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 (144) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 4,020 4,287 5
Proteins 3,788 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 process00.00004078Least InformativeDirect
Biological Process (BP)localization0.0006920.0000009216Least InformativeDirect
Biological Process (BP)cellular component movement0.000085540InformativeDirect
Biological Process (BP)biological adhesion0.000000013790InformativeDirect
Biological Process (BP)locomotion0.00000035350InformativeDirect
Biological Process (BP)localization of cell0.000000029040InformativeDirect
Biological Process (BP)cell adhesion0.0000019180.00000000002569Highly InformativeDirect
Cellular Component (CC)membrane0.00062310Least InformativeDirect
Cellular Component (CC)cell surface0.0000000070340InformativeDirect

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 0.00004078 Least Informative Direct
Biological Process (BP) response to stimulus 0 Least Informative Direct
Biological Process (BP) localization 0.0000009216 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) signal transduction 0 Moderately Informative Direct
Biological Process (BP) nervous system development 0 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.000000000001924 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 0.00001472 Moderately Informative Direct
Biological Process (BP) regulation of localization 0 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 0.00000000009191 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.0000008071 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.0000000219 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0 Moderately Informative Direct
Biological Process (BP) immune system process 0.002224 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 0.02394 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 0.007253 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.03453 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.01883 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) tissue development 0.2952 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.4554 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.00001957 Informative Direct
Biological Process (BP) cellular component movement 0 Informative Direct
Biological Process (BP) central nervous system development 0.00001482 Informative Direct
Biological Process (BP) regulation of nucleoside metabolic process 0.00002025 Informative Direct
Biological Process (BP) response to wounding 0.000005966 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 0.00000000002373 Informative Direct
Biological Process (BP) biological adhesion 0 Informative Direct
Biological Process (BP) cell projection organization 0 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) locomotion 0 Informative Direct
Biological Process (BP) regulation of locomotion 0 Informative Direct
Biological Process (BP) single-organism behavior 0.00004701 Informative Direct
Biological Process (BP) generation of neurons 0 Informative Direct
Biological Process (BP) negative regulation of developmental process 0.0003076 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.000584 Informative Direct
Biological Process (BP) regulation of cellular component movement 0 Informative Direct
Biological Process (BP) organelle localization 0.0005545 Informative Direct
Biological Process (BP) localization of cell 0 Informative Direct
Biological Process (BP) regulation of nervous system development 0.00001782 Informative Direct
Biological Process (BP) regulation of cell development 0.00003447 Informative Direct
Biological Process (BP) regulation of anatomical structure size 0.00000001156 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0.0001143 Informative Direct
Biological Process (BP) regulation of protein localization 1 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.004186 Informative Inherited
Biological Process (BP) gland development 0.2098 Informative Inherited
Biological Process (BP) regulation of growth 0.00393 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 0.04068 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.002646 Informative Inherited
Biological Process (BP) positive regulation of protein metabolic process 0.001361 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.0026 Informative Inherited
Biological Process (BP) growth 0.002689 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.9708 Informative Inherited
Biological Process (BP) epithelium development 0.7238 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.005892 Informative Inherited
Biological Process (BP) tube development 0.002965 Informative Inherited
Biological Process (BP) cardiovascular system development 0.02038 Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0 Highly Informative Direct
Biological Process (BP) angiogenesis 0.00000002118 Highly Informative Direct
Biological Process (BP) chemotaxis 0 Highly Informative Direct
Biological Process (BP) cell adhesion 0.00000000002569 Highly Informative Direct
Biological Process (BP) regulation of cell size 0 Highly Informative Direct
Biological Process (BP) regulation of cell morphogenesis involved in differentiation 0.00000000202 Highly Informative Direct
Biological Process (BP) regulation of neuron projection development 0.00001009 Highly Informative Direct
Biological Process (BP) cell growth 0.0007759 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 0.0001183 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0.000006266 Highly Informative Direct
Biological Process (BP) negative regulation of cell growth 0.000001267 Highly Informative Direct
Biological Process (BP) neuron projection development 0.000000001548 Highly Informative Direct
Biological Process (BP) positive regulation of response to external stimulus 0 Highly Informative Direct
Biological Process (BP) cell part morphogenesis 0.0000000000003182 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 0.0008768 Highly Informative Direct
Biological Process (BP) cell junction organization 0.000005337 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 0.000004321 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 0.0005831 Highly Informative Direct
Biological Process (BP) regulation of developmental growth 0.000003173 Highly Informative Direct
Biological Process (BP) regulation of behavior 0 Highly Informative Direct
Biological Process (BP) leukocyte migration 0.0000556 Highly Informative Direct
Biological Process (BP) positive regulation of cell migration 0.00188 Highly Informative Inherited
Biological Process (BP) negative regulation of response to external stimulus 0.212 Highly Informative Inherited
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0.8059 Highly Informative Inherited
Biological Process (BP) mesenchyme development 0.003822 Highly Informative Inherited
Biological Process (BP) stem cell development 0.4067 Highly Informative Inherited
Biological Process (BP) positive regulation of epithelial cell proliferation 0.01812 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.1565 Highly Informative Inherited
Biological Process (BP) branching morphogenesis of an epithelial tube 0.185 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 0.07842 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.6734 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 0.00002568 Informative Direct
Molecular Function (MF) sulfur compound binding 0.000005008 Informative Direct
Molecular Function (MF) protein dimerization activity 0.1389 Informative Inherited
Molecular Function (MF) kinase activity 0.4681 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.3485 Informative Inherited
Molecular Function (MF) heparin binding 0.000001599 Highly Informative Direct
Molecular Function (MF) protein complex binding 0.0000000000006082 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.000000000007172 Highly Informative Direct
Molecular Function (MF) protein kinase activity 0.1327 Highly Informative Inherited
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) protein complex 0.02912 Least Informative Inherited
Cellular Component (CC) plasma membrane 0 Moderately Informative Direct
Cellular Component (CC) vesicle 0.0006227 Moderately Informative Direct
Cellular Component (CC) cell projection 0.000001471 Moderately Informative Direct
Cellular Component (CC) extracellular region part 0.00000001767 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.02203 Moderately Informative Inherited
Cellular Component (CC) cell surface 0 Informative Direct
Cellular Component (CC) integral to membrane 0 Informative Direct
Cellular Component (CC) cell junction 0.00001948 Informative Direct
Cellular Component (CC) cell leading edge 0.000000007916 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 0.000002806 Informative Direct
Cellular Component (CC) intrinsic to plasma membrane 0.01593 Informative Inherited
Cellular Component (CC) adherens junction 0.000006693 Highly Informative Direct
Cellular Component (CC) cell projection membrane 0.00007408 Highly Informative Direct
Cellular Component (CC) receptor complex 0 Highly Informative Direct
Cellular Component (CC) integral to plasma membrane 0.002226 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 disease0.09874Least InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.08187Moderately InformativeInherited
Disease Ontology (DO)skin disease0.205Moderately InformativeInherited
Disease Ontology (DO)dermatitis herpetiformis0.0000006216InformativeDirect
Disease Ontology (DO)bullous pemphigoid0.0000685InformativeDirect

