informative Direct
Biological Process (BP) positive regulation of protein modification process 0.0138 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.1197 Informative Inherited
Biological Process (BP) epithelium development 0.2254 Informative Inherited
Biological Process (BP) cell-cell signaling 1 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.003077 Informative Inherited
Biological Process (BP) gland development 0.1548 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.003558 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 1 Informative Inherited
Biological Process (BP) phosphorylation 0.05019 Informative Inherited
Biological Process (BP) muscle structure development 0.8206 Informative Inherited
Biological Process (BP) regulation of kinase activity 0.998 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.1163 Informative Inherited
Biological Process (BP) muscle tissue development 0.5366 Informative Inherited
Biological Process (BP) positive regulation of transport 0.1788 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.07979 Informative Inherited
Biological Process (BP) tube development 0.008081 Informative Inherited
Biological Process (BP) cardiovascular system development 0.1569 Informative Inherited
Biological Process (BP) regulation of cell morphogenesis involved in differentiation 2.587e-13 Highly Informative Direct
Biological Process (BP) regulation of neuron projection development 3.234e-06 Highly Informative Direct
Biological Process (BP) axon development 2.94e-09 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in neuron differentiation 0 Highly Informative Direct
Biological Process (BP) cell projection morphogenesis 0 Highly Informative Direct
Biological Process (BP) chemotaxis 0 Highly Informative Direct
Biological Process (BP) regulation of behavior 0 Highly Informative Direct
Biological Process (BP) regulation of cell size 0 Highly Informative Direct
Biological Process (BP) positive regulation of response to external stimulus 0 Highly Informative Direct
Biological Process (BP) regulation of cell growth 1.411e-10 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 9.334e-08 Highly Informative Direct
Biological Process (BP) regulation of developmental growth 2.142e-07 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 4.603e-07 Highly Informative Direct
Biological Process (BP) negative regulation of growth 5.47e-07 Highly Informative Direct
Biological Process (BP) angiogenesis 9.665e-07 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 2.933e-05 Highly Informative Direct
Biological Process (BP) mesenchyme development 0.0001146 Highly Informative Direct
Biological Process (BP) positive regulation of cell migration 0.0002265 Highly Informative Direct
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0.0003793 Highly Informative Direct
Biological Process (BP) positive regulation of protein kinase activity 0.188 Highly Informative Inherited
Biological Process (BP) regulation of organ morphogenesis 0.3652 Highly Informative Inherited
Biological Process (BP) negative regulation of cell differentiation 0.004904 Highly Informative Inherited
Biological Process (BP) negative regulation of response to external stimulus 0.06438 Highly Informative Inherited
Biological Process (BP) protein phosphorylation 0.013 Highly Informative Inherited
Biological Process (BP) muscle organ development 0.3249 Highly Informative Inherited
Biological Process (BP) stem cell development 0.2696 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.1665 Highly Informative Inherited
Biological Process (BP) branching morphogenesis of an epithelial tube 0.359 Highly Informative Inherited
Molecular Function (MF) binding 1.036e-09 Least Informative Direct
Molecular Function (MF) anion binding 0.006161 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.1279 Moderately Informative Inherited
Molecular Function (MF) receptor binding 0 Informative Direct
Molecular Function (MF) molecular transducer activity 0 Informative Direct
Molecular Function (MF) receptor activity 0 Informative Direct
Molecular Function (MF) sulfur compound binding 1.458e-08 Informative Direct
Molecular Function (MF) carbohydrate derivative binding 1.127e-07 Informative Direct
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.03185 Informative Inherited
Molecular Function (MF) kinase activity 0.05707 Informative Inherited
Molecular Function (MF) heparin binding 1.989e-07 Highly Informative Direct
Molecular Function (MF) protein kinase activity 0.005705 Highly Informative Inherited
Cellular Component (CC) membrane 4.743e-11 Least Informative Direct
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) plasma membrane 6.598e-08 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 2.318e-06 Moderately Informative Direct
Cellular Component (CC) integral to membrane 4.76e-10 Informative Direct
Cellular Component (CC) receptor complex 4.843e-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)Receptor protein-tyrosine kinase0InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Mode of Inheritance (MI)Autosomal dominant inheritance0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0Least InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.001548Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.2119Least InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.004938Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.01322Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.0767Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.5422Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.6796Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology3.194e-05InformativeDirect
Mammalian Phenotype (MP)ectopic neuron0.002937InformativeInherited
Mammalian Phenotype (MP)abnormal metencephalon morphology0.008738InformativeInherited
Mammalian Phenotype (MP)abnormal neuron physiology0.02065InformativeInherited
Mammalian Phenotype (MP)abnormal cerebrum morphology0.3956InformativeInherited
Mammalian Phenotype (MP)ectopic cerebellar granule cells3.525e-08Highly InformativeDirect
Mammalian Phenotype (MP)abnormal amacrine cell morphology1.045e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal retinal inner plexiform layer morphology2.451e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal neuronal migration0.0001406Highly InformativeDirect
Mammalian Phenotype (MP)abnormal hippocampus morphology0.1978Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cranial nerve morphology0.2817Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organ system development variant0.0003446Moderately InformativeDirect
Worm Phenotype (WP)male morphology variant1.081e-11InformativeDirect
Worm Phenotype (WP)anchor cell invasion variant2.861e-09InformativeDirect
Worm Phenotype (WP)sensillum morphology variant3.069e-09InformativeDirect
Worm Phenotype (WP)male nervous system morphology variant4.286e-13Highly InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect
Fly Phenotype (FP)neuroanatomy defective0Moderately InformativeDirect

