Summary: Phage integrase, N-terminal
Phage integrase, N-terminal Provide feedback
This is a family of DNA-binding prophage integrases. It is found largely in Proteobacteria.
Internal database links
|Similarity to PfamA using HHSearch:||Phage_int_SAM_1|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR024457
Phage integrase proteins 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].
This entry represents the N-terminal predicted alpha-helical domain found in a family of putative prophage DNA-binding integrases.
- 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
- the Pfam graphic itself.
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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:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
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:||Pfam-B_50 (release 24.0)|
|Number in seed:||22|
|Number in full:||357|
|Average length of the domain:||87.30 aa|
|Average identity of full alignment:||33 %|
|Average coverage of the sequence by the domain:||31.33 %|
|HMM build commands:||
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||2|
|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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