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Table view (25 sequence regions)

Original order	Download FASTA	Accession	Bit score	Type	Start	End	Description	Species	View context
0		X62452.1	N/A	seed	873	682	S. cerevisiae DNA for long ORF (YCR 601)	Saccharomyces cerevisiae (baker's yeast)
1		AABZ01000039.1	N/A	seed	16,243	16,432	Saccharomyces mikatae IFO 1815 contig_216, whole genome shotgun sequence.	Saccharomyces mikatae IFO 1815
2		AACA01000006.1	N/A	seed	89,474	89,283	Saccharomyces bayanus MCYC 623 contig_94, whole genome shotgun sequence.	Saccharomyces bayanus MCYC 623
3		AACI02000034.1	N/A	seed	9,484	9,289	Saccharomyces kudriavzevii IFO 1802 YM6553-Contig02.2075, whole genome shotgun sequence.	Saccharomyces kudriavzevii IFO 1802
0		BK006937.2	237.70	full	178,798	178,607	TPA: Saccharomyces cerevisiae S288C chromosome III, complete sequence.	Saccharomyces cerevisiae S288c
1		JH796485.1	218.20	full	7,924	7,729	Saccharomyces kudriavzevii IFO 1802 unplaced genomic scaffold c2035, whole genome shotgun sequence.	Saccharomyces kudriavzevii IFO 1802
2		CM001565.1	210.30	full	169,001	168,811	Saccharomyces arboricola H-6 chromosome III, whole genome shotgun sequence.	Saccharomyces arboricola H-6
3		HE616747.1	86.20	full	544,805	544,586	Torulaspora delbrueckii CBS 1146 chromosome 6, complete genome	Torulaspora delbrueckii CBS 1146
4		CP058605.1	79.10	full	1,138,446	1,138,246	CP058605.1 Zygotorulaspora mrakii strain NRRL Y-6702 chromosome 2	Zygosaccharomyces mrakii
5		DS480383.1	74.20	full	126,736	126,915	Vanderwaltozyma polyspora DSM 70294 KpolScaffold2002 genomic scaffold, whole genome shotgun sequence.	Vanderwaltozyma polyspora DSM 70294
6		LT598469.1	69.10	full	669,103	669,236	Lachancea mirantina genome assembly, chromosome: G	Lachancea mirantina
7		LT598486.1	67.90	full	348,663	348,825	Lachancea fermentati genome assembly, chromosome: G	Lachancea fermentati
8		HE612860.1	67.50	full	740,259	739,986	Tetrapisispora phaffii CBS 4417 chromosome 5, complete genome	Tetrapisispora phaffii CBS 4417
9		CR382122.1	66.90	full	666,607	666,503	Kluyveromyces lactis strain NRRL Y-1140 chromosome B complete sequence.	Kluyveromyces lactis
10		CU928170.1	66.30	full	344,383	344,555	Lachancea thermotolerans CBS 6340 chromosome F complete sequence.	Lachancea thermotolerans CBS 6340
11		CP059270.1	64.60	full	420,444	420,665	CP059270.1 Torulaspora sp. CBS 2947 strain CBS2947 chromosome 4	Torulaspora sp. CBS 2947
12		HE576760.1	62.80	full	564,497	564,286	Naumovozyma castellii CBS 4309 chromosome 9, complete genome	Naumovozyma castellii CBS 4309
13		AE016818.2	61.60	full	344,509	344,687	Ashbya gossypii ATCC 10895 chromosome V, complete sequence.	Ashbya gossypii ATCC 10895
14		LT598461.1	61.30	full	332,599	332,710	Lachancea dasiensis CBS 10888 genome assembly, chromosome: H	Lachancea dasiensis CBS 10888
15		CU928175.1	60.90	full	951,861	951,664	Zygosaccharomyces rouxii strain CBS732 chromosome C complete sequence.	Zygosaccharomyces rouxii CBS 732
16		LN736370.1	60.20	full	327,537	327,679	Lachancea lanzarotensis strain CBS 12615 genome assembly, scaffold: LALA0S11	Lachancea lanzarotensis
17		JAEUBF010000325.1	55.10	full	30,272	30,143	JAEUBF010000325.1 Wickerhamomyces mucosus strain CBS6341 scaffold51, whole genome shotgun sequence	Wickerhamomyces mucosus
18		CP002504.1	53.60	full	275,962	275,775	Eremothecium cymbalariae DBVPG#7215 chromosome 8, complete sequence.	Eremothecium cymbalariae DBVPG#7215
19		MPUK01000003.1	52.90	full	621,184	620,998	Cyberlindnera fabianii strain 65 BON22_Sc03, whole genome shotgun sequence.	Cyberlindnera fabianii
20		FXLY01000003.1	51.70	full	1,277,959	1,278,150	Kazachstania saulgeensis genome assembly, contig: scaffold_02	Kazachstania saulgeensis

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.