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Table view (23 sequence regions)

Original order	Download FASTA	Accession	Bit score	Type	Start	End	Description	Species	View context
0		CP001124.1	N/A	seed	4,343,880	4,343,790	Geobacter bemidjiensis Bem, complete genome.	Geobacter bemidjiensis Bem
1		CP000698.1	N/A	seed	4,839,082	4,838,991	Geobacter uraniireducens Rf4, complete genome.	Geobacter uraniireducens Rf4
2		AE017180.1	N/A	seed	3,694,623	3,694,713	Geobacter sulfurreducens PCA, complete genome.	Geobacter sulfurreducens PCA
3		CP001390.1	N/A	seed	620,844	620,935	Geobacter sp. FRC-32, complete genome.	Geobacter sp. FRC-32
4		CP000482.1	N/A	seed	292,999	292,905	Pelobacter propionicus DSM 2379, complete genome.	Pelobacter propionicus DSM 2379
5		CP001089.1	N/A	seed	351,026	350,937	Geobacter lovleyi SZ, complete genome.	Geobacter lovleyi SZ
6		CP000148.1	N/A	seed	67,665	67,752	Geobacter metallireducens GS-15, complete genome.	Geobacter metallireducens GS-15
7		AE017180.1	N/A	seed	1,810,322	1,810,409	Geobacter sulfurreducens PCA, complete genome.	Geobacter sulfurreducens PCA
0		AE017180.2	98.00	full	3,694,612	3,694,702	Geobacter sulfurreducens PCA, complete genome.	Geobacter sulfurreducens PCA
1		CP009788.1	86.80	full	58,977	59,064	Geobacter pickeringii strain G13, complete genome.	Geobacter pickeringii
2		BDQG01000001.1	81.80	full	3,787,258	3,787,348	BDQG01000001.1 Geoanaerobacter pelophilus DNA, scaffold: scf_GPEL0_01, strain: Drf2, whole genome shotgun sequence	Geobacter pelophilus
3		VLLN01000013.1	79.10	full	36,259	36,167	VLLN01000013.1 Geobacter argillaceus strain ATCC BAA-1139 Ga0052872_scaffold00013.13, whole genome shotgun sequence	Geobacter argillaceus
4		BAZF01000005.1	78.10	full	175,777	175,685	Geobacter sp. OR-1 DNA, contig: OR1_contig000005.	Geobacter sp. OR-1
5		JAEMHM010000006.1	76.90	full	165,916	166,006	JAEMHM010000006.1 Geomesophilobacter sediminis strain Red875 NODE_6_length_299493_cov_150.316135, whole genome shotgun sequence	Geomesophilobacter sediminis
6		BLXX01000002.1	74.40	full	182,289	182,199	BLXX01000002.1 Geomonas silvestris DNA, sequence02, whole genome shotgun sequence	Geomonas silvestris
7		LT896716.1	69.40	full	3,456,543	3,456,450	LT896716.1 Geobacter sp. DSM 9736 genome assembly, chromosome: I	Geobacter sp. DSM 9736
8		BJBU01000004.1	68.70	full	296,397	296,488	BJBU01000004.1 Geobacter sp. SVR DNA, sequence04, whole genome shotgun sequence	Geobacter sp. SVR
9		SRSD01000006.1	65.60	full	51,747	51,656	SRSD01000006.1 Oryzomonas rubra strain Red88 contig6, whole genome shotgun sequence	Oryzomonas rubra
10		JACABD010000082.1	62.20	full	7,091	7,180	JACABD010000082.1 MAG: Geobacteraceae bacterium isolate Cfx3-08 MAG08_82, whole genome shotgun sequence	Geobacteraceae bacterium
11		AE017180.2	60.40	full	1,810,318	1,810,405	Geobacter sulfurreducens PCA, complete genome.	Geobacter sulfurreducens PCA
12		JWJD01000006.1	60.30	full	78,382	78,476	Geoalkalibacter ferrihydriticus DSM 17813 scaffold6, whole genome shotgun sequence.	Geoalkalibacter ferrihydriticus DSM 17813
13		DUZT01000163.1	54.00	full	2,397	2,304	DUZT01000163.1 MAG TPA_asm: Desulfuromonadales bacterium isolate MAG_21601_9_030 Ga0194061_1017152, whole genome shotgun sequence	Desulfuromonadales bacterium
14		AP022810.1	53.50	full	386,495	386,588	AP022810.1 Desulfuromonas sp. AOP6 DNA, complete genome	Desulfuromonas sp. AOP6

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.