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
Fly Anatomy (FA)multi-tissue structure0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)multi-cell-component structure0Moderately 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)embryo0.4455Least InformativeInherited
Xenopus ANatomical entity (XAN)portion of tissue1Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.1921Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.2857Moderately InformativeInherited
Xenopus ANatomical entity (XAN)cranial placode0.0002138InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Protein-tyrosine kinases0InformativeDirect
Enzyme Commission (EC)Receptor protein-tyrosine kinase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation0Moderately InformativeDirect
Biological processNeurogenesis0InformativeDirect
Biological processAngiogenesis1.694e-13InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentSecreted4.037e-10Moderately InformativeDirect
DiseaseProto-oncogene0Moderately InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainRepeat8.22e-06Least InformativeDirect
DomainImmunoglobulin domain0InformativeDirect
Post-translational modificationTransferase0.1248Least InformativeInherited
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationTyrosine-protein kinase0Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationUbl conjugation6.998e-15Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001627 SSF101912 Protein matches
Abstract

The Sema domain occurs in semaphorins, which are a large family of secreted and transmembrane proteins, some of which function as repellent signals during axon guidance. Sema domains also occur in a hepatocyte growth factor receptor, in SEX protein [PubMed9875845] and in viral proteins.

CD100 (also called SEMA4D) is associated with PTPase and serine kinase activity. CD100 increases PMA, CD3 and CD2 induced T cell proliferation, increases CD45 induced T cell adhesion, induces B cell homotypic adhesion and down-regulates B cell expression of CD23.

The Sema domain is characterised by a conserved set of cysteine residues, which form four disulphide bonds to stabilise the structure. The Sema domain fold is a variation of the beta propeller topology, with seven blades radially arranged around a central axis. Each blade contains a four- stranded (strands A to D) antiparallel beta sheet. The inner strand of each blade (A) lines the channel at the centre of the propeller, with strands B and C of the same repeat radiating outward, and strand D of the next repeat forming the outer edge of the blade. The large size of the Sema domain is not due to a single inserted domain but results from the presence of additionnal secondary structure elements inserted in most of the blades. The Sema domain uses a 'loop and hook' system to close the circle between the first and the last blades. The blades are constructed sequentially with an N-terminal beta- strand closing the circle by providing the outermost strand (D) of the seventh (C-terminal) blade. The beta-propeller is further stabilized by an extension of the N-terminus, providing an additional, fifth beta-strand on the outer edge of blade 6 [PubMed12925274, PubMed12958590, PubMed15167892].

CD molecules are leucocyte antigens on cell surfaces. CD antigens nomenclature is updated at Protein Reviews On The Web (http://mpr.nci.nih.gov/prow/).


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · 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 3 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 Sema 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 3 hidden Markov models representing the Sema 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]