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 (132) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 3,700 3,612 5
Proteins 3,487 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
Biological Process (BP)regulation of cellular process00.0001182Least InformativeDirect
Biological Process (BP)localization0.00068751.342e-06Least InformativeDirect
Biological Process (BP)cellular component movement8.465e-050InformativeDirect
Biological Process (BP)biological adhesion1.194e-080InformativeDirect
Biological Process (BP)locomotion3.364e-070InformativeDirect
Biological Process (BP)localization of cell3.021e-080InformativeDirect
Biological Process (BP)cell adhesion1.768e-063.615e-11Highly InformativeDirect
Cellular Component (CC)membrane0.00046480Least InformativeDirect
Cellular Component (CC)cell surface6.296e-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) 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 0.0001182 Least Informative Direct
Biological Process (BP) response to stimulus 0 Least Informative Direct
Biological Process (BP) localization 1.342e-06 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 3.182e-11 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 1.52e-05 Moderately Informative Direct
Biological Process (BP) regulation of localization 0 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 3.098e-10 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.00079 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 6.096e-13 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 1.91e-08 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 2.892e-06 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0 Moderately Informative Direct
Biological Process (BP) immune system process 0.001762 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) tissue development 0.6194 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.006138 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 0.004172 Moderately Informative Inherited
Biological Process (BP) homeostatic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.02181 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 6.716e-06 Informative Direct
Biological Process (BP) cellular component movement 0 Informative Direct
Biological Process (BP) central nervous system development 1.765e-05 Informative Direct
Biological Process (BP) regulation of nucleoside metabolic process 6.582e-05 Informative Direct
Biological Process (BP) response to wounding 2.475e-06 Informative Direct
Biological Process (BP) embryo development ending in birth or egg hatching 0.000252 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 4.416e-11 Informative Direct
Biological Process (BP) biological adhesion 0 Informative Direct
Biological Process (BP) cell projection organization 0 Informative Direct
Biological Process (BP) regulation of nucleotide catabolic process 5.376e-05 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 0.0002753 Informative Direct
Biological Process (BP) generation of neurons 0 Informative Direct
Biological Process (BP) negative regulation of developmental process 0.0002191 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.0001342 Informative Direct
Biological Process (BP) positive regulation of protein metabolic process 0.0005783 Informative Direct
Biological Process (BP) regulation of cellular component movement 0 Informative Direct
Biological Process (BP) organelle localization 0.0003077 Informative Direct
Biological Process (BP) localization of cell 0 Informative Direct
Biological Process (BP) regulation of nervous system development 1.453e-05 Informative Direct
Biological Process (BP) regulation of cell development 2.952e-05 Informative Direct
Biological Process (BP) regulation of anatomical structure size 5.751e-09 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0.0003082 Informative Direct
Biological Process (BP) epithelium development 0.2414 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.0144 Informative Inherited
Biological Process (BP) gland development 0.1796 Informative Inherited
Biological Process (BP) regulation of growth 0.001437 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) cell activation 0.07764 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.1753 Informative Inherited
Biological Process (BP) muscle tissue development 0.4203 Informative Inherited
Biological Process (BP) positive regulation of cell proliferation 0.6977 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.02605 Informative Inherited
Biological Process (BP) cardiovascular system development 0.02013 Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0 Highly Informative Direct
Biological Process (BP) angiogenesis 1.083e-08 Highly Informative Direct
Biological Process (BP) regulation of cell growth 7.88e-08 Highly Informative Direct
Biological Process (BP) chemotaxis 0 Highly Informative Direct
Biological Process (BP) cell adhesion 3.615e-11 Highly Informative Direct
Biological Process (BP) regulation of cell size 0 Highly Informative Direct
Biological Process (BP) regulation of cell morphogenesis involved in differentiation 2.528e-09 Highly Informative Direct
Biological Process (BP) regulation of neuron projection development 1.47e-05 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 3.888e-05 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 3.892e-06 Highly Informative Direct
Biological Process (BP) neuron projection development 3.044e-09 Highly Informative Direct
Biological Process (BP) positive regulation of response to external stimulus 0 Highly Informative Direct
Biological Process (BP) cell part morphogenesis 0 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 0.0007713 Highly Informative Direct
Biological Process (BP) cell junction organization 5.56e-06 Highly Informative Direct
Biological Process (BP) regulation of Rho protein signal transduction 6.802e-06 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 2.209e-05 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 0.0006595 Highly Informative Direct
Biological Process (BP) negative regulation of growth 2.047e-05 Highly Informative Direct
Biological Process (BP) regulation of developmental growth 4.397e-06 Highly Informative Direct
Biological Process (BP) regulation of behavior 0 Highly Informative Direct
Biological Process (BP) leukocyte migration 0.00017 Highly Informative Direct
Biological Process (BP) morphogenesis of a branching epithelium 0.0009258 Highly Informative Direct
Biological Process (BP) positive regulation of cell migration 0.001098 Highly Informative Inherited
Biological Process (BP) negative regulation of response to external stimulus 0.2107 Highly Informative Inherited
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0.02061 Highly Informative Inherited
Biological Process (BP) mesenchyme development 0.02801 Highly Informative Inherited
Biological Process (BP) stem cell development 0.6809 Highly Informative Inherited