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".

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.

In this page you can view static images showing the secondary structure of this family using a variety of colouring schemes:

Conservation (cons): this plot colours each character by how well conserved it is. A site with 100% sequence conservation is coloured red, 0% is violet.

Covariation (cov): this plot colours each base-pair according to how much the corresponding nucleotides are co-varying. A base-pair position at which every pair of nucleotides is co-variant with respect to every other pair in the alignment gets a score of 2 and is coloured red. Conversely, a base-pair position at every pair is anti-co-variant with respect to every other pair (e.g. lots of mutations to non-canonical pairs) gets a score of -2 and is coloured violet. Further information on this metric can be found in this document.

Sequence entropy (ent): this plot colours each character by how under- or over-represented the residues at the site are. Sites where one or more nucleotides are over-represented while the other nucleotides are either non-existent or near the background frequencies, receive positive scores; sites where all the nucleotides are under-represented receive negative scores. Further information on this metric can be found in this document.

Fraction of canonical basepairs (fcbp): this plot colours each base-pair by the percentage of canonical basepairs (A:U, C:G, G:U) which are found in the corresponding position in the alignment. A pair of sites with 100% canonical pairs is coloured red, a site with 0% is violet.

Maximum parse of the covariance model (maxcm): this plot takes the covariance model for the family and generates the sequence with the maximum possible score for that model. Each character is coloured by how many bits it contributes to the total score.

Sequence: for most of the above cases, the representative sequence used for the backbone is the most informative sequence (MIS). Any residue that has a higher frequency than than the background frequency is projected into the IUPAC redundancy codes.

Normal: this plot simply colours each stem loop

R-chie (rchie): arc diagrams showing secondary structure, calculated using the R-chie package. The consensus secondary structure is visualized as arc diagrams on top of each diagram, where a basepair in an arc, connect two columns of the block of sequences below. The block of sequences below represent the multiple sequence alignment of the Rfam seed, where each sequence is a horizontal strip. Sequences in the alignments are ordered so sequences that best fit the structure are on top, and those that do not fit as well are towards the bottom. For seed alignments for over 500 sequences, 500 random sequences were chosen. Rfam entries without sturcture have a blank plot. Colour information can be found on the R-chie FAQ.

You can also view the secondary structure in the VARNA applet. The applet is shown in a separate pop-up window.

Acknowledgements

The bulk of the code for generating these graphics was kindly supplied by Andreas Gruber and Ivo Hofacker. The statistics were implemented by Rfam.

The VARNA applet is developed by Yann Ponty et al:

The R-chie arc diagrams were calculated using R-chie:

These trees were generated using either a maximum likelihood approach or neighbour-joining. If the number of sequences in the alignment was less than or equal to 64 then the maximum likelihood approach of Rivas and Eddy was used [1]. For families with more than 64 sequences in the alignment the neighbour-joining approach with F84 distances as implemented in phylip was used [2].

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

We do not have tree information for this family. This is most likely due to the size of the family and the number of species covered. For very large families it is too computationally expensive to calculate trees and the resulting tree images would be too large to display in a browser.

There are 1 motifs which match this family.

This section shows the Rfam motifs that match sequences within the seed alignment of this family. Users should be aware that the motifs are structural constructs and do not necessarily conform to taxonomic boundaries in the way that Rfam families do. More...

Original order	Motif Accession	Motif Description	Number of Hits	Fraction of Hits	Sum of Bits	Image
7	RM00008	GNRA tetraloop	5	0.625	47.9