Summary: Structure-specific recognition protein (SSRP1)
Structure-specific recognition protein (SSRP1) Provide feedback
SSRP1 has been implicated in transcriptional initiation and elongation and in DNA replication and repair . This domain belongs to the Pleckstrin homology fold superfamily.
Cao S, Bendall H, Hicks GG, Nashabi A, Sakano H, Shinkai Y, Gariglio M, Oltz EM, Ruley HE; , Mol Cell Biol. 2003;23:5301-5307.: The high-mobility-group box protein SSRP1/T160 is essential for cell viability in day 3.5 mouse embryos. PUBMED:12861016 EPMC:12861016
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR024954This domain is found in structure-specific recognition protein (SSRP1) and related proteins, which are components of the FACT complex - a general chromatin factor that acts to reorganise nucleosome. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication and DNA repair. During transcription elongation the FACT complex acts as a histone chaperone that both destabilises and restores nucleosomal structure.
- 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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Members of this clan share a PH-like fold. Many families in this clan bind to short peptide motifs in proteins and are involved in signalling.
The clan contains the following 38 members:bPH_1 bPH_2 bPH_3 bPH_4 bPH_5 bPH_6 DCP1 DUF1448 DUF1681 FERM_C GRAM ICAP-1_inte_bdg IQ_SEC7_PH IRS Mcp5_PH PH PH_10 PH_11 PH_12 PH_13 PH_2 PH_3 PH_4 PH_5 PH_6 PH_8 PH_9 PH_BEACH PH_TFIIH PID PID_2 PTB Ran_BP1 Rtt106 SSrecog Voldacs Vps36_ESCRT-II WH1
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
|Author:||Griffiths-Jones SR, Mistry J|
|Number in seed:||111|
|Number in full:||760|
|Average length of the domain:||213.80 aa|
|Average identity of full alignment:||40 %|
|Average coverage of the sequence by the domain:||37.64 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||10|
|Download:||download the raw HMM for this family|
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The tree shows the occurrence of this domain across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
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There are 3 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 SSrecog 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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