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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 (130) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 3,637 3,612 5
Proteins 3,429 3,413 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

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) 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) localization 1.354e-05 Least Informative Direct
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.005336 Least Informative Inherited
Biological Process (BP) regulation of developmental process 0 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 0 Moderately Informative Direct
Biological Process (BP) nervous system development 0 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 1.797e-11 Moderately Informative Direct
Biological Process (BP) signal transduction 9.072e-11 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 1.983e-09 Moderately Informative Direct
Biological Process (BP) regulation of localization 2.771e-09 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 1.404e-08 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0.0007841 Moderately Informative Direct
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.004415 Moderately Informative Inherited
Biological Process (BP) immune system process 0.001237 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.3373 Moderately Informative Inherited
Biological Process (BP) homeostatic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.02093 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) tissue development 0.6365 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.3472 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.5025 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.3328 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.7704 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) generation of neurons 0 Informative Direct
Biological Process (BP) regulation of cellular component movement 0 Informative Direct
Biological Process (BP) biological adhesion 0 Informative Direct
Biological Process (BP) cellular component morphogenesis 0 Informative Direct
Biological Process (BP) regulation of locomotion 0 Informative Direct
Biological Process (BP) locomotion 0 Informative Direct
Biological Process (BP) response to external stimulus 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 movement 3.329e-14 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 1.12e-10 Informative Direct
Biological Process (BP) regulation of anatomical structure size 5.159e-07 Informative Direct
Biological Process (BP) response to wounding 6.893e-07 Informative Direct
Biological Process (BP) positive regulation of signal transduction 3.52e-06 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 4.921e-06 Informative Direct
Biological Process (BP) regulation of nervous system development 1.785e-05 Informative Direct
Biological Process (BP) regulation of response to external stimulus 6.556e-05 Informative Direct
Biological Process (BP) single-organism behavior 8.176e-05 Informative Direct
Biological Process (BP) regulation of growth 0.0003478 Informative Direct
Biological Process (BP) negative regulation of developmental process 0.000409 Informative Direct
Biological Process (BP) positive regulation of phosphorus metabolic process 0.0005718 Informative Direct
Biological Process (BP) positive regulation of protein metabolic process 0.0006735 Informative Direct
Biological Process (BP) tissue morphogenesis 0.01144 Informative Inherited
Biological Process (BP) gland development 0.1639 Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 1 Informative Inherited
Biological Process (BP) cell activation 0.07902 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 0.06755 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 0.5404 Informative Inherited
Biological Process (BP) tube development 0.003019 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.006412 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.0256 Informative Inherited
Biological Process (BP) muscle tissue development 0.3991 Informative Inherited
Biological Process (BP) regulation of cell development 0.001219 Informative Inherited
Biological Process (BP) central nervous system development 0.02082 Informative Inherited
Biological Process (BP) epithelium development 0.1252 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.06218 Informative Inherited
Biological Process (BP) cardiovascular system development 0.0353 Informative Inherited
Biological Process (BP) chemotaxis 0 Highly Informative Direct
Biological Process (BP) regulation of cell projection organization 5.43e-14 Highly Informative Direct
Biological Process (BP) regulation of cell morphogenesis 9.526e-14 Highly Informative Direct
Biological Process (BP) cell adhesion 2.313e-12 Highly Informative Direct
Biological Process (BP) regulation of cellular component size 3.79e-09 Highly Informative Direct
Biological Process (BP) positive regulation of MAPK cascade 6.255e-08 Highly Informative Direct
Biological Process (BP) angiogenesis 1.663e-07 Highly Informative Direct
Biological Process (BP) regulation of behavior 2.594e-07 Highly Informative Direct
Biological Process (BP) axonogenesis 2.715e-06 Highly Informative Direct
Biological Process (BP) regulation of Ras protein signal transduction 3.032e-05 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 5.418e-05 Highly Informative Direct
Biological Process (BP) regulation of developmental growth 8.398e-05 Highly Informative Direct
Biological Process (BP) organelle localization 8.435e-05 Highly Informative Direct
Biological Process (BP) negative regulation of cell growth 0.0001698 Highly Informative Direct
Biological Process (BP) regulation of purine nucleotide catabolic process 0.0003703 Highly Informative Direct
Biological Process (BP) regulation of nucleoside metabolic process 0.0004725 Highly Informative Direct
Biological Process (BP) leukocyte migration 0.0005546 Highly Informative Direct
Biological Process (BP) morphogenesis of a branching epithelium 0.001566 Highly Informative Inherited
Biological Process (BP) regulation of neuron differentiation 0.0244 Highly Informative Inherited
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0.01567 Highly Informative Inherited
Biological Process (BP) negative regulation of cell development 0.2335 Highly Informative Inherited
Biological Process (BP) stem cell development 0.6728 Highly Informative Inherited
Biological Process (BP) epithelial tube morphogenesis 0.07495 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.1298 Highly Informative Inherited
Molecular Function (MF) binding 4.288e-14 Least Informative Direct
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) protein binding 4.179e-13 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.3979 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) protein dimerization activity 0.7584 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.1563 Informative Inherited
Molecular Function (MF) kinase activity 0.2313 Informative Inherited
Molecular Function (MF) protein complex binding 1.898e-14 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 7.987e-06 Highly Informative Direct
Molecular Function (MF) protein kinase activity 0.07299 Highly Informative Inherited
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) protein complex 0.009876 Least Informative Inherited
Cellular Component (CC) plasma membrane 0 Moderately Informative Direct
Cellular Component (CC) extracellular region 0.0002717 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.0006073 Moderately Informative Direct
Cellular Component (CC) integral to membrane 0 Informative Direct
Cellular Component (CC) cell surface 3.129e-15 Informative Direct
Cellular Component (CC) cell leading edge 1.053e-07 Informative Direct
Cellular Component (CC) cell junction 7.374e-05 Informative Direct
Cellular Component (CC) intrinsic to plasma membrane 0.0006398 Informative Direct
Cellular Component (CC) receptor complex 0 Highly Informative Direct
Cellular Component (CC) cell-substrate junction 1.48e-06 Highly Informative Direct
Cellular Component (CC) adherens junction 0.0002182 Highly Informative Direct
Cellular Component (CC) integral to plasma membrane 0.001869 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 disease0.2055Least InformativeInherited
Disease Ontology (DO)skin disease0.1159Moderately InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.2012Moderately InformativeInherited
Disease Ontology (DO)dermatitis herpetiformis1.126e-06InformativeDirect
Disease Ontology (DO)bullous pemphigoid6.643e-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 phenotype0.005391Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.01916Least InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.001639Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.003372Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.1586Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.5637Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.9143Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell migration3.657e-06InformativeDirect
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology0.0009727InformativeDirect
Mammalian Phenotype (MP)abnormal neuron physiology0.003911InformativeInherited
Mammalian Phenotype (MP)abnormal hindbrain morphology0.1517InformativeInherited
Mammalian Phenotype (MP)abnormal cerebrum morphology0.3362InformativeInherited
Mammalian Phenotype (MP)ectopic cerebellar granule cells3.297e-09Highly InformativeDirect
Mammalian Phenotype (MP)abnormal amacrine cell morphology3.384e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal hippocampal mossy fiber morphology7.079e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal retinal inner plexiform layer morphology0.0002213Highly InformativeDirect
Mammalian Phenotype (MP)abnormal retinal ganglion cell morphology0.0004172Highly InformativeDirect
Mammalian Phenotype (MP)abnormal neuronal migration0.0004612Highly InformativeDirect

