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 inheritance0.0001362InformativeDirect
Mode of Inheritance (MI)Y-linked inheritance0.000406Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.2788Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the musculature0.3773Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.3781Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.4308Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.5751Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal skeletal muscle morphology0.1599Moderately InformativeInherited
Phenotypic Abnormality (PA)Behavioral abnormality0.2717Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of central motor function0.4066Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the respiratory system0.4867Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.5406Moderately InformativeInherited
Phenotypic Abnormality (PA)Neurodevelopmental abnormality0.6003Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper respiratory tract0.009006InformativeInherited
Phenotypic Abnormality (PA)Fatigable weakness0.01248InformativeInherited
Phenotypic Abnormality (PA)Abnormal muscle fiber morphology0.02556InformativeInherited
Phenotypic Abnormality (PA)Neurological speech impairment0.2475InformativeInherited
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0.6183InformativeInherited
Phenotypic Abnormality (PA)Abnormal motor neuron morphology0.0000002097Highly InformativeDirect
Phenotypic Abnormality (PA)Fatigable weakness of swallowing muscles0.000001573Highly InformativeDirect
Phenotypic Abnormality (PA)Fatigable weakness of respiratory muscles0.00004053Highly InformativeDirect
Phenotypic Abnormality (PA)Paralysis0.0003323Highly InformativeDirect
Phenotypic Abnormality (PA)Agitation0.0003662Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of salivation0.0006831Highly InformativeDirect
Phenotypic Abnormality (PA)Azoospermia0.003574Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal larynx physiology0.02651Highly InformativeInherited
Phenotypic Abnormality (PA)Atrophy/Degeneration affecting the central nervous system0.04696Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0.2853Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.9999Least InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.7554Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.8892Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell differentiation0.7837InformativeInherited
Mammalian Phenotype (MP)premature neuronal precursor differentiation0.0006292Highly 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 variant0.00000000000000806Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.0000001426Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.000001921Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.0004276Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.008526Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.7615Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.8452Least InformativeInherited
Worm Phenotype (WP)neuron development variant0.0001688Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.0002511Moderately InformativeDirect
Worm Phenotype (WP)metabolic pathway variant0.00336Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.01457Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.04876Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.1322Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.2794Moderately InformativeInherited
Worm Phenotype (WP)apoptosis variant0.326Moderately InformativeInherited
Worm Phenotype (WP)germ cell development variant0.9824Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant1Moderately InformativeInherited
Worm Phenotype (WP)sterile progeny1Moderately InformativeInherited
Worm Phenotype (WP)RNA expression variant0.0000000004649InformativeDirect
Worm Phenotype (WP)sick0.000000355InformativeDirect
Worm Phenotype (WP)brood size variant0.00001037InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.00003138InformativeDirect
Worm Phenotype (WP)alimentary system development variant0.0002464InformativeDirect
Worm Phenotype (WP)cell number increased0.001248InformativeInherited
Worm Phenotype (WP)pericellular component morphology variant0.001853InformativeInherited
Worm Phenotype (WP)vulva development variant0.01102InformativeInherited
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.02632InformativeInherited
Worm Phenotype (WP)egg laying variant0.03875InformativeInherited
Worm Phenotype (WP)organism pathogen response variant0.1131InformativeInherited
Worm Phenotype (WP)oocyte morphology variant0.244InformativeInherited
Worm Phenotype (WP)cell fate specification variant0.5924InformativeInherited
Worm Phenotype (WP)cell proliferation increased0Highly InformativeDirect
Worm Phenotype (WP)sex determination variant0.00000002767Highly InformativeDirect
Worm Phenotype (WP)neurite development variant0.0000004418Highly InformativeDirect
Worm Phenotype (WP)embryonic lethal late emb0.000001918Highly InformativeDirect
Worm Phenotype (WP)RNA processing variant0.00000423Highly InformativeDirect
Worm Phenotype (WP)no induction of antimicrobial peptide expression after infection0.0000197Highly InformativeDirect
Worm Phenotype (WP)developmental morphology variant0.0001226Highly InformativeDirect
Worm Phenotype (WP)embryonic arrest0.0003888Highly InformativeDirect
Worm Phenotype (WP)organism starvation response variant0.03699Highly InformativeInherited
Worm Phenotype (WP)P granule abnormal0.05243Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0.007584Least InformativeInherited
Fly Phenotype (FP)lethal0.00004993Moderately InformativeDirect

Document: FP 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)embryo0.00000000000009245Least InformativeDirect
Xenopus ANatomical entity (XAN)urogenital system0.000001145Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.000004542Least InformativeDirect
Xenopus ANatomical entity (XAN)nervous system0.001915Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.006201Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.01598Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.4061Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.000000000003278Moderately InformativeDirect
Xenopus ANatomical entity (XAN)testis0.0000001868Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0.000001407Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.000001983Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0.00002817Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.0001851Moderately InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0.002516Moderately InformativeInherited
Xenopus ANatomical entity (XAN)brain0.01095Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.02085Moderately InformativeInherited
Xenopus ANatomical entity (XAN)germ cell0.02221Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro0InformativeDirect
Xenopus ANatomical entity (XAN)immune system0.000000000007994InformativeDirect
Xenopus ANatomical entity (XAN)endocrine system0.00000000005788InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm0.00000004128InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0.0000008106InformativeDirect
Xenopus ANatomical entity (XAN)intestine0.00001711InformativeDirect
Xenopus ANatomical entity (XAN)eye0.00005186InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.0006267InformativeDirect
Xenopus ANatomical entity (XAN)neural crest0.0006548InformativeDirect
Xenopus ANatomical entity (XAN)limb0.0006992InformativeDirect
Xenopus ANatomical entity (XAN)hindbrain0.0001531Highly InformativeDirect
Xenopus ANatomical entity (XAN)marginal zone0.001026Highly InformativeInherited
Xenopus ANatomical entity (XAN)vegetal hemisphere0.009266Highly InformativeInherited
Xenopus DEvelopment stage (XDE)post-embryonic stage0.002094Least InformativeInherited
Xenopus DEvelopment stage (XDE)unspecified stage0.0002316Moderately InformativeDirect
Xenopus DEvelopment stage (XDE)climax stage0.008847Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)NF stage 660.0005085InformativeDirect

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)Hydrolases0.01499Least InformativeInherited
Enzyme Commission (EC)Transferring phosphorus-containing groups1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups0.000000003457Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0.0000001241Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.00007272Moderately InformativeDirect
Enzyme Commission (EC)Aminoacyltransferases0.007358Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases0.0197Moderately InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0.04617Moderately InformativeInherited
Enzyme Commission (EC)RNA helicase0.00000000000001388InformativeDirect
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0.00000003461InformativeDirect
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0.0006119InformativeDirect
Enzyme Commission (EC)Peptidylprolyl isomerase0Highly InformativeDirect
Enzyme Commission (EC)Polynucleotide adenylyltransferase0.000000000000003019Highly InformativeDirect
Enzyme Commission (EC)Poly(A)-specific ribonuclease0.0000000000003649Highly 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 Phenotype (FP) · 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 Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]