Summary: Ribonuclease HII
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Ribonuclease HII Provide feedback
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Internal database links
|SCOOP:||EVI2A Apo-VLDL-II DUF1160 Root_cap YcbB DUF1836 DUF2526 DUF3891 DUF4375 Lipin_mid DUF5101|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR024567
Ribonuclease HII and HIII are endonucleases that specifically degrade the RNA of RNA-DNA hybrids. Proteins which belong to this family have been found in bacteria, archaea, and eukaryota.
The domain represented by this entry is found in ribonucleases HII aand HIII.
- 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
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This clan includes a diverse set of nucleases that share a similar structure to Ribonuclease H.
The clan contains the following 48 members:CAF1 DDE_1 DDE_2 DDE_3 DDE_5 DDE_Tnp_1 DDE_Tnp_1_2 DDE_Tnp_1_3 DDE_Tnp_1_4 DDE_Tnp_1_5 DDE_Tnp_1_6 DDE_Tnp_1_7 DDE_Tnp_2 DDE_Tnp_4 DDE_Tnp_IS1 DDE_Tnp_IS1595 DDE_Tnp_IS240 DDE_Tnp_IS66 DDE_Tnp_ISAZ013 DDE_Tnp_ISL3 DNA_pol_A_exo1 DNA_pol_B_exo1 DNA_pol_B_exo2 DUF2779 DUF3882 DUF4152 DUF5051 Maelstrom MULE NurA OrfB_IS605 Piwi Plant_tran Pox_A22 RNase_H RNase_H_2 RNase_HII RNase_T RNaseH_like RuvC rve rve_2 rve_3 RVT_3 Transposase_1 Transposase_mut UPF0236 Ydc2-catalyt
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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Curation and family details
|Seed source:||Bateman A|
|Number in seed:||11|
|Number in full:||26937|
|Average length of the domain:||183.50 aa|
|Average identity of full alignment:||38 %|
|Average coverage of the sequence by the domain:||73.24 %|
|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:||14|
|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 are 6 interactions 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 RNase_HII domain has been found. There are 35 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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