Summary: Phage integrase, N-terminal SAM-like domain
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Phage integrase, N-terminal SAM-like domain Provide feedback
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Internal database links
|Similarity to PfamA using HHSearch:||Phage_int_SAM_2 Phage_int_SAM_4 Phage_int_SAM_4|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR004107
Proteins containing this domain cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [PUBMED:9082984, PUBMED:9288963].
The phage integrase N-terminal SAM-like domain is almost always found with the signature that defines the phage integrase family (see INTERPRO).
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||DNA binding (GO:0003677)|
|Biological process||DNA integration (GO:0015074)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
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This superfamily is characterised by families having 4-5 helices in a bundle of two orthogonally packed alpha-hairpins that are involved in interactions with DNA and proteins.
The clan contains the following 5 members:Phage_int_SAM_1 Phage_int_SAM_2 Phage_int_SAM_3 Phage_int_SAM_4 Phage_int_SAM_5
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
|Seed source:||Structural domain|
|Number in seed:||37|
|Number in full:||10422|
|Average length of the domain:||83.20 aa|
|Average identity of full alignment:||22 %|
|Average coverage of the sequence by the domain:||26.81 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||12|
|Download:||download the raw HMM for this family|
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The tree shows the occurrence of this domain across different species. More...
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There is 1 interaction for this family. More...
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Phage_int_SAM_1 domain has been found. There are 13 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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