Biological Process (BP) positive regulation of epithelial cell proliferation 0.02104 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.1395 Highly Informative Inherited
Biological Process (BP) epithelial tube morphogenesis 0.09863 Highly Informative Inherited
Molecular Function (MF) binding 1.555e-15 Least Informative Direct
Molecular Function (MF) anion binding 0.04669 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.5784 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 1.149e-05 Informative Direct
Molecular Function (MF) sulfur compound binding 1.837e-06 Informative Direct
Molecular Function (MF) protein dimerization activity 0.8358 Informative Inherited
Molecular Function (MF) kinase activity 0.3885 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.2821 Informative Inherited
Molecular Function (MF) heparin binding 1.768e-06 Highly Informative Direct
Molecular Function (MF) protein complex binding 3.641e-14 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 1.953e-05 Highly Informative Direct
Molecular Function (MF) protein kinase activity 0.09943 Highly Informative Inherited
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) protein complex 0.01159 Least Informative Inherited
Cellular Component (CC) intrinsic to membrane 0.0008279 Moderately Informative Direct
Cellular Component (CC) extracellular region part 2.34e-07 Moderately Informative Direct
Cellular Component (CC) plasma membrane part 0 Moderately Informative Direct
Cellular Component (CC) vesicle 0.002355 Moderately Informative Inherited
Cellular Component (CC) cell surface 0 Informative Direct
Cellular Component (CC) integral to membrane 0 Informative Direct
Cellular Component (CC) intrinsic to plasma membrane 0.0005875 Informative Direct
Cellular Component (CC) cell leading edge 2.271e-07 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 3.653e-05 Informative Direct
Cellular Component (CC) adherens junction 2.95e-05 Highly Informative Direct
Cellular Component (CC) cell-substrate junction 3.233e-08 Highly Informative Direct
Cellular Component (CC) receptor complex 0 Highly Informative Direct
Cellular Component (CC) integral to plasma membrane 0.001216 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 disease0.06552Least InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.05987Moderately InformativeInherited
Disease Ontology (DO)skin disease0.1664Moderately InformativeInherited
Disease Ontology (DO)dermatitis herpetiformis6.898e-07InformativeDirect
Disease Ontology (DO)bullous pemphigoid4.228e-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 phenotype0.005713Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.0259Least InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.00164Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.001877Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.1849Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.5442Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.7943Moderately InformativeInherited
Mammalian Phenotype (MP)ectopic neuron0.00122InformativeInherited
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology0.001223InformativeInherited
Mammalian Phenotype (MP)abnormal metencephalon morphology0.008467InformativeInherited
Mammalian Phenotype (MP)abnormal neuron physiology0.01353InformativeInherited
Mammalian Phenotype (MP)abnormal cerebrum morphology0.3347InformativeInherited
Mammalian Phenotype (MP)ectopic cerebellar granule cells2.961e-09Highly InformativeDirect
Mammalian Phenotype (MP)abnormal amacrine cell morphology6.464e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal retinal inner plexiform layer morphology0.0003098Highly InformativeDirect
Mammalian Phenotype (MP)abnormal neuronal migration0.000437Highly InformativeDirect
Mammalian Phenotype (MP)abnormal retinal ganglion cell morphology0.0004903Highly InformativeDirect
Mammalian Phenotype (MP)abnormal hippocampus morphology0.2786Highly 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

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)anatomical group0.09945Least InformativeInherited
Fly Anatomy (FA)larva0.1723Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)multi-cell-component structure0Moderately InformativeDirect
Fly Anatomy (FA)late embryo0.01302Moderately InformativeInherited
Fly Anatomy (FA)central nervous system0.02299Moderately InformativeInherited
Fly Anatomy (FA)peripheral nervous system0.05973Moderately InformativeInherited
Fly Anatomy (FA)adult nervous system0.1118Moderately InformativeInherited
Fly Anatomy (FA)adult segment0.5414Moderately InformativeInherited
Fly Anatomy (FA)head0.6008Moderately InformativeInherited
Fly Anatomy (FA)larval abdominal segment6.957e-06InformativeDirect
Fly Anatomy (FA)embryonic/larval peripheral nervous system0.0003672InformativeDirect
Fly Anatomy (FA)synaptic neuropil block0.0008205InformativeDirect
Fly Anatomy (FA)adult procephalic segment0.002051InformativeInherited
Fly Anatomy (FA)nerve0.003674InformativeInherited
Fly Anatomy (FA)ganglion0.006131InformativeInherited
Fly Anatomy (FA)adult central nervous system0.01923InformativeInherited
Fly Anatomy (FA)brain0.05781InformativeInherited
Fly Anatomy (FA)tract0.1881InformativeInherited
Fly Anatomy (FA)protocerebrum0.6285InformativeInherited
Fly Anatomy (FA)fascicle1.754e-07Highly InformativeDirect
Fly Anatomy (FA)intersegmental nerve4.953e-06Highly 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)embryo0.525Least InformativeInherited
Xenopus ANatomical entity (XAN)portion of tissue1Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.1567Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.3107Moderately InformativeInherited
Xenopus ANatomical entity (XAN)cranial placode2.629e-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 interaction3.266e-05Moderately InformativeDirect
Biological processCell adhesion0InformativeDirect
Biological processNeurogenesis0InformativeDirect
Biological processAngiogenesis1.738e-12InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCell projection1.026e-10Moderately InformativeDirect
Cellular componentEndosome7.965e-07Moderately InformativeDirect
Cellular componentCell junction5.777e-06Moderately InformativeDirect
Cellular componentSecreted2.314e-05Moderately InformativeDirect
DiseaseProto-oncogene0Moderately InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainRepeat1.228e-15Least InformativeDirect
DomainImmunoglobulin domain0InformativeDirect
Post-translational modificationTransferase0.9471Least InformativeInherited
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationKinase2.369e-14Moderately InformativeDirect
Post-translational modificationTyrosine-protein kinase0Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationUbl conjugation3.962e-11Moderately InformativeDirect
Post-translational modificationPyrrolidone carboxylic acid0.0006798InformativeDirect

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 ]