SUPERFAMILY 1.75 HMM library and genome assignments server


Penicillin binding protein dimerisation domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Penicillin binding protein dimerisation domain [ 56518]
Superfamily:   Penicillin binding protein dimerisation domain [ 56519]
Families:   Penicillin binding protein dimerisation domain [ 56520] (2)


Superfamily statistics
Genomes (2,459) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,742 42,257 6
Proteins 5,735 42,214 6


Functional annotation
General category General
Detailed category Protein interaction

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) nitrogen compound metabolic process 0.007345 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.002137 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.01622 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.01137 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.04318 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.005927 Least Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 2.643e-06 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 1.479e-05 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 3.244e-05 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 6.687e-05 Moderately Informative Direct
Biological Process (BP) aminoglycan biosynthetic process 8.501e-13 Highly Informative Direct
Biological Process (BP) cellular component macromolecule biosynthetic process 1.282e-12 Highly Informative Direct
Biological Process (BP) glycosaminoglycan metabolic process 7.039e-12 Highly Informative Direct
Biological Process (BP) cell wall macromolecule metabolic process 2.682e-11 Highly Informative Direct
Biological Process (BP) cell wall biogenesis 3.789e-11 Highly Informative Direct
Molecular Function (MF) binding 0.0001934 Least Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Glycosyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Peptidoglycan glycosyltransferase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Glycosyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Hexosyltransferases0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle0Moderately InformativeDirect
Biological processAntibiotic resistance0InformativeDirect
Biological processCell wall biogenesis/degradation0InformativeDirect
Biological processCell shape0InformativeDirect
Biological processPeptidoglycan synthesis0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCell membrane1.276e-05Moderately InformativeDirect
DomainTransmembrane1.226e-15Least InformativeDirect
Post-translational modificationTransferase0.01017Least InformativeInherited
Post-translational modificationGlycosyltransferase1.415e-12InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR005311 SSF56519 Protein matches
Abstract

This domain is found at the N-terminus of Class B High Molecular Weight Penicillin-Binding Proteins. Its function has not been precisely defined, but is strongly implicated in PBP polymerisation. The domain forms a largely disordered "sugar tongs" structure.


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) · Enzyme Commission (EC) · 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 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 Penicillin binding protein dimerisation 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 Penicillin binding protein dimerisation 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) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]