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 disease0.0547Least InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.2507Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.3433Moderately InformativeInherited
Disease Ontology (DO)disease by infectious agent0.6147Moderately InformativeInherited
Disease Ontology (DO)myopia0.0009111InformativeDirect
Disease Ontology (DO)inherited blood coagulation disease0.004245InformativeInherited
Disease Ontology (DO)filariasis0.000003989Highly InformativeDirect
Disease Ontology (DO)opportunistic mycosis0.0001599Highly InformativeDirect

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.1957Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.5868Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.9696Least InformativeInherited
Mammalian Phenotype (MP)growth/size/body region phenotype0.9902Least InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.2593Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell physiology0.2775Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.4395Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle morphology0.4845Moderately InformativeInherited
Mammalian Phenotype (MP)reproductive system phenotype0.6475Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal leukocyte physiology0.6522Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.692Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.7775Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle physiology0.8522Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.8722Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0.8916Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal spinal cord morphology0.03538InformativeInherited
Mammalian Phenotype (MP)abnormal macrophage physiology0.03688InformativeInherited
Mammalian Phenotype (MP)abnormal compact bone morphology0.05843InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.1954InformativeInherited
Mammalian Phenotype (MP)abnormal skin physiology0.2198InformativeInherited
Mammalian Phenotype (MP)abnormal interleukin secretion0.3017InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.6171InformativeInherited
Mammalian Phenotype (MP)decreased interleukin-12b secretion0.0001048Highly InformativeDirect
Mammalian Phenotype (MP)abnormal skin tensile strength0.0001237Highly InformativeDirect
Mammalian Phenotype (MP)abnormal spinal cord ventral commissure morphology0.0002423Highly InformativeDirect
Mammalian Phenotype (MP)abnormal tendon morphology0.0003297Highly InformativeDirect
Mammalian Phenotype (MP)decreased macrophage cytokine production0.0004929Highly InformativeDirect
Mammalian Phenotype (MP)abnormal nervous system regeneration0.0006048Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cornea morphology0.004643Highly InformativeInherited
Mammalian Phenotype (MP)abnormal epididymis morphology0.05635Highly InformativeInherited
Mammalian Phenotype (MP)abnormal susceptibility to weight loss0.06719Highly InformativeInherited
Mammalian Phenotype (MP)abnormal spinal cord white matter morphology0.1342Highly InformativeInherited
Mammalian Phenotype (MP)decreased bone mass0.2108Highly 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
Worm Phenotype (WP)myopodia present0.0007423Highly InformativeDirect

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)nervous system0.6072Least InformativeInherited
Fly Anatomy (FA)somatic cell0.7551Least InformativeInherited
Fly Anatomy (FA)neuron0.1229Moderately InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA 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)Aminoacyltransferases0.000001036Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.702Moderately 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 transferase0.0000000003591InformativeDirect
Enzyme Commission (EC)Acting on a peroxide as acceptor0.0005085InformativeDirect
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)Protein-serine/threonine phosphatase0.00000002495Highly InformativeDirect
Enzyme Commission (EC)Adenylate cyclase0.00000004263Highly InformativeDirect

Document: EC annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · 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 26 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 26 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]