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 disease0.01961InformativeInherited
Disease Ontology (DO)ischemia0.2899Highly 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 inheritance0.00002766InformativeDirect
Mode of Inheritance (MI)Y-linked inheritance0.0005819Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.06682Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.1047Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the musculature0.1192Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.1904Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.3338Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.9022Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of muscle morphology0.05368Moderately InformativeInherited
Phenotypic Abnormality (PA)Muscle weakness0.1193Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of central motor function0.337Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the respiratory system0.5515Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper respiratory tract0.007646InformativeInherited
Phenotypic Abnormality (PA)Behavioral abnormality0.4072InformativeInherited
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0.4173InformativeInherited
Phenotypic Abnormality (PA)Amyotrophic lateral sclerosis0.00000003869Highly InformativeDirect
Phenotypic Abnormality (PA)Fatigable weakness of bulbar muscles0.0000005954Highly InformativeDirect
Phenotypic Abnormality (PA)Fatigable weakness of respiratory muscles0.0000009112Highly InformativeDirect
Phenotypic Abnormality (PA)Xerostomia0.00000823Highly InformativeDirect
Phenotypic Abnormality (PA)Agitation0.00003577Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal larynx morphology0.00009841Highly InformativeDirect
Phenotypic Abnormality (PA)Elevated serum creatine phosphokinase0.0004348Highly InformativeDirect
Phenotypic Abnormality (PA)Paralysis0.0004815Highly InformativeDirect
Phenotypic Abnormality (PA)Muscle cramps0.000542Highly InformativeDirect
Phenotypic Abnormality (PA)Azoospermia0.001017Highly InformativeInherited
Phenotypic Abnormality (PA)Infertility0.002299Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of muscle fibers0.01169Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0.2659Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype1Least InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.8154Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.8818Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell differentiation0.7833InformativeInherited
Mammalian Phenotype (MP)premature neuronal precursor differentiation0.0006107Highly 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 variant0.000000000000006201Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.000001599Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.0001611Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.0002464Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.001268Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.003228Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.824Least InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.000354Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.07549Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.1134Moderately InformativeInherited
Worm Phenotype (WP)apoptosis variant0.2169Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.468Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.5211Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.697Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant1Moderately InformativeInherited
Worm Phenotype (WP)sterile progeny1Moderately InformativeInherited
Worm Phenotype (WP)RNA expression variant0.00000000003032InformativeDirect
Worm Phenotype (WP)sick0.0000002289InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.00003098InformativeDirect
Worm Phenotype (WP)alimentary system development variant0.0006245InformativeDirect
Worm Phenotype (WP)cell number increased0.001432InformativeInherited
Worm Phenotype (WP)VPC competence variant0.007486InformativeInherited
Worm Phenotype (WP)vulva development variant0.01755InformativeInherited
Worm Phenotype (WP)egg laying variant0.05107InformativeInherited
Worm Phenotype (WP)organism pathogen response variant0.06188InformativeInherited
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.2053InformativeInherited
Worm Phenotype (WP)oocyte morphology variant0.323InformativeInherited
Worm Phenotype (WP)cell proliferation increased8.875e-16Highly InformativeDirect
Worm Phenotype (WP)sex determination variant0.0000001181Highly InformativeDirect
Worm Phenotype (WP)dendrite development variant0.0000002853Highly InformativeDirect
Worm Phenotype (WP)embryonic lethal late emb0.000002084Highly InformativeDirect
Worm Phenotype (WP)RNA processing variant0.000002525Highly InformativeDirect
Worm Phenotype (WP)no induction of antimicrobial peptide expression after infection0.00002302Highly InformativeDirect
Worm Phenotype (WP)developmental morphology variant0.00009678Highly InformativeDirect
Worm Phenotype (WP)embryonic arrest0.0002787Highly InformativeDirect
