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 (3,254) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 21,749 139,626 21
Proteins 21,742 139,606 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)biosynthetic process0.062870.03077Least InformativeInherited
Biological Process (BP)protein metabolic process0.022730.3109Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.0071678.345e-08Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.33452.49e-05Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.46327.13e-05Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.32961.681e-05Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.40916.769e-05Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.16510.002076Least InformativeInherited
Biological Process (BP)gene expression2.977e-063.627e-14Moderately InformativeDirect
Biological Process (BP)RNA metabolic process0.087221.757e-09Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.052590.0006361Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.00050660.001124Moderately InformativeInherited
Biological Process (BP)ribonucleoprotein complex biogenesis3.11e-055.224e-12InformativeDirect
Biological Process (BP)ncRNA metabolic process0.00015792.387e-09InformativeDirect
Biological Process (BP)RNA processing0.31130.1407InformativeInherited
Biological Process (BP)rRNA processing6.226e-060Highly InformativeDirect
Molecular Function (MF)binding0.56531Least InformativeInherited
Molecular Function (MF)structural molecule activity8.754e-067.79e-07Moderately InformativeDirect
Molecular Function (MF)nucleic acid binding1.37e-050.1659Moderately InformativeInherited
Molecular Function (MF)RNA binding4.332e-070.0006623InformativeDirect
Molecular Function (MF)structural constituent of ribosome8.587e-071.861e-10InformativeDirect
Cellular Component (CC)intracellular organelle part0.12130.08511Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.30720.002972Least InformativeInherited
Cellular Component (CC)intracellular non-membrane-bounded organelle0.0010930.001031Least InformativeInherited
Cellular Component (CC)ribonucleoprotein complex4.132e-099.579e-12Moderately InformativeDirect
Cellular Component (CC)cytosol0.0045430.1768Moderately InformativeInherited
Cellular Component (CC)small ribosomal subunit2.549e-090InformativeDirect

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 2.49e-05 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 7.13e-05 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 8.345e-08 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 1.681e-05 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 6.769e-05 Least Informative Direct
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.03077 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.002076 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.3109 Least Informative Inherited
Biological Process (BP) gene expression 3.627e-14 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 1.757e-09 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.0006361 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0.0164 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.06789 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.001124 Moderately Informative Inherited
Biological Process (BP) mitochondrion organization 9.334e-05 Informative Direct
Biological Process (BP) RNA modification 1.116e-10 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 5.224e-12 Informative Direct
Biological Process (BP) ncRNA metabolic process 2.387e-09 Informative Direct
Biological Process (BP) RNA processing 0.1407 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 7.79e-07 Moderately Informative Direct
Molecular Function (MF) isomerase activity 1.494e-10 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.1659 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.0006623 Informative Direct
Molecular Function (MF) structural constituent of ribosome 1.861e-10 Informative Direct
Molecular Function (MF) ligase activity 2.076e-05 Informative Direct
Molecular Function (MF) intramolecular transferase activity 0 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.08511 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.002972 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.001031 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 9.579e-12 Moderately Informative Direct
Cellular Component (CC) cytosol 0.1768 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.02717 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.02806 Moderately Informative Inherited
Cellular Component (CC) mitochondrial matrix 0.0006272 Informative Direct
Cellular Component (CC) small ribosomal subunit 0 Informative Direct
Cellular Component (CC) cytosolic ribosome 0.111 Informative Inherited
Cellular Component (CC) cytosolic small ribosomal subunit 0.000344 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)Isomerases1.001e-12Least 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)Isomerases5.056e-13Moderately 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-binding9.085e-15Moderately InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationIsomerase4.449e-09Moderately InformativeDirect
Post-translational modificationAminoacyl-tRNA synthetase0InformativeDirect
Post-translational modificationRibosomal protein5.85e-11InformativeDirect

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 ]