SUPERFAMILY 1.75 HMM library and genome assignments server

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 (3,255) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 21,759 139,626 21
Proteins 21,752 139,606 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)heterocycle metabolic process0.33850.00001739Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.41280.000071Least InformativeInherited
Biological Process (BP)biosynthetic process0.062160.0271Least InformativeInherited
Biological Process (BP)protein metabolic process0.024090.3159Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.16880.002801Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.34370.00002576Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.47610.00007094Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.0071790.00000008726Least InformativeInherited
Biological Process (BP)gene expression0.0000042770.00000000000009141Moderately InformativeDirect
Biological Process (BP)cellular component biogenesis0.050250.0004996Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.086660.000000001926Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.00050220.001118Moderately InformativeInherited
Biological Process (BP)ribonucleoprotein complex biogenesis0.000030820.000000000004697InformativeDirect
Biological Process (BP)ncRNA metabolic process0.00015640.000000002095InformativeDirect
Biological Process (BP)RNA processing0.27540.1006InformativeInherited
Biological Process (BP)rRNA processing0.0000061790Highly InformativeDirect
Molecular Function (MF)binding0.57271Least InformativeInherited
Molecular Function (MF)structural molecule activity0.0000087990.0000007803Moderately InformativeDirect
Molecular Function (MF)nucleic acid binding0.000022080.1154Moderately InformativeInherited
Molecular Function (MF)RNA binding0.0000010670.0004757InformativeDirect
Molecular Function (MF)structural constituent of ribosome0.00000086050.0000000001877InformativeDirect
Cellular Component (CC)intracellular organelle part0.12160.07627Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.30980.00308Least InformativeInherited
Cellular Component (CC)non-membrane-bounded organelle0.0014690.001564Least InformativeInherited
Cellular Component (CC)ribonucleoprotein complex0.0000000042680.000000000009412Moderately InformativeDirect
Cellular Component (CC)cytosol0.0045140.1781Moderately InformativeInherited
Cellular Component (CC)small ribosomal subunit0.0000000025110InformativeDirect

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 0.00002576 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.00007094 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.00000008726 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00001739 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000071 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.9456 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.0271 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.3159 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.002801 Least Informative Inherited
Biological Process (BP) gene expression 0.00000000000009141 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.000000001926 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.0004996 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0.01524 Moderately Informative Inherited
Biological Process (BP) single-organism organelle organization 0.121 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.001118 Moderately Informative Inherited
Biological Process (BP) mitochondrion organization 0.00007319 Informative Direct
Biological Process (BP) RNA modification 0.000000000106 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.000000000004697 Informative Direct
Biological Process (BP) ncRNA metabolic process 0.000000002095 Informative Direct
Biological Process (BP) RNA processing 0.1006 Informative Inherited
Biological Process (BP) rRNA processing 0 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) structural molecule activity 0.0000007803 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0.0000000001499 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.1154 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.0004757 Informative Direct
Molecular Function (MF) structural constituent of ribosome 0.0000000001877 Informative Direct
Molecular Function (MF) ligase activity 0.0000001583 Informative Direct
Molecular Function (MF) intramolecular transferase activity 0 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.07627 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.00308 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.001564 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.9489 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 0.000000000009412 Moderately Informative Direct
Cellular Component (CC) cytosol 0.1781 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.02855 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.01362 Moderately Informative Inherited
Cellular Component (CC) mitochondrial matrix 0.0009579 Informative Direct
Cellular Component (CC) small ribosomal subunit 0 Informative Direct
Cellular Component (CC) cytosolic ribosome 0.0937 Informative Inherited
Cellular Component (CC) cytosolic small ribosomal subunit 0.0002589 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)growth variant0Least InformativeDirect
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Moderately InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP 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)Isomerases0.0000000000005056Moderately InformativeDirect
Enzyme Commission (EC)Intramolecular transferases (mutases)0InformativeDirect
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-binding1Least InformativeInherited
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionATP-binding0.000000000000009085Moderately InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationIsomerase0.000000004449Moderately InformativeDirect
Post-translational modificationAminoacyl-tRNA synthetase0InformativeDirect
Post-translational modificationRibosomal protein0.0000000000585InformativeDirect

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) · 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) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]