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)muscle tissue disease0.01924InformativeInherited
Disease Ontology (DO)ischemia0.29Highly 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 inheritance0.00006071InformativeDirect
Mode of Inheritance (MI)Y-linked inheritance0.0002914Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.1013Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.1098Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the musculature0.1165Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.1672Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.6014Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal muscle morphology0.1199Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal respiratory system morphology0.224Moderately InformativeInherited
Phenotypic Abnormality (PA)Behavioral abnormality0.3973Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.5373Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of central motor function0.6015Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal peripheral nervous system morphology0.6433Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper respiratory tract0.002722InformativeInherited
Phenotypic Abnormality (PA)Fatigable weakness0.005891InformativeInherited
Phenotypic Abnormality (PA)Abnormal muscle fiber morphology0.03556InformativeInherited
Phenotypic Abnormality (PA)Neurological speech impairment0.1632InformativeInherited
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0.4546InformativeInherited
Phenotypic Abnormality (PA)Abnormal motor neuron morphology0.00000003937Highly InformativeDirect
Phenotypic Abnormality (PA)Fatigable weakness of swallowing muscles0.000000593Highly InformativeDirect
Phenotypic Abnormality (PA)Xerostomia0.000007051Highly InformativeDirect
Phenotypic Abnormality (PA)Fatigable weakness of respiratory muscles0.00001768Highly InformativeDirect
Phenotypic Abnormality (PA)Agitation0.0001104Highly InformativeDirect
Phenotypic Abnormality (PA)Paralysis0.000758Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal spermatogenesis0.002888Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal larynx physiology0.02271Highly InformativeInherited
Phenotypic Abnormality (PA)Atrophy/Degeneration affecting the central nervous system0.03357Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0.286Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.9998Least InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.7546Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.8885Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell differentiation0.7838InformativeInherited
Mammalian Phenotype (MP)premature neuronal precursor differentiation0.0006299Highly 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 variant9.238e-16Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.0000008986Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.000006321Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.0005876Least InformativeDirect
Worm Phenotype (WP)blast cell physiology variant0.001456Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.001468Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.006337Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.8565Least InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.0003581Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.009628Moderately InformativeInherited
Worm Phenotype (WP)body region morphology variant0.03184Moderately InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.03184Moderately InformativeInherited
Worm Phenotype (WP)developmental morphology variant0.03212Moderately InformativeInherited
Worm Phenotype (WP)adult body morphology variant0.03239Moderately InformativeInherited
Worm Phenotype (WP)body morphology variant0.03956Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.08639Moderately InformativeInherited
Worm Phenotype (WP)apoptosis variant0.2083Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.5668Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.6352Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant1Moderately InformativeInherited
Worm Phenotype (WP)germ cell development variant1Moderately InformativeInherited
Worm Phenotype (WP)sterile progeny1Moderately InformativeInherited
Worm Phenotype (WP)RNA expression variant0.0000000002052InformativeDirect
Worm Phenotype (WP)sick0.000000257InformativeDirect
Worm Phenotype (WP)brood size variant0.000005704InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.00003119InformativeDirect
Worm Phenotype (WP)alimentary system development variant0.0004193InformativeDirect
Worm Phenotype (WP)cell number increased0.001508InformativeInherited
Worm Phenotype (WP)pericellular component morphology variant0.001793InformativeInherited
Worm Phenotype (WP)VPC competence variant0.006586InformativeInherited
Worm Phenotype (WP)vulva development variant0.01569InformativeInherited
Worm Phenotype (WP)egg laying variant0.03529InformativeInherited
Worm Phenotype (WP)organism pathogen response variant0.06659InformativeInherited
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.07255InformativeInherited
Worm Phenotype (WP)oocyte morphology variant0.315InformativeInherited
Worm Phenotype (WP)cell proliferation increased4.623e-16Highly InformativeDirect
Worm Phenotype (WP)sex determination variant0.00000001796Highly InformativeDirect
Worm Phenotype (WP)neurite development variant0.0000002038Highly InformativeDirect
Worm Phenotype (WP)embryonic lethal late emb0.000001472Highly InformativeDirect
Worm Phenotype (WP)RNA processing variant0.00000678Highly InformativeDirect
Worm Phenotype (WP)egg morphology variant0.0000147Highly InformativeDirect
Worm Phenotype (WP)no induction of antimicrobial peptide expression after infection0.00001877Highly InformativeDirect
Worm Phenotype (WP)embryonic arrest0.0002862Highly InformativeDirect
Worm Phenotype (WP)P granule defective0.05408Highly 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)embryo0.0000000000004874Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.00001458Least InformativeDirect
Xenopus ANatomical entity (XAN)trunk0.007206Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.0172Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.4131Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical system1Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.00000000003789Moderately InformativeDirect
Xenopus ANatomical entity (XAN)testis0.0000003047Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0.000002185Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.00002262Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0.00003309Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.0005946Moderately InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0.003974Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.01596Moderately InformativeInherited
Xenopus ANatomical entity (XAN)brain0.02038Moderately InformativeInherited
Xenopus ANatomical entity (XAN)germ cell0.02461Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro0InformativeDirect
Xenopus ANatomical entity (XAN)immune system0.00000000002203InformativeDirect
Xenopus ANatomical entity (XAN)endocrine system0.0000000001519InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm0.00000003542InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0.000004648InformativeDirect
Xenopus ANatomical entity (XAN)intestine0.000008594InformativeDirect
Xenopus ANatomical entity (XAN)eye0.00004691InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.0003537InformativeDirect
Xenopus ANatomical entity (XAN)hindbrain0.0001939Highly InformativeDirect
Xenopus ANatomical entity (XAN)marginal zone0.0007763Highly InformativeDirect
Xenopus ANatomical entity (XAN)vegetal hemisphere0.008855Highly InformativeInherited
Xenopus DEvelopment stage (XDE)post-embryonic stage0.002751Least InformativeInherited
Xenopus DEvelopment stage (XDE)unspecified stage0.0001983Moderately InformativeDirect
Xenopus DEvelopment stage (XDE)climax stage0.008749Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)NF stage 660.0007451InformativeDirect

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)Hydrolases0.02114Least InformativeInherited
Enzyme Commission (EC)Transferring phosphorus-containing groups1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups0.0000000005044Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0.0000001871Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.00006764Moderately InformativeDirect
Enzyme Commission (EC)Aminoacyltransferases0.007864Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases0.0179Moderately InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0.05298Moderately InformativeInherited
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect
Enzyme Commission (EC)RNA helicase0.00000000000001916InformativeDirect
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0.00000003403InformativeDirect
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0.0006515InformativeDirect
Enzyme Commission (EC)Peptidylprolyl isomerase0Highly InformativeDirect
Enzyme Commission (EC)Polynucleotide adenylyltransferase0.00000000000000449Highly InformativeDirect
Enzyme Commission (EC)Poly(A)-specific ribonuclease0.0000000000005529Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Post-translational modificationRNA-binding0InformativeDirect

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 ]