SUPERFAMILY 1.75 HMM library and genome assignments server

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SET domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   beta-clip [ 51268] (7)
Superfamily:   SET domain [ 82199] (3)
Families:   Histone lysine methyltransferases [ 82200] (3)
  Viral histone H3 Lysine 27 Methyltransferase [ 82207]
  RuBisCo LSMT catalytic domain [ 82210]


Superfamily statistics
Genomes (940) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 18,958 56,585 13
Proteins 18,582 55,527 13


Functional annotation
General category Processes_IC
Detailed category Ion metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring one-carbon groups0Least InformativeDirect
Enzyme Commission (EC)Methyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)primary immunodeficiency disease0.03462InformativeInherited
Disease Ontology (DO)phagocyte bactericidal dysfunction0.000007305Highly InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Mode of Inheritance (MI)Autosomal dominant inheritance0.0003885Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of limbs0.01178Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.05661Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.06955Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.1022Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the digestive system0.1704Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.2001Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.2212Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limb bone morphology0.0006328Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the upper limb0.0007519Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.002425Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin adnexa morphology0.0071Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal joint morphology0.02578Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal oral cavity morphology0.02809Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.07002Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin morphology0.08626Moderately InformativeInherited
Phenotypic Abnormality (PA)Growth abnormality0.1059Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of digestive system physiology0.1068Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lower limb0.1398Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the testis0.00009691InformativeDirect
Phenotypic Abnormality (PA)Abnormality of pelvic girdle bone morphology0.0003659InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the lower urinary tract0.0004265InformativeDirect
Phenotypic Abnormality (PA)Regional abnormality of skin0.00327InformativeInherited
Phenotypic Abnormality (PA)Abnormal ear morphology0.005674InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the synovia0.01616InformativeInherited
Phenotypic Abnormality (PA)Abnormality of lower limb joint0.02767InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the forehead0.03148InformativeInherited
Phenotypic Abnormality (PA)Joint dislocation0.03685InformativeInherited
Phenotypic Abnormality (PA)Abnormality of body weight0.1615InformativeInherited
Phenotypic Abnormality (PA)Abnormality of joint mobility0.2229InformativeInherited
Phenotypic Abnormality (PA)Abdominal symptom0.2547InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the palm0.314InformativeInherited
Phenotypic Abnormality (PA)Hypospadias0.000001623Highly InformativeDirect
Phenotypic Abnormality (PA)Ventriculomegaly0.000003458Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the pinna0.00004633Highly InformativeDirect
Phenotypic Abnormality (PA)Posteriorly rotated ears0.00009125Highly InformativeDirect
Phenotypic Abnormality (PA)Precocious puberty0.0001251Highly InformativeDirect
Phenotypic Abnormality (PA)Downturned corners of mouth0.0003698Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the frontal hairline0.0006261Highly InformativeDirect
Phenotypic Abnormality (PA)Talipes0.0007827Highly InformativeDirect
Phenotypic Abnormality (PA)Feeding difficulties0.0009337Highly InformativeDirect
Phenotypic Abnormality (PA)Single transverse palmar crease0.0009859Highly InformativeDirect
Phenotypic Abnormality (PA)Hearing impairment0.002715Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the middle ear0.003741Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the radius0.00525Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the voice0.009696Highly InformativeInherited
Phenotypic Abnormality (PA)Synostosis of joints0.07122Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)hematopoietic system phenotype0.3252Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.3505Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.3751Least InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.0008856Moderately InformativeDirect
Mammalian Phenotype (MP)neoplasm0.2003Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology/development0.2351Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology0.3217Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.9597Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal B cell differentiation0.0008988InformativeDirect
Mammalian Phenotype (MP)increased hemolymphoid system tumor incidence0.001484InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.07152Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.1372Least InformativeInherited
Worm Phenotype (WP)cell development variant0.3243Least InformativeInherited
Worm Phenotype (WP)life span variant0Moderately InformativeDirect
Worm Phenotype (WP)protein expression variant0.000001334Moderately InformativeDirect
Worm Phenotype (WP)reproductive system development variant0.0418Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.1891Moderately InformativeInherited
Worm Phenotype (WP)sterile progeny0.6081Moderately InformativeInherited
Worm Phenotype (WP)apoptosis variant0.8167Moderately InformativeInherited
Worm Phenotype (WP)protein modification variant0.00000002101InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.00003429InformativeDirect
Worm Phenotype (WP)vulva development variant0.007893InformativeInherited
Worm Phenotype (WP)VPC competence variant0.1052InformativeInherited
Worm Phenotype (WP)transgenerational loss of fertility0.00000000002338Highly InformativeDirect
Worm Phenotype (WP)apoptosis increased0.0000003712Highly InformativeDirect
Worm Phenotype (WP)RNAi response variant0.000002425Highly InformativeDirect
Worm Phenotype (WP)spontaneous mutation rate increased0.00002718Highly InformativeDirect
Worm Phenotype (WP)shortened life span0.0002538Highly InformativeDirect
Worm Phenotype (WP)cell number decreased0.01682Highly InformativeInherited
Worm Phenotype (WP)germline proliferation variant0.02484Highly InformativeInherited
Worm Phenotype (WP)antibody staining variant0.2491Highly InformativeInherited
Worm Phenotype (WP)transgene silencing variant0.4958Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)modifier of variegation0.00000000195InformativeDirect
Fly Phenotype (FP)suppressor of variegation0.0000000004313Highly InformativeDirect
Fly Phenotype (FP)non-suppressor of variegation0.00002026Highly InformativeDirect
Fly Phenotype (FP)homeotic0.00009455Highly InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)adult0.4398Least InformativeInherited
Fly Anatomy (FA)organ system subdivision0.4504Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)thoracic segment0.1341Moderately InformativeInherited
Fly Anatomy (FA)appendage0.4263Moderately InformativeInherited
Fly Anatomy (FA)tagmatic subdivision of integument0.4429Moderately InformativeInherited
Fly Anatomy (FA)adult integumentary system0.5914Moderately InformativeInherited
Fly Anatomy (FA)adult thorax0.6055Moderately InformativeInherited
Fly Anatomy (FA)adult segment0.77Moderately InformativeInherited
Fly Anatomy (FA)leg0.04624InformativeInherited
Fly Anatomy (FA)adult metathoracic segment0.002489Highly InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring one-carbon groups0Moderately InformativeDirect
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect

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 Phenotype (FP) · 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 5 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 SET domain 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 5 hidden Markov models representing the SET domain 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 Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]