SUPERFAMILY 1.75 HMM library and genome assignments server

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RNA-binding domain, RBD superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ferredoxin-like [ 54861] (59)
Superfamily:   RNA-binding domain, RBD [ 54928] (5)
Families:   Canonical RBD [ 54929] (67)
  Non-canonical RBD domain [ 54954]
  Splicing factor U2AF subunits [ 64276]
  Smg-4/UPF3 [ 102987]
  GUCT domain [ 160314]


Superfamily statistics
Genomes (1,025) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 114,462 318,313 138
Proteins 83,107 233,604 130


Functional annotation
General category Regulation
Detailed category RNA binding, 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 groups0.00000000004189Least InformativeDirect
Enzyme Commission (EC)Isomerases0.000002211Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.01123Least InformativeInherited
Enzyme Commission (EC)Acting on ester bonds0.003436Least InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0.02837Least InformativeInherited
Enzyme Commission (EC)Methyltransferases0.000000000000009651Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0.00000004046Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.02062Moderately InformativeInherited
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect
Enzyme Commission (EC)Peptidylprolyl isomerase0InformativeDirect
Enzyme Commission (EC)Polynucleotide adenylyltransferase0Highly InformativeDirect
Enzyme Commission (EC)RNA uridylyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Poly(A)-specific ribonuclease0.00000000000004272Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)cardiovascular system disease1Least InformativeInherited
Disease Ontology (DO)muscle tissue disease0.01969InformativeInherited
Disease Ontology (DO)ischemia0.2901Highly InformativeInherited

