SUPERFAMILY 1.75 HMM library and genome assignments server

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L domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) [ 52046] (3)
Superfamily:   L domain-like [ 52058] (8)
Families:   Internalin LRR domain [ 52059] (3)
  Leucine rich effector protein YopM [ 69433]
  Ngr ectodomain-like [ 75142] (6)
  Polygalacturonase inhibiting protein PGIP [ 89569]
  Rab geranylgeranyltransferase alpha-subunit, C-terminal domain [ 52062]
  mRNA export factor tap [ 52065]
  U2A'-like [ 52068]
  L domain [ 52071] (5)


Superfamily statistics
Genomes (1,419) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 119,601 298,005 63
Proteins 93,513 237,507 49


Functional annotation
General category General
Detailed category General

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on ester bonds0.00000756Least InformativeDirect
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Protein-serine/threonine kinases0Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.3857Moderately InformativeInherited
Enzyme Commission (EC)Receptor protein-tyrosine kinase0InformativeDirect
Enzyme Commission (EC)Phosphoprotein phosphatase0.00000000441InformativeDirect
Enzyme Commission (EC)Peroxidases0.0001357InformativeDirect
Enzyme Commission (EC)Phosphorus-oxygen lyases1InformativeInherited
Enzyme Commission (EC)Poly(A)-specific ribonuclease0Highly InformativeDirect
Enzyme Commission (EC)Adenylate cyclase0.00000000003813Highly InformativeDirect
Enzyme Commission (EC)Peroxidase0.0000000001091Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)nervous system disease0.05437Least InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.2511Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.3445Moderately InformativeInherited
Disease Ontology (DO)disease by infectious agent0.6163Moderately InformativeInherited
Disease Ontology (DO)myopia0.0009218InformativeDirect
Disease Ontology (DO)inherited blood coagulation disease0.004274InformativeInherited
Disease Ontology (DO)filariasis0.000004058Highly InformativeDirect
Disease Ontology (DO)opportunistic mycosis0.0001611Highly InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Incomplete penetrance0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.7036Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.7541Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the digestive system0.7589Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.8219Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.9928Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal cardiovascular system physiology0.4908Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper urinary tract0.6958Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the urinary system physiology0.7116Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of digestive system physiology0.7118Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the gastrointestinal tract0.9108Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues1Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal urine cytology0.05882InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the coagulation cascade0.122InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood circulation0.3607InformativeInherited
Phenotypic Abnormality (PA)Abnormal renal physiology0.5228InformativeInherited
Phenotypic Abnormality (PA)Abnormal renal morphology0.5847InformativeInherited
Phenotypic Abnormality (PA)Abnormal thrombocyte morphology0.6464InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.686InformativeInherited
Phenotypic Abnormality (PA)Functional abnormality of the gastrointestinal tract0.6874InformativeInherited
Phenotypic Abnormality (PA)Abnormal bleeding0.7729InformativeInherited
Phenotypic Abnormality (PA)Prolonged bleeding following procedure0.0007361Highly InformativeDirect
Phenotypic Abnormality (PA)Epistaxis0.06812Highly InformativeInherited
Phenotypic Abnormality (PA)Gastrointestinal hemorrhage0.1534Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of bone marrow cell morphology0.2015Highly InformativeInherited
Phenotypic Abnormality (PA)Thrombocytopenia0.5382Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.1703Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.6112Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.9748Least InformativeInherited
Mammalian Phenotype (MP)growth/size/body region phenotype0.9942Least InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.216Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell physiology0.2841Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.4571Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle morphology0.4965Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal leukocyte physiology0.6634Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.692Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.8205Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle physiology0.8596Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.8709Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0.9037Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system morphology0.9423Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal macrophage physiology0.03858InformativeInherited
Mammalian Phenotype (MP)abnormal spinal cord morphology0.04032InformativeInherited
Mammalian Phenotype (MP)abnormal compact bone morphology0.05819InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.2009InformativeInherited
Mammalian Phenotype (MP)abnormal skin physiology0.245InformativeInherited
Mammalian Phenotype (MP)abnormal interleukin secretion0.3088InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.6243InformativeInherited
Mammalian Phenotype (MP)decreased interleukin-12b secretion0.0001084Highly InformativeDirect
Mammalian Phenotype (MP)abnormal skin tensile strength0.0001237Highly InformativeDirect
Mammalian Phenotype (MP)abnormal spinal cord ventral commissure morphology0.0002486Highly InformativeDirect
Mammalian Phenotype (MP)abnormal tendon morphology0.0003412Highly InformativeDirect
Mammalian Phenotype (MP)decreased macrophage cytokine production0.0005059Highly InformativeDirect
Mammalian Phenotype (MP)abnormal nervous system regeneration0.0006055Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cornea morphology0.004875Highly InformativeInherited
Mammalian Phenotype (MP)abnormal epididymis morphology0.05783Highly InformativeInherited
Mammalian Phenotype (MP)abnormal susceptibility to weight loss0.06716Highly InformativeInherited
Mammalian Phenotype (MP)abnormal spinal cord white matter morphology0.1342Highly InformativeInherited
Mammalian Phenotype (MP)decreased bone mass0.2104Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell morphology variant1Least InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)adult0.1761Least InformativeInherited
Fly Anatomy (FA)larva0.2721Least InformativeInherited
Fly Anatomy (FA)nervous system0.6292Least InformativeInherited
Fly Anatomy (FA)somatic cell0.7618Least InformativeInherited
Fly Anatomy (FA)neuron0.1534Moderately InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)multi-tissue structure0.04044Least InformativeInherited
Zebrafish Anatomy (ZA)organism subdivision0.7036Least InformativeInherited
Zebrafish Anatomy (ZA)surface structure0.8019InformativeInherited
Zebrafish Anatomy (ZA)scale0.0001008Highly InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus DEvelopment stage (XDE)embryonic stage0.000721Moderately InformativeDirect
Xenopus DEvelopment stage (XDE)early tailbud stage0.07321Highly InformativeInherited

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)portion of meristem tissue1Least InformativeInherited

Document: AP 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)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Protein-serine/threonine kinases0Moderately InformativeDirect
Enzyme Commission (EC)Aminoacyltransferases0.000001152Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.7475Moderately InformativeInherited
Enzyme Commission (EC)Protein-tyrosine kinases0InformativeDirect
Enzyme Commission (EC)Non-specific serine/threonine protein kinase0InformativeDirect
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0.0000000004382InformativeDirect
Enzyme Commission (EC)Acting on a peroxide as acceptor0.0005002InformativeDirect
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than methyl groups1InformativeInherited
Enzyme Commission (EC)Phosphorus-oxygen lyases1InformativeInherited
Enzyme Commission (EC)Receptor protein-tyrosine kinase0Highly InformativeDirect
Enzyme Commission (EC)Poly(A)-specific ribonuclease0Highly InformativeDirect
Enzyme Commission (EC)Adenylate cyclase0.00000001816Highly InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine phosphatase0.00000002376Highly InformativeDirect

Document: EC annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 50 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 L domain-like 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 50 hidden Markov models representing the L domain-like 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 · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]