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Alpha-L RNA-binding motif superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Alpha-L RNA-binding motif [ 55173]
Superfamily:   Alpha-L RNA-binding motif [ 55174] (5)
Families:   Ribosomal protein S4 [ 55178]
  Heat shock protein 15 kD [ 55182]
  Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain [ 75465]
  YbcJ-like [ 103046]
  Pseudouridine synthase RsuA N-terminal domain [ 75468]


Superfamily statistics
Genomes (3,261) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 21,785 133,986 21
Proteins 21,778 133,913 21


Functional annotation
General category Regulation
Detailed category RNA binding, metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)cellular nitrogen compound metabolic process0.0040810Least InformativeInherited
Biological Process (BP)primary metabolic process0.15330.0000004143Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.29670.0000001197Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.29920.00000008528Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.38050.0000004699Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.0091170.005932Least InformativeInherited
Biological Process (BP)macromolecule metabolic process0.0085580.00000000002176Least InformativeInherited
Biological Process (BP)biosynthetic process0.059160.007346Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.19870.8364Least InformativeInherited
Biological Process (BP)peptide metabolic process0.0000037290Moderately InformativeDirect
Biological Process (BP)gene expression0.000002150Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.00033470.000007387Moderately InformativeDirect
Biological Process (BP)amide biosynthetic process0.000008760Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization0.0095630.07861Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.078660.000000000009274Moderately InformativeInherited
Biological Process (BP)ribosome biogenesis0.0000000047780InformativeDirect
Biological Process (BP)ribonucleoprotein complex subunit organization0.000020030.00002694InformativeDirect
Molecular Function (MF)binding0.51141Least InformativeInherited
Molecular Function (MF)structural molecule activity0.0000000024460.0000000001043Moderately InformativeDirect
Molecular Function (MF)nucleic acid binding0.000039150.0575Moderately InformativeInherited
Molecular Function (MF)RNA binding0.0000017590.00004336InformativeDirect
Cellular Component (CC)non-membrane-bounded organelle0.00047080.0007627Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.12780.4054Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.2010.0001832Least InformativeInherited
Cellular Component (CC)ribosome0.000013960.000000001418Moderately InformativeDirect
Cellular Component (CC)cytosolic part0.000038410.000009308Moderately InformativeDirect
Cellular Component (CC)small ribosomal subunit0.00000000015470InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular aromatic compound metabolic process 0.0000001197 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.00000000002176 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0000004143 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00000008528 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0000004699 Least Informative Direct
Biological Process (BP) biosynthetic process 0.007346 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.3877 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.8364 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.005932 Least Informative Inherited
Biological Process (BP) peptide metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0.00008762 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.000000000009274 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.000007387 Moderately Informative Direct
Biological Process (BP) amide biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.07861 Moderately Informative Inherited
Biological Process (BP) RNA modification 0.0000000000001847 Informative Direct
Biological Process (BP) ribosome biogenesis 0 Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0.00002694 Informative Direct
Biological Process (BP) tRNA metabolic process 0.8404 Informative Inherited
Biological Process (BP) ncRNA processing 0.006814 Informative Inherited
Biological Process (BP) rRNA metabolic process 0.002557 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) structural molecule activity 0.0000000001043 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0.00000000000107 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.0575 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.00004336 Informative Direct
Molecular Function (MF) ligase activity 0.0000000002144 Informative Direct
Molecular Function (MF) intramolecular transferase activity 0 Highly Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.0007627 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.0001832 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.4054 Least Informative Inherited
Cellular Component (CC) ribosome 0.000000001418 Moderately Informative Direct
Cellular Component (CC) cytosolic part 0.000009308 Moderately Informative Direct
Cellular Component (CC) small ribosomal subunit 0 Informative Direct
Cellular Component (CC) cytosolic ribosome 0.02713 Informative Inherited
Cellular Component (CC) cytosolic small ribosomal subunit 0.00005239 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Least InformativeDirect
Enzyme Commission (EC)Isomerases0.000000000001001Least InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compoun0Moderately InformativeDirect
Enzyme Commission (EC)Transferring other groups0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processrRNA processing0InformativeDirect
Biological processProtein biosynthesis0InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Molecular functionNucleotide-binding0.00003119Least InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationIsomerase0.0000000001163Moderately InformativeDirect
Post-translational modificationAminoacyl-tRNA synthetase0InformativeDirect
Post-translational modificationRibosomal protein0.000000000008033InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · 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 9 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 Alpha-L RNA-binding motif 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 9 hidden Markov models representing the Alpha-L RNA-binding motif 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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]