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

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)larva0.1587Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)multi-cell-component structure0Moderately InformativeDirect
Fly Anatomy (FA)anatomical group0.005705Moderately InformativeInherited
Fly Anatomy (FA)late embryo0.009259Moderately InformativeInherited
Fly Anatomy (FA)peripheral nervous system0.05711Moderately InformativeInherited
Fly Anatomy (FA)adult segment0.2976Moderately InformativeInherited
Fly Anatomy (FA)head0.6171Moderately InformativeInherited
Fly Anatomy (FA)neuromere1.185e-05InformativeDirect
Fly Anatomy (FA)embryonic/larval peripheral nervous system0.0001616InformativeDirect
Fly Anatomy (FA)larval abdominal segment0.0002046InformativeDirect
Fly Anatomy (FA)labral segment0.0004776InformativeDirect
Fly Anatomy (FA)adult procephalic segment0.001664InformativeInherited
Fly Anatomy (FA)nerve0.002461InformativeInherited
Fly Anatomy (FA)ganglion0.006052InformativeInherited
Fly Anatomy (FA)adult central nervous system0.01509InformativeInherited
Fly Anatomy (FA)brain0.05374InformativeInherited
Fly Anatomy (FA)tract0.4768InformativeInherited
Fly Anatomy (FA)intersegmental nerve1.596e-06Highly InformativeDirect
Fly Anatomy (FA)adult labral segment0.0001538Highly InformativeDirect
Fly Anatomy (FA)protocerebrum0.6146Highly InformativeInherited

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

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XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.5065Least InformativeInherited
Xenopus ANatomical entity (XAN)portion of tissue1Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.133Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.2965Moderately InformativeInherited
Xenopus ANatomical entity (XAN)cranial placode0.0002697Highly InformativeDirect

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 interaction2.68e-05Moderately InformativeDirect
Biological processCell adhesion0InformativeDirect
Biological processNeurogenesis0InformativeDirect
Biological processAngiogenesis7.409e-13InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentSecreted2.749e-05Moderately InformativeDirect
DiseaseProto-oncogene0Moderately InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainRepeat5.03e-14Least InformativeDirect
DomainImmunoglobulin domain0InformativeDirect
Post-translational modificationTransferase0.9822Least InformativeInherited
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationKinase2.066e-14Moderately InformativeDirect
Post-translational modificationTyrosine-protein kinase0Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationUbl conjugation1.917e-11Moderately InformativeDirect
Post-translational modificationPyrrolidone carboxylic acid0.0009777InformativeDirect

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 ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

Please send feedback, comments or questions to superfamily@cs.bris.ac.uk or use the feedback form.

© Copyright 2013 The SUPERFAMILY authors and Julian Gough.