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 (141) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,599 3,801 3
Proteins 3,457 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)multicellular organismal process0.0000027060Least InformativeDirect
Biological Process (BP)developmental process0.00000089860Least InformativeDirect
Biological Process (BP)single-organism cellular process0.00000550Least InformativeDirect
Biological Process (BP)regulation of cellular process0.00025220Least InformativeDirect
Biological Process (BP)response to stimulus0.00093430Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.007760Least InformativeInherited
Biological Process (BP)localization0.0013680.001344Least InformativeInherited
Biological Process (BP)cell differentiation0.0000000060280Moderately InformativeDirect
Biological Process (BP)regulation of developmental process0.00030590.00000001771Moderately InformativeDirect
Biological Process (BP)anatomical structure morphogenesis0.062130.0000000000005487Moderately InformativeInherited
Biological Process (BP)tissue development0.0014770.3717Moderately InformativeInherited
Biological Process (BP)regulation of multicellular organismal process0.0010660Moderately InformativeInherited
Biological Process (BP)nervous system development0.0092990Moderately InformativeInherited
Biological Process (BP)regulation of cellular component organization0.0048850.00000001042Moderately InformativeInherited
Biological Process (BP)signal transduction0.053830Moderately InformativeInherited
Biological Process (BP)cellular component movement0.00000370InformativeDirect
Biological Process (BP)regulation of anatomical structure morphogenesis0.000000045610InformativeDirect
Biological Process (BP)cell projection organization0.00055980InformativeDirect
Biological Process (BP)locomotion0.00000000094530InformativeDirect
Biological Process (BP)generation of neurons0.00000014480InformativeDirect
Biological Process (BP)localization of cell0.00018890InformativeDirect
Biological Process (BP)regulation of cell development0.00000093490InformativeDirect
Biological Process (BP)epithelium development0.35010.2154InformativeInherited
Biological Process (BP)cellular component morphogenesis0.0038160InformativeInherited
Biological Process (BP)regulation of nervous system development0.023130.000001033InformativeInherited
Biological Process (BP)tissue morphogenesis0.0011590.003189InformativeInherited
Biological Process (BP)chemotaxis0.00000060580Highly InformativeDirect
Biological Process (BP)regulation of cell morphogenesis involved in differentiation0.00000002020.000000000000204Highly InformativeDirect
Biological Process (BP)regulation of neuron projection development0.000000033590.00000252Highly InformativeDirect
Biological Process (BP)neuron projection development0.00000040080Highly InformativeDirect
Biological Process (BP)cell part morphogenesis0.00000062170Highly InformativeDirect
Biological Process (BP)cell morphogenesis involved in differentiation0.010920Highly InformativeInherited
Molecular Function (MF)binding0.016950.000000002385Least InformativeInherited
Molecular Function (MF)receptor binding0.0004510InformativeDirect

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) multicellular organismal process 0 Least Informative Direct
Biological Process (BP) developmental process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0 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) 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) localization 0.001344 Least Informative Inherited
Biological Process (BP) signal transduction 0 Moderately Informative Direct
Biological Process (BP) nervous system development 0 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.0000000000005487 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 0.000001576 Moderately Informative Direct
Biological Process (BP) cell differentiation 0 Moderately Informative Direct
Biological Process (BP) regulation of localization 0 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.0003414 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 0.000000000001817 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.00008969 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.00000001771 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.00000001042 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.004394 Moderately Informative Inherited
Biological Process (BP) tissue development 0.3717 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.8146 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.9334 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) positive regulation of molecular function 0.3396 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) regulation of biological quality 0.1108 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.000006303 Informative Direct
Biological Process (BP) cellular component movement 0 Informative Direct
Biological Process (BP) central nervous system development 0.00009416 Informative Direct
Biological Process (BP) regulation of nucleoside metabolic process 0.000002408 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 0 Informative Direct
