SUPERFAMILY 1.75 HMM library and genome assignments server


Plexin repeat superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   Trefoil/Plexin domain-like [ 57491] (3)
Superfamily:   Plexin repeat [ 103575]
Families:   Plexin repeat [ 103576] (3)


Superfamily statistics
Genomes (145) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 4,047 4,287 5
Proteins 3,814 4,046 5


Functional annotation
General category Regulation
Detailed category Receptor activity

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)single-organism cellular process00Least InformativeDirect
Biological Process (BP)regulation of cellular process03.869e-05Least InformativeDirect
Biological Process (BP)localization0.0006847.94e-07Least InformativeDirect
Biological Process (BP)biological adhesion1.282e-080InformativeDirect
Biological Process (BP)localization of cell2.943e-080InformativeDirect
Biological Process (BP)locomotion3.592e-070InformativeDirect
Biological Process (BP)cellular component movement8.543e-050InformativeDirect
Biological Process (BP)cell adhesion1.859e-062.863e-11Highly InformativeDirect
Cellular Component (CC)membrane0.00060620Least InformativeDirect
Cellular Component (CC)cell surface6.995e-090InformativeDirect

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) single-organism cellular process 0 Least Informative Direct
Biological Process (BP) regulation of cellular process 3.869e-05 Least Informative Direct
Biological Process (BP) localization 7.94e-07 Least Informative Direct
Biological Process (BP) developmental process 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0 Least Informative Direct
Biological Process (BP) multicellular organismal process 0 Least Informative Direct
Biological Process (BP) response to stimulus 0 Least Informative Direct
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) signal transduction 0 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0 Moderately Informative Direct
Biological Process (BP) regulation of localization 0 Moderately Informative Direct
Biological Process (BP) nervous system development 0 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 1.798e-12 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 4.165e-12 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 9.944e-11 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 1.927e-08 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 6.698e-07 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 1.395e-05 Moderately Informative Direct
Biological Process (BP) immune system process 0.002216 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.02038 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) regulation of catalytic activity 0.007967 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.03433 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.02037 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) tissue development 0.2918 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.4426 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) biological adhesion 0 Informative Direct
Biological Process (BP) localization of cell 0 Informative Direct
Biological Process (BP) locomotion 0 Informative Direct
Biological Process (BP) cellular component movement 0 Informative Direct
Biological Process (BP) generation of neurons 0 Informative Direct
Biological Process (BP) regulation of cellular component movement 0 Informative Direct
Biological Process (BP) cellular component morphogenesis 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) cell projection organization 0 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 2.594e-11 Informative Direct
Biological Process (BP) regulation of establishment of protein localization 9.316e-08 Informative Direct
Biological Process (BP) response to wounding 5.83e-06 Informative Direct
Biological Process (BP) central nervous system development 1.368e-05 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 1.734e-05 Informative Direct
Biological Process (BP) regulation of nervous system development 1.878e-05 Informative Direct
Biological Process (BP) regulation of nucleoside metabolic process 2.817e-05 Informative Direct
Biological Process (BP) regulation of cell development 2.887e-05 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0.0001419 Informative Direct
Biological Process (BP) negative regulation of developmental process 0.0002868 Informative Direct
Biological Process (BP) organelle localization 0.0005502 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.0005588 Informative Direct
Biological Process (BP) single-organism behavior 0.0006894 Informative Direct
Biological Process (BP) tissue morphogenesis 0.004362 Informative Inherited
Biological Process (BP) gland development 0.2039 Informative Inherited
Biological Process (BP) regulation of growth 0.003851 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) leukocyte activation 0.04073 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.002889 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.002561 Informative Inherited
