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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 process0.0036390Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.30090.0000001354Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.30330.00000009529Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.38320.0000004967Least InformativeInherited
Biological Process (BP)macromolecule metabolic process0.0072310.00000000002902Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.0270.01026Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.19570.8278Least InformativeInherited
Biological Process (BP)primary metabolic process0.14030.000000578Least InformativeInherited
Biological Process (BP)biosynthetic process0.05550.007389Least InformativeInherited
Biological Process (BP)peptide metabolic process0.0000034490Moderately InformativeDirect
Biological Process (BP)gene expression0.0000015740Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.0003450.000006971Moderately InformativeDirect
Biological Process (BP)amide biosynthetic process0.000008220Moderately InformativeDirect
Biological Process (BP)RNA metabolic process0.081220.00000000001008Moderately InformativeInherited
Biological Process (BP)ribosome biogenesis0.00000015210InformativeDirect
Molecular Function (MF)binding0.62021Least InformativeInherited
Molecular Function (MF)structural molecule activity0.000000064560.000000001745Moderately InformativeDirect
Molecular Function (MF)nucleic acid binding0.000033150.05329Moderately InformativeInherited
Molecular Function (MF)RNA binding0.0000015590.00004744InformativeDirect
Cellular Component (CC)cytoplasmic part0.25420.0003265Least InformativeInherited
Cellular Component (CC)macromolecular complex0.0020120.01838Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.20530.4908Least InformativeInherited
Cellular Component (CC)non-membrane-bounded organelle0.0014630.001528Least InformativeInherited
Cellular Component (CC)ribosome0.00012870.00000001759Moderately InformativeDirect
Cellular Component (CC)cytosolic part0.0003710.00007394Moderately InformativeDirect
Cellular Component (CC)small ribosomal subunit0.0000000090050InformativeDirect

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 0.0000001354 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.00000000002902 Least Informative Direct
Biological Process (BP) primary metabolic process 0.000000578 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00000009529 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0000004967 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.8278 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.4217 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.007389 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.01026 Least Informative Inherited
Biological Process (BP) peptide metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0.00008921 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.00000000001008 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.000006971 Moderately Informative Direct
Biological Process (BP) amide biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) RNA modification 0.0000000000002408 Informative Direct
Biological Process (BP) ribosome biogenesis 0 Informative Direct
Biological Process (BP) tRNA metabolic process 0.8317 Informative Inherited
Biological Process (BP) ncRNA processing 0.007935 Informative Inherited
Biological Process (BP) rRNA metabolic process 0.002659 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) structural molecule activity 0.000000001745 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0.000000000001418 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.05329 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.00004744 Informative Direct
Molecular Function (MF) ligase activity 0.000000000178 Informative Direct
Molecular Function (MF) intramolecular transferase activity 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.0003265 Least Informative Direct
Cellular Component (CC) macromolecular complex 0.01838 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.4908 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.001528 Least Informative Inherited
Cellular Component (CC) ribosome 0.00000001759 Moderately Informative Direct
Cellular Component (CC) cytosolic part 0.00007394 Moderately Informative Direct
Cellular Component (CC) small ribosomal subunit 0 Informative Direct
Cellular Component (CC) cytosolic ribosome 0.0506 Informative Inherited
Cellular Component (CC) cytosolic small ribosomal subunit 0.0002128 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

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)general pace of development variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Least InformativeDirect
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval growth variant0Least InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)anatomical cluster0Least InformativeDirect
Xenopus ANatomical entity (XAN)female genitalia0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)egg0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)anatomical entity in vitro0InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0.000000000000001469Moderately InformativeDirect
Enzyme Commission (EC)Intramolecular transferases0InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compounds0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processProtein biosynthesis0InformativeDirect
Biological processrRNA processing0InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Molecular functionNucleotide-binding0.00002357Least InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationIsomerase0.0000000001245Moderately InformativeDirect
Post-translational modificationAminoacyl-tRNA synthetase0InformativeDirect
Post-translational modificationRibosomal protein0.000000000008385InformativeDirect

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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · 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 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]