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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 (147) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 3,650 10,052 3
Proteins 3,507 9,882 3


Functional annotation
General category Processes_EC
Detailed category Cell adhesion

Document:
Function annotation of SCOP domain superfamilies

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 nervous system physiology0.139Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.4451Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the ear0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the nose0.05339Moderately InformativeInherited
Phenotypic Abnormality (PA)Hearing impairment0.0004742InformativeDirect
Phenotypic Abnormality (PA)Functional abnormality of the inner ear0.0006256InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the sense of smell0.0002501Highly 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 phenotype0.0003688Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0.1706Least InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.003084Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.008152Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal renal/urinary system morphology0.01511Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.06128Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.4624Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal renal/urinary system physiology0.4875Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.6643Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology0.00003171InformativeDirect
Mammalian Phenotype (MP)abnormal metencephalon morphology0.002069InformativeInherited
Mammalian Phenotype (MP)abnormal neuron physiology0.00992InformativeInherited
Mammalian Phenotype (MP)abnormal kidney physiology0.01695InformativeInherited
Mammalian Phenotype (MP)abnormal response to injury0.04863InformativeInherited
Mammalian Phenotype (MP)abnormal sensory neuron morphology0.0617InformativeInherited
Mammalian Phenotype (MP)abnormal limbic system morphology0.0878InformativeInherited
Mammalian Phenotype (MP)abnormal renal tubule morphology0.1097InformativeInherited
Mammalian Phenotype (MP)abnormal cerebral hemisphere morphology0.1385InformativeInherited
Mammalian Phenotype (MP)abnormal cranial nerve morphology0.3359InformativeInherited
Mammalian Phenotype (MP)ectopic cerebellar granule cells0.0000000003472Highly InformativeDirect
Mammalian Phenotype (MP)abnormal retinal inner plexiform layer morphology0.000003716Highly InformativeDirect
Mammalian Phenotype (MP)abnormal amacrine cell morphology0.000003951Highly InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to kidney reperfusion injury0.000005144Highly InformativeDirect
Mammalian Phenotype (MP)abnormal hippocampal mossy fiber morphology0.00004611Highly InformativeDirect
Mammalian Phenotype (MP)abnormal kidney epithelium morphology0.00006577Highly InformativeDirect
Mammalian Phenotype (MP)abnormal neuronal migration0.0003231Highly InformativeDirect
Mammalian Phenotype (MP)abnormal brain white matter morphology0.0368Highly 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 morphology variant0.0001371Least InformativeDirect
Worm Phenotype (WP)cell development variant0.0002379Least InformativeDirect
Worm Phenotype (WP)nervous system morphology variant0.0000001912Moderately InformativeDirect
Worm Phenotype (WP)reproductive system development variant0.00003744Moderately InformativeDirect
Worm Phenotype (WP)male morphology variant0.0000000001009InformativeDirect
Worm Phenotype (WP)axon outgrowth variant0.0000000003905InformativeDirect
Worm Phenotype (WP)anchor cell invasion variant0.000000002321InformativeDirect
Worm Phenotype (WP)sensillum morphology variant0.00000001032InformativeDirect
Worm Phenotype (WP)male ray morphology variant0.000000000004292Highly InformativeDirect
Worm Phenotype (WP)axon guidance variant0.00000000003236Highly InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

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

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)larva0Least InformativeDirect
Fly Anatomy (FA)adult0Least InformativeDirect
Fly Anatomy (FA)nervous system0Least InformativeDirect
Fly Anatomy (FA)multi-tissue structure0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect
Fly Anatomy (FA)somatic cell0Least InformativeDirect
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)central nervous system0Moderately InformativeDirect
Fly Anatomy (FA)peripheral nervous system0Moderately InformativeDirect
Fly Anatomy (FA)neuron0Moderately InformativeDirect
Fly Anatomy (FA)ganglion0Moderately InformativeDirect
Fly Anatomy (FA)late embryo0Moderately InformativeDirect
Fly Anatomy (FA)multi-cell-component structure0Moderately InformativeDirect
Fly Anatomy (FA)sensory system0Moderately InformativeDirect
Fly Anatomy (FA)abdominal segment0InformativeDirect
Fly Anatomy (FA)ventral nerve cord0InformativeDirect
Fly Anatomy (FA)larval segment0InformativeDirect
Fly Anatomy (FA)larval abdomen0InformativeDirect
Fly Anatomy (FA)nerve0InformativeDirect
Fly Anatomy (FA)embryonic/larval peripheral nervous system0InformativeDirect
Fly Anatomy (FA)presumptive embryonic/larval system0.03905InformativeInherited
Fly Anatomy (FA)tract0.2083InformativeInherited
Fly Anatomy (FA)intersegmental nerve0Highly InformativeDirect
Fly Anatomy (FA)abdominal segmental nerve0Highly InformativeDirect
Fly Anatomy (FA)fascicle0.0000008494Highly InformativeDirect
Fly Anatomy (FA)connective0.00002275Highly InformativeDirect
Fly Anatomy (FA)presumptive embryonic/larval central nervous system0.00005452Highly InformativeDirect

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)nervous system0.317Least InformativeInherited
Zebrafish Anatomy (ZA)cell0.4479Least InformativeInherited
Zebrafish Anatomy (ZA)electrically active cell0.05201Moderately InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.3255Moderately InformativeInherited
Zebrafish Anatomy (ZA)neuron0.01449InformativeInherited
Zebrafish Anatomy (ZA)primary germ layer0.01786InformativeInherited
Zebrafish Anatomy (ZA)primary motor neuron0.00003939Highly InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.2014Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.5738Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.7055Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.7524Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical system1Least InformativeInherited
Xenopus ANatomical entity (XAN)sensory system0.00002376Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.0000855Moderately InformativeDirect
Xenopus ANatomical entity (XAN)embryonic structure0.0005601Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0.04492Moderately InformativeInherited
Xenopus ANatomical entity (XAN)brain0.2322Moderately InformativeInherited
Xenopus ANatomical entity (XAN)cranial placode0.00000001628InformativeDirect
Xenopus ANatomical entity (XAN)neural plate0.001036InformativeInherited
Xenopus ANatomical entity (XAN)pharyngeal region0.06305InformativeInherited
Xenopus ANatomical entity (XAN)vestibuloauditory system0.5177InformativeInherited
Xenopus ANatomical entity (XAN)cranial neural crest0.000007155Highly InformativeDirect
Xenopus ANatomical entity (XAN)otic placode0.000009379Highly InformativeDirect
Xenopus ANatomical entity (XAN)presumptive midbrain-hindbrain boundary0.0002163Highly InformativeDirect
Xenopus ANatomical entity (XAN)branchial arch0.0002836Highly InformativeDirect
Xenopus ANatomical entity (XAN)involuted dorsal mesoderm0.0002843Highly InformativeDirect
Xenopus ANatomical entity (XAN)midbrain-hindbrain boundary0.0008158Highly InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

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

Document: EC 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 · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) ]

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 · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · Internal database links ]