Biological Process (BP) growth 0.002616 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.9689 Informative Inherited
Biological Process (BP) epithelium development 0.7179 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.005427 Informative Inherited
Biological Process (BP) tube development 0.002998 Informative Inherited
Biological Process (BP) cardiovascular system development 0.02071 Informative Inherited
Biological Process (BP) cell adhesion 2.863e-11 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in differentiation 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) chemotaxis 0 Highly Informative Direct
Biological Process (BP) cell part morphogenesis 3.263e-13 Highly Informative Direct
Biological Process (BP) neuron projection development 1.872e-09 Highly Informative Direct
Biological Process (BP) regulation of cell morphogenesis involved in differentiation 2.895e-09 Highly Informative Direct
Biological Process (BP) angiogenesis 2.208e-08 Highly Informative Direct
Biological Process (BP) negative regulation of cell growth 1.422e-06 Highly Informative Direct
Biological Process (BP) regulation of developmental growth 3.46e-06 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 4.942e-06 Highly Informative Direct
Biological Process (BP) cell junction organization 5.886e-06 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 6.34e-06 Highly Informative Direct
Biological Process (BP) regulation of neuron projection development 1.061e-05 Highly Informative Direct
Biological Process (BP) leukocyte migration 5.347e-05 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 0.000114 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 0.0005433 Highly Informative Direct
Biological Process (BP) cell growth 0.0007457 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 0.0009714 Highly Informative Direct
Biological Process (BP) positive regulation of cell migration 0.00185 Highly Informative Inherited
Biological Process (BP) negative regulation of response to external stimulus 0.1824 Highly Informative Inherited
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0.8074 Highly Informative Inherited
Biological Process (BP) mesenchyme development 0.003854 Highly Informative Inherited
Biological Process (BP) stem cell development 0.4099 Highly Informative Inherited
Biological Process (BP) positive regulation of epithelial cell proliferation 0.01864 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.1587 Highly Informative Inherited
Biological Process (BP) branching morphogenesis of an epithelial tube 0.1857 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) anion binding 0.07619 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.6763 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 4.978e-06 Informative Direct
Molecular Function (MF) carbohydrate derivative binding 2.611e-05 Informative Direct
Molecular Function (MF) protein dimerization activity 0.1404 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.3511 Informative Inherited
Molecular Function (MF) kinase activity 0.4712 Informative Inherited
Molecular Function (MF) protein complex binding 5.922e-13 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 7.156e-12 Highly Informative Direct
Molecular Function (MF) heparin binding 1.673e-06 Highly Informative Direct
Molecular Function (MF) protein kinase activity 0.1345 Highly Informative Inherited
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) protein complex 0.0297 Least Informative Inherited
Cellular Component (CC) plasma membrane 0 Moderately Informative Direct
Cellular Component (CC) extracellular region part 1.725e-08 Moderately Informative Direct
Cellular Component (CC) cell projection 3.169e-06 Moderately Informative Direct
Cellular Component (CC) vesicle 0.0006194 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.02297 Moderately Informative Inherited
Cellular Component (CC) cell surface 0 Informative Direct
Cellular Component (CC) integral to membrane 0 Informative Direct
Cellular Component (CC) cell leading edge 6.273e-09 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 2.839e-06 Informative Direct
Cellular Component (CC) cell junction 1.964e-05 Informative Direct
Cellular Component (CC) intrinsic to plasma membrane 0.01625 Informative Inherited
Cellular Component (CC) receptor complex 0 Highly Informative Direct
Cellular Component (CC) adherens junction 6.779e-06 Highly Informative Direct
Cellular Component (CC) cell projection membrane 7.749e-05 Highly Informative Direct
Cellular Component (CC) integral to plasma membrane 0.002208 Highly Informative Inherited

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

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)immune system disease0.09775Least InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.0808Moderately InformativeInherited
Disease Ontology (DO)skin disease0.2039Moderately InformativeInherited
Disease Ontology (DO)dermatitis herpetiformis6.223e-07InformativeDirect
Disease Ontology (DO)bullous pemphigoid6.888e-05InformativeDirect