Biological Process (BP) cell projection organization 0 Informative Direct
Biological Process (BP) regulation of cellular catabolic process 0.0001439 Informative Direct
Biological Process (BP) regulation of response to external stimulus 0 Informative Direct
Biological Process (BP) cellular component morphogenesis 0 Informative Direct
Biological Process (BP) regulation of growth 0.00007145 Informative Direct
Biological Process (BP) locomotion 0 Informative Direct
Biological Process (BP) regulation of locomotion 0 Informative Direct
Biological Process (BP) single-organism behavior 0.00002234 Informative Direct
Biological Process (BP) generation of neurons 0 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.00005195 Informative Direct
Biological Process (BP) positive regulation of protein metabolic process 0.0001829 Informative Direct
Biological Process (BP) regulation of cellular component movement 0 Informative Direct
Biological Process (BP) organelle localization 0.0005653 Informative Direct
Biological Process (BP) localization of cell 0 Informative Direct
Biological Process (BP) regulation of nervous system development 0.000001033 Informative Direct
Biological Process (BP) regulation of cell development 0 Informative Direct
Biological Process (BP) regulation of anatomical structure size 0.00000000001987 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0.00001482 Informative Direct
Biological Process (BP) positive regulation of phosphate metabolic process 0.1354 Informative Inherited
Biological Process (BP) epithelium development 0.2154 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.003189 Informative Inherited
Biological Process (BP) gland development 0.1512 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.00363 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 0.05425 Informative Inherited
Biological Process (BP) muscle structure development 0.8339 Informative Inherited
Biological Process (BP) regulation of kinase activity 0.9721 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.1192 Informative Inherited
Biological Process (BP) muscle tissue development 0.5479 Informative Inherited
Biological Process (BP) positive regulation of transport 0.1803 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.09041 Informative Inherited
Biological Process (BP) tube development 0.007453 Informative Inherited
Biological Process (BP) cardiovascular system development 0.1519 Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0 Highly Informative Direct
Biological Process (BP) angiogenesis 0.00000091 Highly Informative Direct
Biological Process (BP) chemotaxis 0 Highly Informative Direct
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0.0004516 Highly Informative Direct
Biological Process (BP) regulation of cell size 0 Highly Informative Direct
Biological Process (BP) regulation of cell morphogenesis involved in differentiation 0.000000000000204 Highly Informative Direct
Biological Process (BP) regulation of neuron projection development 0.00000252 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 0.00004082 Highly Informative Direct
Biological Process (BP) negative regulation of cell growth 0.000000001361 Highly Informative Direct
Biological Process (BP) positive regulation of cell migration 0.0002208 Highly Informative Direct
Biological Process (BP) neuron projection development 0 Highly Informative Direct
Biological Process (BP) positive regulation of response to external stimulus 0 Highly Informative Direct
Biological Process (BP) cell part morphogenesis 0 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 0.0000008344 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 0.00000008535 Highly Informative Direct
Biological Process (BP) regulation of developmental growth 0.0000001011 Highly Informative Direct
Biological Process (BP) regulation of behavior 0 Highly Informative Direct
Biological Process (BP) mesenchyme development 0.000121 Highly Informative Direct
Biological Process (BP) positive regulation of protein kinase activity 0.1672 Highly Informative Inherited
Biological Process (BP) regulation of organ morphogenesis 0.3466 Highly Informative Inherited
Biological Process (BP) negative regulation of cell differentiation 0.004828 Highly Informative Inherited
Biological Process (BP) negative regulation of response to external stimulus 0.05804 Highly Informative Inherited
Biological Process (BP) protein phosphorylation 0.01409 Highly Informative Inherited
Biological Process (BP) muscle organ development 0.3538 Highly Informative Inherited
Biological Process (BP) stem cell development 0.2844 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.1588 Highly Informative Inherited
Biological Process (BP) branching morphogenesis of an epithelial tube 0.3487 Highly Informative Inherited
Molecular Function (MF) binding 0.000000002385 Least Informative Direct
Molecular Function (MF) transferase activity 0.8581 Least Informative Inherited
Molecular Function (MF) anion binding 0.008125 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.1439 Moderately Informative Inherited