Worm Phenotype (WP)P granule defective0.07642Highly 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)embryo0.0000000000001687Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0.0000003313Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.000001485Least InformativeDirect
Xenopus ANatomical entity (XAN)nervous system0.00141Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.00571Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.01718Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.4176Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.0000000002667Moderately InformativeDirect
Xenopus ANatomical entity (XAN)germ line cell0.00000007349Moderately InformativeDirect
Xenopus ANatomical entity (XAN)testis0.0000004213Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0.0000007147Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.0000371Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0.00004463Moderately InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0.001548Moderately InformativeInherited
Xenopus ANatomical entity (XAN)musculoskeletal system0.001763Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.007568Moderately InformativeInherited
Xenopus ANatomical entity (XAN)brain0.01366Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro0InformativeDirect
Xenopus ANatomical entity (XAN)immune system0.00000000001883InformativeDirect
Xenopus ANatomical entity (XAN)endocrine system0.00000000009033InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm0.0000001249InformativeDirect
Xenopus ANatomical entity (XAN)skeletal muscle0.000008086InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0.00000983InformativeDirect
Xenopus ANatomical entity (XAN)intestine0.00001129InformativeDirect
Xenopus ANatomical entity (XAN)eye0.0001321InformativeDirect
Xenopus ANatomical entity (XAN)hindbrain0.0002162InformativeDirect
Xenopus ANatomical entity (XAN)limb0.000899InformativeDirect
Xenopus ANatomical entity (XAN)oocyte0.0000001145Highly InformativeDirect
Xenopus ANatomical entity (XAN)marginal zone0.0002233Highly InformativeDirect
Xenopus ANatomical entity (XAN)vegetal hemisphere0.005974Highly InformativeInherited
Xenopus DEvelopment stage (XDE)post-embryonic stage0.002254Least InformativeInherited
Xenopus DEvelopment stage (XDE)climax stage0.0001394Moderately InformativeDirect
Xenopus DEvelopment stage (XDE)unspecified stage0.0003251Moderately InformativeDirect
Xenopus DEvelopment stage (XDE)NF stage 660.0003353InformativeDirect

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 cell0.00000008502Least InformativeDirect
Plant ANatomical entity (PAN)seed0.000006117Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0.0001148Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0.002602Least InformativeInherited
Plant ANatomical entity (PAN)leaf0.005038Least InformativeInherited
Plant ANatomical entity (PAN)inflorescence0.009955Least InformativeInherited
Plant ANatomical entity (PAN)whole plant0.02104Least InformativeInherited
Plant ANatomical entity (PAN)flower0.1691Least InformativeInherited
Plant ANatomical entity (PAN)collective phyllome structure0.2Least InformativeInherited
Plant ANatomical entity (PAN)shoot axis0.2113Least InformativeInherited
Plant ANatomical entity (PAN)gamete0.00005279InformativeDirect
Plant ANatomical entity (PAN)cultured plant cell0.0001433Highly InformativeDirect
Plant ANatomical entity (PAN)bud0.03185Highly InformativeInherited
Plant structure DEvelopment stage (PDE)D bilateral stage0.00001301Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0.00004974Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0.0001061Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0.000115Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0.03649Least InformativeInherited
Enzyme Commission (EC)Transferring phosphorus-containing groups1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups0.0000000003604Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0.0000000976Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.001989Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases0.01748Moderately InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0.04585Moderately InformativeInherited
Enzyme Commission (EC)Acyltransferases0.7487Moderately InformativeInherited
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect
Enzyme Commission (EC)RNA helicase0.0000000000000112InformativeDirect
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0.00000003327InformativeDirect
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0.0005114InformativeDirect
Enzyme Commission (EC)Peptidylprolyl isomerase0Highly InformativeDirect
Enzyme Commission (EC)Polynucleotide adenylyltransferase2.512e-16Highly InformativeDirect
Enzyme Commission (EC)Poly(A)-specific ribonuclease0.0000000000004606Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Post-translational modificationRNA-binding0.000000000000002487InformativeDirect

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 98 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 98 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 ]