5  structures 3  species 5  sequences

Family: Phage_pRNA (RF00044)

Description: Bacteriophage pRNA

Summary

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry Bacteriophage pRNA. More...

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

Sequences

Alignment

There are various ways to view or download the seed alignments that we store. You can use a sequence viewer to look at them, or you can look at a plain text version of the sequence in a variety of different formats. More...

View options

You can view Rfam seed alignments in your browser in various ways. Choose the viewer that you want to use and click the "View" button to show the alignment in a pop-up window.

Viewer:

Formatting options

You can view or download Rfam seed alignments in several formats. Check either the "download" button, to save the formatted alignment, or "view", to see it in your browser window, and click "Generate".

Alignment format:
Download/view:

Download

Download a gzip-compressed, Stockholm-format file containing the seed alignment for this family. You may find RALEE useful when viewing sequence alignments.

Submit a new alignment

We're happy receive updated seed alignments for new or existing families. Submit your new alignment and we'll take a look.

Secondary structure

This section shows a variety of different secondary structure representations for this family. More...

You can view the secondary structure of the family using the VARNA applet. You can see more information about VARNA iself here.

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Tree controls

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The tree shows the occurrence of this RNA across different species. More...

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Trees

This page displays the predicted phylogenetic tree for the alignment. More...

This tree was built using the fasttree method.

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Note: You can also download the data file for the seed tree.

Structures

For those sequences which have a structure in the Protein DataBank, we generate a mapping between EMBL, PDB and Rfam coordinate systems. The table below shows the structures on which the Phage_pRNA family has been found.

Loading structure mapping...

References

This section shows the database cross-references that we have for this Rfam family.

Literature references

  1. Guo P Prog Nucleic Acid Res Mol Biol 2002;72:415-472. Structure and function of phi29 hexameric RNA that drives the viral DNA packaging motor: review. PUBMED:12206459

  2. Morais MC, Tao Y, Olson NH, Grimes S, Jardine PJ, Anderson DL, Baker TS, Rossmann MG J Struct Biol 2001;135:38-46. Cryoelectron-microscopy image reconstruction of symmetry mismatches in bacteriophage phi29. PUBMED:11562164

  3. Simpson AA, Tao Y, Leiman PG, Badasso MO, He Y, Jardine PJ, Olson NH, Morais MC, Grimes S, Anderson DL, Baker TS, Rossmann MG Nature 2000;408:745-750. Structure of the bacteriophage phi29 DNA packaging motor. PUBMED:11130079

  4. Badasso MO, Leiman PG, Tao Y, He Y, Ohlendorf DH, Rossmann MG, Anderson D Acta Crystallogr D Biol Crystallogr 2000;56:1187-1190. Purification, crystallization and initial X-ray analysis of the head-tail connector of bacteriophage phi29. PUBMED:10957642

  5. Guo PX, Erickson S, Anderson D Science 1987;236:690-694. A small viral RNA is required for in vitro packaging of bacteriophage phi 29 DNA. PUBMED:3107124

  6. Bailey S, Wichitwechkarn J, Johnson D, Reilly BE, Anderson DL, Bodley JW J Biol Chem 1990;265:22365-22370. Phylogenetic analysis and secondary structure of the Bacillus subtilis bacteriophage RNA required for DNA packaging. PUBMED:2125049

External database links

Curation and family details

This section shows the detailed information about the Rfam family. We're happy to receive updated or improved alignments for new or existing families. Submit your new alignment and we'll take a look.

Curation

Seed source Finn RD
Structure source Predicted; ILM
Type Gene;
Author Finn RDORCID logo
Alignment details
Alignment Number of
sequences
full 2
seed 3

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
Gathering cutoff 40.0
Trusted cutoff 61.9
Noise cutoff 35.9
Covariance model Download