Molecular Function (MF) receptor activity 0 Informative Direct
Molecular Function (MF) receptor binding 0 Informative Direct
Molecular Function (MF) molecular transducer activity 0 Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.000000114 Informative Direct
Molecular Function (MF) sulfur compound binding 0.00000001669 Informative Direct
Molecular Function (MF) kinase activity 0.06449 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.03581 Informative Inherited
Molecular Function (MF) heparin binding 0.0000001722 Highly Informative Direct
Molecular Function (MF) protein kinase activity 0.006561 Highly Informative Inherited
Cellular Component (CC) membrane 0.0000000001209 Least Informative Direct
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) plasma membrane 0.0000001464 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.000001852 Moderately Informative Direct
Cellular Component (CC) extracellular region part 0.0009961 Moderately Informative Direct
Cellular Component (CC) integral to membrane 0.0000000006568 Informative Direct
Cellular Component (CC) receptor complex 0.00005456 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 phenotype0.001614Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.2344Least InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.005478Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.01413Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.08339Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.5491Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.6776Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology0.0000366InformativeDirect
Mammalian Phenotype (MP)abnormal telencephalon morphology0.0008977InformativeDirect
Mammalian Phenotype (MP)ectopic neuron0.003146InformativeInherited
Mammalian Phenotype (MP)abnormal metencephalon morphology0.009404InformativeInherited
Mammalian Phenotype (MP)abnormal neuron physiology0.01995InformativeInherited
Mammalian Phenotype (MP)ectopic cerebellar granule cells0.00000003354Highly InformativeDirect
Mammalian Phenotype (MP)abnormal amacrine cell morphology0.00000179Highly InformativeDirect
Mammalian Phenotype (MP)abnormal retinal inner plexiform layer morphology0.000003331Highly InformativeDirect
Mammalian Phenotype (MP)abnormal neuronal migration0.00009616Highly InformativeDirect
Mammalian Phenotype (MP)abnormal hippocampus morphology0.1906Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cranial nerve morphology0.3013Highly 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 variant0.00000000001081InformativeDirect
Worm Phenotype (WP)anchor cell invasion variant0.000000002861InformativeDirect
Worm Phenotype (WP)sensillum morphology variant0.000000003069InformativeDirect
Worm Phenotype (WP)male nervous system morphology variant0.0000000000004286Highly InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
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)anatomical group0.1344Least InformativeInherited
Fly Anatomy (FA)larva0.2221Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)multi-cell-component structure0Moderately InformativeDirect
Fly Anatomy (FA)late embryo0.02809Moderately InformativeInherited
Fly Anatomy (FA)central nervous system0.04404Moderately InformativeInherited
Fly Anatomy (FA)developing material anatomical entity0.08607Moderately InformativeInherited
Fly Anatomy (FA)peripheral nervous system0.09581Moderately InformativeInherited
Fly Anatomy (FA)embryonic/larval peripheral nervous system0.000002743InformativeDirect
Fly Anatomy (FA)nerve0.00001619InformativeDirect
Fly Anatomy (FA)larval abdominal segment0.00005855InformativeDirect
Fly Anatomy (FA)neuromere0.0001514InformativeDirect
Fly Anatomy (FA)ipsilateral tract0.0005135InformativeDirect
Fly Anatomy (FA)embryonic/larval central nervous system0.3579InformativeInherited
Fly Anatomy (FA)abdominal segmental nerve0.0000000537Highly InformativeDirect
Fly Anatomy (FA)intersegmental nerve0.0000006472Highly InformativeDirect
Fly Anatomy (FA)fascicle0.000009226Highly InformativeDirect
Fly Anatomy (FA)presumptive embryonic/larval central nervous system0.000274Highly InformativeDirect
Fly Anatomy (FA)longitudinal connective0.0002828Highly 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)embryo0.4507Least InformativeInherited
Xenopus ANatomical entity (XAN)portion of tissue1Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.1997Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.2924Moderately InformativeInherited
Xenopus ANatomical entity (XAN)cranial placode0.0002352InformativeDirect

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 processAngiogenesis0.0000000000001658InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentSecreted0.0000000004093Moderately InformativeDirect
DiseaseProto-oncogene0Moderately InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainRepeat0.000008366Least InformativeDirect
DomainImmunoglobulin domain0InformativeDirect
Post-translational modificationTransferase0.125Least 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 conjugation0.00000000000001053Moderately 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 ]