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Mode of Inheritance (MI)Gonosomal inheritance0.00004413InformativeDirect
Mode of Inheritance (MI)Y-linked inheritance0.0004177Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.07171Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.1047Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the musculature0.1218Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.1711Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.3242Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.9023Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal muscle morphology0.05363Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of central motor function0.4692Moderately InformativeInherited
Phenotypic Abnormality (PA)Behavioral abnormality0.4839Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the respiratory system0.5529Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper respiratory tract0.006971InformativeInherited
Phenotypic Abnormality (PA)Abnormality of muscle fibers0.03352InformativeInherited
Phenotypic Abnormality (PA)Muscle weakness0.1247InformativeInherited
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0.4057InformativeInherited
Phenotypic Abnormality (PA)Amyotrophic lateral sclerosis0.00000003601Highly InformativeDirect
Phenotypic Abnormality (PA)Fatigable weakness of swallowing muscles0.000000463Highly InformativeDirect
Phenotypic Abnormality (PA)Laryngospasm0.0000008647Highly InformativeDirect
Phenotypic Abnormality (PA)Xerostomia0.000006431Highly InformativeDirect
Phenotypic Abnormality (PA)Fatigable weakness of respiratory muscles0.000009627Highly InformativeDirect
Phenotypic Abnormality (PA)Agitation0.0000685Highly InformativeDirect
Phenotypic Abnormality (PA)Paralysis0.0006086Highly InformativeDirect
Phenotypic Abnormality (PA)Elevated serum creatine phosphokinase0.0007441Highly InformativeDirect
Phenotypic Abnormality (PA)Neurodegeneration0.0009232Highly InformativeDirect
Phenotypic Abnormality (PA)Azoospermia0.001307Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0.2656Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype1Least InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.8153Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.8825Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell differentiation0.7833InformativeInherited
Mammalian Phenotype (MP)premature neuronal precursor differentiation0.0006105Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell development variant0.00000000000000178Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.000001458Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.0001657Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.0002384Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.001266Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.003329Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.8254Least InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.0003419Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.06939Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.1086Moderately InformativeInherited
Worm Phenotype (WP)apoptosis variant0.2129Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.4116Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.5259Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.708Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant1Moderately InformativeInherited
Worm Phenotype (WP)sterile progeny1Moderately InformativeInherited
Worm Phenotype (WP)RNA expression variant0.00000000003033InformativeDirect
Worm Phenotype (WP)sick0.0000003102InformativeDirect
Worm Phenotype (WP)brood size variant0.000006399InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.00002943InformativeDirect
Worm Phenotype (WP)alimentary system development variant0.0006643InformativeDirect
Worm Phenotype (WP)cell number increased0.001559InformativeInherited
Worm Phenotype (WP)VPC competence variant0.007618InformativeInherited
Worm Phenotype (WP)vulva development variant0.01813InformativeInherited
Worm Phenotype (WP)egg laying variant0.05634InformativeInherited
Worm Phenotype (WP)organism pathogen response variant0.06241InformativeInherited
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.1985InformativeInherited
Worm Phenotype (WP)oocyte morphology variant0.3424InformativeInherited
Worm Phenotype (WP)cell proliferation increased8.906e-16Highly InformativeDirect
Worm Phenotype (WP)sex determination variant0.00000001553Highly InformativeDirect
Worm Phenotype (WP)neurite development variant0.0000001571Highly InformativeDirect
Worm Phenotype (WP)RNA processing variant0.000001746Highly InformativeDirect
Worm Phenotype (WP)embryonic lethal late emb0.000002111Highly InformativeDirect
Worm Phenotype (WP)no induction of antimicrobial peptide expression after infection0.0000234Highly InformativeDirect
Worm Phenotype (WP)developmental morphology variant0.0001121Highly InformativeDirect
Worm Phenotype (WP)embryonic arrest0.0003438Highly InformativeDirect
Worm Phenotype (WP)P granule defective0.08137Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.0000000000003012Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0.0000003161Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.00000221Least InformativeDirect
Xenopus ANatomical entity (XAN)nervous system0.001446Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.006134Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.01735Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.4144Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.0000000003399Moderately InformativeDirect
Xenopus ANatomical entity (XAN)germ line cell0.00000007432Moderately InformativeDirect
Xenopus ANatomical entity (XAN)testis0.0000004104Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0.0000005819Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0.00002761Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.00003079Moderately InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0.001609Moderately InformativeInherited
Xenopus ANatomical entity (XAN)musculoskeletal system0.001906Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.007672Moderately InformativeInherited
Xenopus ANatomical entity (XAN)brain0.01594Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro0InformativeDirect
Xenopus ANatomical entity (XAN)immune system0.000000000006367InformativeDirect
Xenopus ANatomical entity (XAN)endocrine system0.00000000003542InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm0.00000007605InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0.000006543InformativeDirect
Xenopus ANatomical entity (XAN)skeletal muscle0.000008595InformativeDirect
Xenopus ANatomical entity (XAN)intestine0.00001128InformativeDirect
Xenopus ANatomical entity (XAN)eye0.00008427InformativeDirect
Xenopus ANatomical entity (XAN)hindbrain0.0004852InformativeDirect
Xenopus ANatomical entity (XAN)oocyte0.000000284Highly InformativeDirect
Xenopus ANatomical entity (XAN)marginal zone0.0004732Highly InformativeDirect
Xenopus ANatomical entity (XAN)vegetal hemisphere0.005969Highly InformativeInherited
Xenopus DEvelopment stage (XDE)post-embryonic stage0.002598Least InformativeInherited
Xenopus DEvelopment stage (XDE)climax stage0.0002738Moderately InformativeDirect
Xenopus DEvelopment stage (XDE)unspecified stage0.0005094Moderately InformativeDirect
Xenopus DEvelopment stage (XDE)NF stage 660.0006278InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0.00000008591Least InformativeDirect
Plant ANatomical entity (PAN)seed0.00000613Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0.0001151Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0.002607Least InformativeInherited
Plant ANatomical entity (PAN)leaf0.005049Least InformativeInherited
Plant ANatomical entity (PAN)inflorescence0.009978Least InformativeInherited
Plant ANatomical entity (PAN)whole plant0.02106Least InformativeInherited
Plant ANatomical entity (PAN)flower0.1693Least InformativeInherited
Plant ANatomical entity (PAN)collective phyllome structure0.2001Least InformativeInherited
Plant ANatomical entity (PAN)shoot axis0.2113Least InformativeInherited
Plant ANatomical entity (PAN)gamete0.00005335InformativeDirect
Plant ANatomical entity (PAN)cultured plant cell0.0001439Highly InformativeDirect
Plant ANatomical entity (PAN)bud0.03197Highly InformativeInherited
Plant structure DEvelopment stage (PDE)D bilateral stage0.00001302Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0.00004978Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0.0001063Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0.0001151Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0.04451Least InformativeInherited
Enzyme Commission (EC)Transferring phosphorus-containing groups1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups0.0000000001121Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0.0000001131Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.001835Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases0.01661Moderately InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0.04834Moderately InformativeInherited
Enzyme Commission (EC)Acyltransferases0.7768Moderately InformativeInherited
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect
Enzyme Commission (EC)RNA helicase0.0000000000000132InformativeDirect
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0.00000003101InformativeDirect
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0.0005747InformativeDirect
Enzyme Commission (EC)Peptidylprolyl isomerase0Highly InformativeDirect
Enzyme Commission (EC)Polynucleotide adenylyltransferase2.531e-16Highly InformativeDirect
Enzyme Commission (EC)Poly(A)-specific ribonuclease0.000000000000493Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Post-translational modificationRNA-binding0.000000000000002511InformativeDirect

Document: KW 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) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 194 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 RNA-binding domain, RBD 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 194 hidden Markov models representing the RNA-binding domain, RBD 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) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]