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 disease0.01971InformativeInherited
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 inheritance0.00006053InformativeDirect
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 system0.1095Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the musculature0.1168Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.1668Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.6045Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal muscle morphology0.1204Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal respiratory system morphology0.2227Moderately InformativeInherited
Phenotypic Abnormality (PA)Behavioral abnormality0.3967Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.5385Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of central motor function0.6023Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal peripheral nervous system morphology0.6451Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper respiratory tract0.002716InformativeInherited
Phenotypic Abnormality (PA)Fatigable weakness0.005837InformativeInherited
Phenotypic Abnormality (PA)Abnormal muscle fiber morphology0.03542InformativeInherited
Phenotypic Abnormality (PA)Neurological speech impairment0.164InformativeInherited
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0.4556InformativeInherited
Phenotypic Abnormality (PA)Abnormal motor neuron morphology0.0000000393Highly InformativeDirect
Phenotypic Abnormality (PA)Fatigable weakness of swallowing muscles0.0000005918Highly InformativeDirect
Phenotypic Abnormality (PA)Xerostomia0.000007029Highly InformativeDirect
Phenotypic Abnormality (PA)Fatigable weakness of respiratory muscles0.00001765Highly InformativeDirect
Phenotypic Abnormality (PA)Agitation0.0001101Highly InformativeDirect
Phenotypic Abnormality (PA)Paralysis0.0007564Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal spermatogenesis0.002882Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal larynx physiology0.0227Highly InformativeInherited
Phenotypic Abnormality (PA)Atrophy/Degeneration affecting the central nervous system0.03403Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0.2863Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.9999Least InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.7567Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.8893Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell differentiation0.7833InformativeInherited
Mammalian Phenotype (MP)premature neuronal precursor differentiation0.0006307Highly 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 variant8.943e-16Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.000001553Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.0002657Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.0003372Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.001177Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.006154Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.8537Least InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.0003533Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.05602Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.1224Moderately InformativeInherited
Worm Phenotype (WP)apoptosis variant0.2082Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.3913Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.5687Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.7345Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant1Moderately InformativeInherited
Worm Phenotype (WP)sterile progeny1Moderately InformativeInherited
Worm Phenotype (WP)RNA expression variant0.000000000139InformativeDirect
Worm Phenotype (WP)sick0.0000002504InformativeDirect
Worm Phenotype (WP)brood size variant0.000005447InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.00003196InformativeDirect
Worm Phenotype (WP)alimentary system development variant0.0004151InformativeDirect
Worm Phenotype (WP)cell number increased0.001483InformativeInherited
Worm Phenotype (WP)pericellular component morphology variant0.001678InformativeInherited
Worm Phenotype (WP)VPC competence variant0.006509InformativeInherited
Worm Phenotype (WP)vulva development variant0.01558InformativeInherited
Worm Phenotype (WP)egg laying variant0.04396InformativeInherited
Worm Phenotype (WP)organism pathogen response variant0.06674InformativeInherited
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.3162InformativeInherited
Worm Phenotype (WP)oocyte morphology variant0.3363InformativeInherited
Worm Phenotype (WP)cell proliferation increased4.475e-16Highly InformativeDirect
Worm Phenotype (WP)sex determination variant0.00000001713Highly InformativeDirect
Worm Phenotype (WP)neurite development variant0.0000001978Highly InformativeDirect
Worm Phenotype (WP)embryonic lethal late emb0.000001617Highly InformativeDirect
Worm Phenotype (WP)RNA processing variant0.000005364Highly InformativeDirect
Worm Phenotype (WP)no induction of antimicrobial peptide expression after infection0.00001885Highly InformativeDirect
Worm Phenotype (WP)developmental morphology variant0.0001115Highly InformativeDirect
Worm Phenotype (WP)embryonic arrest0.0003059Highly InformativeDirect
Worm Phenotype (WP)P granule defective0.05154Highly 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)tissue0.00001267Least InformativeDirect
Xenopus ANatomical entity (XAN)trunk0.007033Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.0165Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.4137Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical system1Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.000000000005234Moderately InformativeDirect
Xenopus ANatomical entity (XAN)testis0.0000003207Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0.000002089Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.00001354Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0.00002447Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.0005121Moderately InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0.003431Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.01561Moderately InformativeInherited
Xenopus ANatomical entity (XAN)brain0.01872Moderately InformativeInherited
Xenopus ANatomical entity (XAN)germ cell0.02643Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro0InformativeDirect
Xenopus ANatomical entity (XAN)immune system0.00000000002141InformativeDirect
Xenopus ANatomical entity (XAN)endocrine system0.0000000001362InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm0.00000004914InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0.000004308InformativeDirect
Xenopus ANatomical entity (XAN)intestine0.000008446InformativeDirect
Xenopus ANatomical entity (XAN)eye0.00003735InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.0008048InformativeDirect
Xenopus ANatomical entity (XAN)hindbrain0.0008699InformativeDirect
Xenopus ANatomical entity (XAN)marginal zone0.001911Highly InformativeInherited
Xenopus ANatomical entity (XAN)vegetal hemisphere0.006361Highly InformativeInherited
Xenopus DEvelopment stage (XDE)post-embryonic stage0.00275Least InformativeInherited
Xenopus DEvelopment stage (XDE)unspecified stage0.0002075Moderately InformativeDirect
Xenopus DEvelopment stage (XDE)climax stage0.00919Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)NF stage 660.0007666InformativeDirect

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)Hydrolases0.02288Least InformativeInherited
Enzyme Commission (EC)Transferring phosphorus-containing groups1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups0.0000000005031Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0.0000001865Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.00008954Moderately InformativeDirect
Enzyme Commission (EC)Aminoacyltransferases0.007887Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases0.01797Moderately InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0.0533Moderately InformativeInherited
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect
Enzyme Commission (EC)RNA helicase0.00000000000001933InformativeDirect
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0.00000003416InformativeDirect
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0.0006518InformativeDirect
Enzyme Commission (EC)Peptidylprolyl isomerase0Highly InformativeDirect
Enzyme Commission (EC)Polynucleotide adenylyltransferase0.000000000000004469Highly InformativeDirect
Enzyme Commission (EC)Poly(A)-specific ribonuclease0.0000000000005549Highly 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 ]