SUPERFAMILY 1.75 HMM library and genome assignments server


lambda integrase-like, N-terminal domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   SAM domain-like [ 47768] (16)
Superfamily:   lambda integrase-like, N-terminal domain [ 47823]
Families:   lambda integrase-like, N-terminal domain [ 47824] (3)


Superfamily statistics
Genomes (1,375) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,860 12,269 18
Proteins 2,855 12,263 18


Functional annotation
General category Regulation
Detailed category DNA-binding

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) cellular aromatic compound metabolic process 6.68e-05 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0001835 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0004561 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 6.036e-05 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0001029 Least Informative Direct
Biological Process (BP) DNA metabolic process 3.816e-08 Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle0Moderately InformativeDirect
Biological processDNA recombination0InformativeDirect
Biological processDNA integration0Highly InformativeDirect
Biological processChromosome partition0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR010998 SSF47823 Protein matches
Abstract

Phage integrases are enzymes that mediate unidirectional site-specific recombination between two DNA recognition sequences, the phage attachment site, attP, and the bacterial attachment site, attB [PubMed14687564]. Integrases may be grouped into two major families, the tyrosine recombinases and the serine recombinases, based on their mode of catalysis. Tyrosine family integrases, such as lambda integrase, utilise a catalytic tyrosine to mediate strand cleavage, tend to recognize longer attP sequences, and require other proteins encoded by the phage or the host bacteria.

The 356 amino acid lambda integrase consists of two domains: an N-terminal domain (NTD) that includes residues 1 - 64 and is responsible for binding the arm-type sites of attP, and a C-terminal domain that binds the lower affinity core-type sites and contains the catalytic site. The NTD adopts a 4-5 helical bundle fold with two orthogonally packed alpha-hairpins.

The recombinases Cre from P1 phage, XerD from Escherichia coli, and Flp from yeast are members of the tyrosine recombinase family, and have a two-domain motif resembling that of lambda integrase, as well as sharing a conserved binding mechanism [PubMed12560475, PubMed16139195].

The phage integrase NTD is almost always found with the signature that defines the phage integrase family (see )


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) · 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 lambda integrase-like, N-terminal 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 lambda integrase-like, N-terminal 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) · UniProtKB KeyWords (KW) · Internal database links ]