Summary: Phage integrase SAM-like domain
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Phage integrase SAM-like domain Provide feedback
A family of uncharacterised proteins found by clustering human gut metagenomic sequences . This family appears related to the N-terminal domain of phage integrases.
Ellrott K, Jaroszewski L, Weizhong L, Wooley J, Godzik, A, PLoS Computational Biology, 2010: Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families PUBMED:20532204 EPMC:20532204
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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 6 members:Flp_N 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 UniProtKB sequence database using the family HMM
- 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:
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:||JCSG - Joint Center for Structural Genomics|
|Author:||Ellrott K, Bateman A|
|Number in seed:||193|
|Number in full:||1052|
|Average length of the domain:||151.10 aa|
|Average identity of full alignment:||17 %|
|Average coverage of the sequence by the domain:||39.40 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||3|
|Download:||download the raw HMM for this family|
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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_5 domain has been found. There are 1 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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