SUPERFAMILY 1.75 HMM library and genome assignments server

L28p-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   L28p-like [ 143799]
Superfamily:   L28p-like [ 143800] (2)
Families:   Ribosomal protein L28 [ 143801]
  Ribosomal protein L31p [ 143804]


Superfamily statistics
Genomes (3,002) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 6,499 38,171 8
Proteins 6,498 38,169 8


Functional annotation
General category Information
Detailed category Translation

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 macromolecule metabolic process0.0084690.01226Least InformativeInherited
Biological Process (BP)biosynthetic process0.0076110.00001786Least InformativeInherited
Biological Process (BP)protein metabolic process0.0032270.0115Least InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.00008970.0001634Moderately InformativeDirect
Biological Process (BP)gene expression0.00012390.0000005027Moderately InformativeDirect
Molecular Function (MF)structural molecule activity0.0000010660.0000000000009506Moderately InformativeDirect
Molecular Function (MF)structural constituent of ribosome0.00000014090InformativeDirect

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) biosynthetic process 0.00001786 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.01226 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.0115 Least Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.0001634 Moderately Informative Direct
Biological Process (BP) gene expression 0.0000005027 Moderately Informative Direct
Molecular Function (MF) structural molecule activity 0.0000000000009506 Moderately Informative Direct
Molecular Function (MF) structural constituent of ribosome 0 Informative Direct
Cellular Component (CC) intracellular organelle part 0.00000001147 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.000001296 Least Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.000005723 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.6084 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 0.000000001025 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.00002601 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.06471 Moderately Informative Inherited
Cellular Component (CC) large ribosomal subunit 0.0000000000009486 Informative Direct
Cellular Component (CC) mitochondrial matrix 0.000004014 Informative Direct
Cellular Component (CC) mitochondrial ribosome 0.00000000000002881 Highly Informative Direct

Document: GO annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Molecular functionZinc0Least InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionrRNA-binding0InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Arabidopsis Plant Ontology (AP) · 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 6 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 L28p-like 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 6 hidden Markov models representing the L28p-like 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) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]