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.006449Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.04446Least InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.0005741Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal neuron morphology0.001829Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.1064Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.4894Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.5439Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology0.0002677InformativeDirect
Mammalian Phenotype (MP)ectopic neuron0.001235InformativeInherited
Mammalian Phenotype (MP)abnormal telencephalon morphology0.002115InformativeInherited
Mammalian Phenotype (MP)abnormal metencephalon morphology0.009558InformativeInherited
Mammalian Phenotype (MP)abnormal neuron physiology0.04322InformativeInherited
Mammalian Phenotype (MP)ectopic cerebellar granule cells0.000000002648Highly InformativeDirect
Mammalian Phenotype (MP)abnormal retinal inner plexiform layer morphology0.000003331Highly InformativeDirect
Mammalian Phenotype (MP)abnormal amacrine cell morphology0.00002155Highly InformativeDirect
Mammalian Phenotype (MP)abnormal neuronal migration0.0003126Highly InformativeDirect
Mammalian Phenotype (MP)abnormal hippocampus morphology0.2749Highly 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 variant0.000000002861InformativeDirect
Worm Phenotype (WP)male morphology variant0.000000005127InformativeDirect
Worm Phenotype (WP)sensillum morphology variant0.0000005455InformativeDirect
Worm Phenotype (WP)male nervous system morphology variant0.0000000003534Highly 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 defective0.000717InformativeDirect

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 structure0.05045Least InformativeInherited
Fly Anatomy (FA)larva0.1206Least InformativeInherited
Fly Anatomy (FA)anatomical group0.2174Least InformativeInherited
Fly Anatomy (FA)adult0.2263Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)multi-cell-component structure0.00008913Moderately InformativeDirect
Fly Anatomy (FA)late embryo0.005599Moderately InformativeInherited
Fly Anatomy (FA)peripheral nervous system0.03578Moderately InformativeInherited
Fly Anatomy (FA)central nervous system0.0674Moderately InformativeInherited
Fly Anatomy (FA)adult head0.1921Moderately InformativeInherited
Fly Anatomy (FA)adult nervous system0.1927Moderately InformativeInherited
Fly Anatomy (FA)adult segment0.5203Moderately InformativeInherited
Fly Anatomy (FA)larval abdominal segment0.00003261InformativeDirect
Fly Anatomy (FA)neuromere0.0001015InformativeDirect
Fly Anatomy (FA)ipsilateral tract0.0001251InformativeDirect
Fly Anatomy (FA)embryonic/larval peripheral nervous system0.001439InformativeInherited
Fly Anatomy (FA)labral segment0.00166InformativeInherited
Fly Anatomy (FA)adult brain0.002153InformativeInherited
Fly Anatomy (FA)synaptic neuropil0.002183InformativeInherited
Fly Anatomy (FA)adult procephalic segment0.004976InformativeInherited
Fly Anatomy (FA)nerve0.01159InformativeInherited
Fly Anatomy (FA)supraesophageal ganglion0.04706InformativeInherited
Fly Anatomy (FA)fascicle0.0000007616Highly InformativeDirect
Fly Anatomy (FA)intersegmental nerve0.00001192Highly 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)embryo0.5343Least InformativeInherited
Xenopus ANatomical entity (XAN)portion of tissue1Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.1722Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.3211Moderately InformativeInherited
Xenopus ANatomical entity (XAN)cranial placode0.00003324InformativeDirect

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 interaction0.00003237Moderately InformativeDirect
Biological processCell adhesion0InformativeDirect
Biological processNeurogenesis0InformativeDirect
Biological processAngiogenesis0.000000000001686InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCell projection0.000000000143Moderately InformativeDirect
Cellular componentEndosome0.0000008554Moderately InformativeDirect
Cellular componentCell junction0.000006356Moderately InformativeDirect
Cellular componentSecreted0.00002561Moderately InformativeDirect
DiseaseProto-oncogene0Moderately InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainRepeat0.000000000000001223Least InformativeDirect
DomainImmunoglobulin domain0InformativeDirect
Post-translational modificationTransferase0.9463Least InformativeInherited
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationKinase0.00000000000002436Moderately InformativeDirect
Post-translational modificationTyrosine-protein kinase0Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationUbl conjugation0.0000000000654Moderately InformativeDirect
Post-translational modificationPyrrolidone carboxylic acid0.0006998InformativeDirect

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 ]