SUPERFAMILY 1.75 HMM library and genome assignments server

DNA-binding pseudobarrel domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   DNA-binding pseudobarrel domain [ 101935]
Superfamily:   DNA-binding pseudobarrel domain [ 101936] (2)
Families:   Type II restriction endonuclease effector domain [ 101937]
  B3 DNA binding domain [ 117343] (2)


Superfamily statistics
Genomes (96) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 9,606 6,376 3
Proteins 7,278 4,948 3


Functional annotation
General category Metabolism
Detailed category Other enzymes

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) multicellular organismal process 0.0000007934 Least Informative Direct
Biological Process (BP) developmental process 0.00000005846 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.004402 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.0162 Least Informative Inherited
Biological Process (BP) reproduction 0.000000000002597 Moderately Informative Direct
Biological Process (BP) response to endogenous stimulus 0.000000001411 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.0003552 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.00000002759 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.0004494 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.07443 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.2818 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.5315 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) organ development 0.7909 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.008395 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.001919 Moderately Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.0000000001462 Informative Direct
Biological Process (BP) response to hormone stimulus 0.00000005774 Informative Direct
Biological Process (BP) reproductive system development 0.0000000000001857 Informative Direct
Biological Process (BP) post-embryonic development 0 Highly Informative Direct
Biological Process (BP) post-embryonic organ development 0.000001224 Highly Informative Direct
Biological Process (BP) response to alcohol 0.00007319 Highly Informative Direct
Biological Process (BP) regulation of reproductive process 0.0000006402 Highly Informative Direct
Biological Process (BP) pattern specification process 0.001023 Highly Informative Inherited
Molecular Function (MF) binding 0.1847 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.000000003675 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding transcription factor activity 0 Informative Direct
Molecular Function (MF) DNA binding 0.0111 Informative Inherited
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.00006025 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)shoot axis0.968Least InformativeInherited
Plant ANatomical entity (PAN)portion of meristem tissue1Least InformativeInherited
Plant ANatomical entity (PAN)flower1Least InformativeInherited
Plant ANatomical entity (PAN)collective phyllome structure1Least InformativeInherited
Plant ANatomical entity (PAN)primordium0.00000854InformativeDirect
Plant ANatomical entity (PAN)plant ovule0.0000002388Highly InformativeDirect
Plant ANatomical entity (PAN)reproductive shoot apex0.00006075Highly InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processAuxin signaling pathway0Highly InformativeDirect
Biological processEthylene signaling pathway0.000000001229Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
DomainRepeat0.00000000000004318Least InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Post-translational modificationActivator0.00007463Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR015300 SSF101936 Protein matches
Abstract

This entry represents the N-terminal effector-binding domain of the type II restriction endonuclease EcoRII, which has a DNA recognition fold, allowing for binding to 5'-CCWGG sequences. It assumes a structure composed of an eight-stranded beta-sheet with the strands in the order of b2, b5, b4, b3, b7, b6, b1 and b8. They are mostly antiparallel to each other except that b3 is parallel to b7. Alternatively, it may also be viewed as consisting of two mini beta-sheets of four antiparallel beta-strands, sheet I from beta-strands b2, b5, b4, b3 and sheet II from strands b7, b6, b1, b8, folded into an open mixed beta-barrel with a novel topology. Sheet I has a simple Greek key motif while sheet II does not [PubMed14659759].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · 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 3 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 DNA-binding pseudobarrel domain 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 3 hidden Markov models representing the DNA-binding pseudobarrel domain 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]