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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)

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HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Mode of Inheritance (MI)Autosomal dominant inheritance0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.3435Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.4046Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.01599Moderately InformativeInherited
Phenotypic Abnormality (PA)Neoplasm0.02118Moderately InformativeInherited
Phenotypic Abnormality (PA)Neoplasm of the endocrine system0.01749InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.03658InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the thyroid gland0.06117InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.0001605Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0.1348Least InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.003038Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.006125Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal renal/urinary system morphology0.034Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.06133Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.461Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal renal/urinary system physiology0.5851Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.6645Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology0.0000235InformativeDirect
Mammalian Phenotype (MP)abnormal cerebellum morphology0.001078InformativeInherited
Mammalian Phenotype (MP)abnormal neuron physiology0.00991InformativeInherited
Mammalian Phenotype (MP)abnormal kidney physiology0.04883InformativeInherited
Mammalian Phenotype (MP)abnormal sensory neuron morphology0.06194InformativeInherited
Mammalian Phenotype (MP)abnormal limbic system morphology0.08779InformativeInherited
Mammalian Phenotype (MP)abnormal response to injury0.1095InformativeInherited
Mammalian Phenotype (MP)abnormal cerebral hemisphere morphology0.1384InformativeInherited
Mammalian Phenotype (MP)abnormal renal tubule morphology0.1593InformativeInherited
Mammalian Phenotype (MP)abnormal cranial nerve morphology0.3358InformativeInherited
Mammalian Phenotype (MP)ectopic cerebellar granule cells0.0000000002648Highly InformativeDirect
Mammalian Phenotype (MP)abnormal retinal inner plexiform layer morphology0.00000372Highly InformativeDirect
Mammalian Phenotype (MP)abnormal amacrine cell morphology0.000003957Highly InformativeDirect
Mammalian Phenotype (MP)abnormal hippocampal mossy fiber morphology0.0000461Highly InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to kidney reperfusion injury0.0001253Highly InformativeDirect
Mammalian Phenotype (MP)abnormal neuronal migration0.0003232Highly InformativeDirect
Mammalian Phenotype (MP)abnormal kidney epithelium morphology0.0004384Highly InformativeDirect
Mammalian Phenotype (MP)abnormal brain white matter morphology0.0369Highly 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 variant0.0001549Least InformativeDirect
Worm Phenotype (WP)cell development variant0.0002937Least InformativeDirect
Worm Phenotype (WP)neuron development variant0.00000001473Moderately InformativeDirect
Worm Phenotype (WP)nervous system morphology variant0.0000002156Moderately InformativeDirect
Worm Phenotype (WP)body region morphology variant0.00002456Moderately InformativeDirect
Worm Phenotype (WP)organism segment morphology variant0.00002456Moderately InformativeDirect
Worm Phenotype (WP)developmental morphology variant0.00002467Moderately InformativeDirect
Worm Phenotype (WP)adult body morphology variant0.00002477Moderately InformativeDirect
Worm Phenotype (WP)body morphology variant0.00002744Moderately InformativeDirect
Worm Phenotype (WP)reproductive system development variant0.00004022Moderately InformativeDirect
Worm Phenotype (WP)male morphology variant0.0000000001106InformativeDirect
Worm Phenotype (WP)axon outgrowth variant0.0000000004048InformativeDirect
Worm Phenotype (WP)anchor cell invasion variant0.000000002505InformativeDirect
Worm Phenotype (WP)sensillum morphology variant0.00000001186InformativeDirect
Worm Phenotype (WP)male ray morphology variant0.000000000004703Highly InformativeDirect
Worm Phenotype (WP)axon guidance variant0.00000000003398Highly 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)

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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)multi-cell-component structure0Moderately InformativeDirect
Fly Anatomy (FA)sensory system0Moderately InformativeDirect
Fly Anatomy (FA)embryo0.08273Moderately InformativeInherited
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 system0.003406InformativeInherited
Fly Anatomy (FA)tract0.2029InformativeInherited
Fly Anatomy (FA)intersegmental nerve0Highly InformativeDirect
Fly Anatomy (FA)abdominal segmental nerve0Highly InformativeDirect
Fly Anatomy (FA)fascicle0.0000009997Highly InformativeDirect
Fly Anatomy (FA)connective0.00002412Highly InformativeDirect
Fly Anatomy (FA)presumptive embryonic/larval central nervous system0.00005367Highly InformativeDirect
Fly Anatomy (FA)neuron projection bundle of ventral nerve cord0.0009129Highly InformativeDirect

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

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ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)nervous system0.3335Least InformativeInherited
Zebrafish Anatomy (ZA)cell0.4563Least InformativeInherited
Zebrafish Anatomy (ZA)electrically active cell0.05273Moderately InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.3547Moderately InformativeInherited
Zebrafish Anatomy (ZA)neuron0.01372InformativeInherited
Zebrafish Anatomy (ZA)primary germ layer0.01704InformativeInherited
Zebrafish Anatomy (ZA)primary motor neuron0.00003745Highly InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

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XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.2174Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.5737Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.7641Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical system1Least InformativeInherited
Xenopus ANatomical entity (XAN)sensory system0.00002886Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.0001544Moderately InformativeDirect
Xenopus ANatomical entity (XAN)embryonic structure0.0008058Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0.05012Moderately InformativeInherited
Xenopus ANatomical entity (XAN)cranial placode0.00000002275InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0.09213InformativeInherited
Xenopus ANatomical entity (XAN)vestibuloauditory system0.6114InformativeInherited
Xenopus ANatomical entity (XAN)otic placode0.000006855Highly InformativeDirect
Xenopus ANatomical entity (XAN)periocular region0.000006969Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.000007695Highly InformativeDirect
Xenopus ANatomical entity (XAN)presumptive midbrain-hindbrain boundary0.0002194Highly InformativeDirect
Xenopus ANatomical entity (XAN)involuted dorsal mesoderm0.0002699Highly InformativeDirect
Xenopus ANatomical entity (XAN)branchial arch0.0003474Highly InformativeDirect
Xenopus ANatomical entity (XAN)anatomical line0.0005901Highly 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 ]