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.005989Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.04065Least InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.0005151Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal neuron morphology0.001672Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.09895Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.4973Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.541Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology0.0002448InformativeDirect
Mammalian Phenotype (MP)ectopic neuron0.001095InformativeInherited
Mammalian Phenotype (MP)abnormal metencephalon morphology0.008768InformativeInherited
Mammalian Phenotype (MP)abnormal neuron physiology0.04473InformativeInherited
Mammalian Phenotype (MP)abnormal cerebrum morphology0.3497InformativeInherited
Mammalian Phenotype (MP)ectopic cerebellar granule cells2.666e-09Highly InformativeDirect
Mammalian Phenotype (MP)abnormal retinal inner plexiform layer morphology2.868e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal amacrine cell morphology1.408e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal neuronal migration0.0004389Highly InformativeDirect
Mammalian Phenotype (MP)abnormal hippocampus morphology0.2882Highly 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)anchor cell invasion variant2.861e-09InformativeDirect
Worm Phenotype (WP)male morphology variant5.127e-09InformativeDirect
Worm Phenotype (WP)sensillum morphology variant5.455e-07InformativeDirect
Worm Phenotype (WP)male nervous system morphology variant3.534e-10Highly 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
Fly Phenotype (FP)sensory perception defective0.0007181InformativeDirect

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)organ system subdivision0Least InformativeDirect
Fly Anatomy (FA)multi-tissue structure0.05061Least InformativeInherited
Fly Anatomy (FA)larva0.1209Least InformativeInherited
Fly Anatomy (FA)anatomical group0.2177Least InformativeInherited
Fly Anatomy (FA)adult0.226Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)multi-cell-component structure8.947e-05Moderately InformativeDirect
Fly Anatomy (FA)late embryo0.005613Moderately InformativeInherited
Fly Anatomy (FA)peripheral nervous system0.03595Moderately InformativeInherited
Fly Anatomy (FA)central nervous system0.06762Moderately InformativeInherited
Fly Anatomy (FA)adult head0.1924Moderately InformativeInherited
Fly Anatomy (FA)adult nervous system0.1931Moderately InformativeInherited
Fly Anatomy (FA)adult segment0.5198Moderately InformativeInherited
Fly Anatomy (FA)larval abdominal segment3.27e-05InformativeDirect
Fly Anatomy (FA)neuromere0.0001018InformativeDirect
Fly Anatomy (FA)ipsilateral tract0.0001252InformativeDirect
Fly Anatomy (FA)embryonic/larval peripheral nervous system0.001439InformativeInherited
Fly Anatomy (FA)labral segment0.001664InformativeInherited
Fly Anatomy (FA)adult brain0.002158InformativeInherited
Fly Anatomy (FA)synaptic neuropil0.002183InformativeInherited
Fly Anatomy (FA)adult procephalic segment0.004986InformativeInherited
Fly Anatomy (FA)nerve0.0116InformativeInherited
Fly Anatomy (FA)supraesophageal ganglion0.04705InformativeInherited
Fly Anatomy (FA)fascicle7.632e-07Highly InformativeDirect
Fly Anatomy (FA)intersegmental nerve1.195e-05Highly 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)embryo0.5312Least InformativeInherited
Xenopus ANatomical entity (XAN)portion of tissue1Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.1701Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.3177Moderately InformativeInherited
Xenopus ANatomical entity (XAN)cranial placode3.294e-05InformativeDirect

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 processHost-virus interaction3.221e-05Moderately InformativeDirect
Biological processCell adhesion0InformativeDirect
Biological processNeurogenesis0InformativeDirect
Biological processAngiogenesis1.699e-12InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCell projection1.322e-10Moderately InformativeDirect
Cellular componentEndosome8.016e-07Moderately InformativeDirect
Cellular componentCell junction6.323e-06Moderately InformativeDirect
Cellular componentSecreted2.579e-05Moderately InformativeDirect
DiseaseProto-oncogene0Moderately InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainRepeat9.229e-16Least InformativeDirect
DomainImmunoglobulin domain0InformativeDirect
Post-translational modificationTransferase0.946Least InformativeInherited
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationKinase2.412e-14Moderately InformativeDirect
Post-translational modificationTyrosine-protein kinase0Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationUbl conjugation5.605e-11Moderately InformativeDirect
Post-translational modificationPyrrolidone carboxylic acid0.0007047InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · 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 4 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 Plexin repeat 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 4 hidden Markov models representing the Plexin repeat 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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]