The Wikipedia text that you see displayed on our web site was retrieved from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button above ("Edit wikipedia entry") takes you to the edit page for the article directly within Wikipedia.

Before you edit for the first time

Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.

You should take a few minutes to view the following pages:

• Five pillars
• Policies and quidelines
• Wikipedia help contents
• Wikipedia Tips
• Editing help

Things you should know

How your contribution will be recorded

Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia entry" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer’s IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.

If you have problems editing a particular page, contact us at rfam-help@ebi.ac.uk and we will try to help.

Information we would like to see added

We would value contributions that are referenced directly to the primary literature. Information on structure and function will be especially valuable.

Adding references is explained by this Wikipedia how-to article.

For a good example of what is possible in wikipedia, look at the Hammerhead Ribozyme entry.

Does Rfam agree with the content of the Wikipedia entry ?

Rfam has chosen to create Wikipedia entries for all of our RNA families and to open them up to community annotation. While the original Wikipedia article that we import was (in most cases) generated from Rfam annotations, the Wikipedia article you see now may bear little resemblance to that original text. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Rfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.

Contact us

If you have problems editing or experience problems with these pages please contact us.

If you are interested in contributing to a wide range of articles relating to RNA, see the Wikiproject RNA page.

Quick actions

Table view (49 sequence regions)

Original order	Download FASTA	Accession	Bit score	Type	Start	End	Description	Species	View context
0		FN424405.1	N/A	seed	74,844	74,921	Salmonella enterica subsp. enterica serovar Typhimurium str. D23580 complete genome	Salmonella enterica subsp. enterica serovar Typhimurium str. D23580
1		FR877557.1	N/A	seed	55,147	55,225	Salmonella bongori NCTC 12419, culture collection SGSC SARC11, complete genome	Salmonella bongori NCTC 12419
2		CP000964.1	N/A	seed	4,759,511	4,759,434	Klebsiella pneumoniae 342, complete genome.	Klebsiella pneumoniae 342
3		FN543502.1	N/A	seed	41,079	41,156	Citrobacter rodentium ICC168, complete genome	Citrobacter rodentium ICC168
4		CP002824.1	N/A	seed	2,339,682	2,339,760	Enterobacter aerogenes KCTC 2190, complete genome.	Enterobacter aerogenes KCTC 2190
5		FN543093.2	N/A	seed	720,844	720,920	Cronobacter turicensis z3032 complete genome	Cronobacter turicensis z3032
0		CP000880.1	99.60	full	2,870,610	2,870,533	Salmonella enterica subsp. arizonae serovar 62:z4,z23:--, complete genome.	Salmonella enterica subsp. arizonae serovar 62:z4,z23:--
1		AE006468.2	99.60	full	74,844	74,921	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2, complete genome.	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
2		PYKI01000680.1	99.60	full	142	219	PYKI01000680.1 Salmonella enterica subsp. enterica serovar Poona strain 22sa NODE_2714_length_544_cov_4.0621, whole genome shotgun sequence	Salmonella enterica subsp. enterica serovar Poona
3		LS483466.1	99.60	full	3,785,556	3,785,479	LS483466.1 Salmonella enterica subsp. arizonae strain NCTC7307 genome assembly, chromosome: 1	Salmonella enterica subsp. arizonae
4		CP000822.1	93.30	full	3,124,362	3,124,285	Citrobacter koseri ATCC BAA-895, complete genome.	Citrobacter koseri ATCC BAA-895
5		JABXSS010000001.1	92.00	full	3,474,197	3,474,119	JABXSS010000001.1 Citrobacter freundii strain RHB34-C11 RHB34-C11_1, whole genome shotgun sequence	Citrobacter freundii
6		KK036986.1	90.90	full	5,447,874	5,447,796	KK036986.1 Klebsiella michiganensis strain MGH 27 adjbQ-supercont1.1, whole genome shotgun sequence	Klebsiella michiganensis
7		CP019445.1	88.60	full	453,844	453,767	CP019445.1 Kosakonia cowanii JCM 10956 = DSM 18146 strain 888-76 chromosome, complete genome	Kosakonia cowanii JCM 10956 = DSM 18146
8		VCHQ01000024.1	87.00	full	130,703	130,781	VCHQ01000024.1 Klebsiella indica strain TOUT106 salmonela_mira_c24, whole genome shotgun sequence	Klebsiella indica
9		CP002272.1	86.40	full	3,963,758	3,963,681	Enterobacter cloacae SCF1, complete genome.	Enterobacter cloacae SCF1
10		WAAG01075990.1	85.70	full	90,034	89,957	WAAG01075990.1 Tichodroma muraria voucher UWBM:61504 isolate B10K-DU-012-47 scaffold14438_3, whole genome shotgun sequence	Tichodroma muraria
11		WJYB01000005.1	85.70	full	122,450	122,527	WJYB01000005.1 Enterobacteriaceae bacterium RIT714 5, whole genome shotgun sequence	Enterobacteriaceae bacterium RIT714
12		BBMZ01000002.1	83.80	full	357,931	357,854	Escherichia vulneris NBRC 102420 DNA, contig: EV10242002.	Escherichia vulneris NBRC 102420
13		CP022114.1	81.30	full	4,178,038	4,177,961	CP022114.1 Kluyvera genomosp. 3 strain YDC799 chromosome, complete genome	Kluyvera genomosp. 3
14		CP000653.1	81.30	full	663,750	663,827	Enterobacter sp. 638, complete genome.	Enterobacter sp. 638
15		CAADJD010000021.1	81.00	full	251,613	251,690	CAADJD010000021.1 Kluyvera cryocrescens strain NCTC12993 genome assembly, contig: ERS473437SCcontig000021, whole genome shotgun sequence	Kluyvera cryocrescens
16		CP003200.1	80.80	full	791,014	791,091	CP003200.1 Klebsiella pneumoniae subsp. pneumoniae HS11286, complete genome	Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)
17		UGLZ01000005.1	79.70	full	3,368,515	3,368,438	UGLZ01000005.1 Klebsiella pneumoniae subsp. ozaenae strain NCTC5050 genome assembly, contig: ERS513128SCcontig000005, whole genome shotgun sequence	Klebsiella pneumoniae subsp. ozaenae
18		CP000783.1	79.70	full	3,232,305	3,232,229	Cronobacter sakazakii ATCC BAA-894, complete genome.	Cronobacter sakazakii ATCC BAA-894
19		JNGI01000030.1	79.40	full	2,730	2,808	JNGI01000030.1 Trabulsiella odontotermitis strain 12 SAMPLE12_CONTIG_30, whole genome shotgun sequence	Trabulsiella odontotermitis
20		JMPI01000060.1	79.30	full	17,032	16,956	Buttiauxella agrestis ATCC 33320 GBAG.assembly.060, whole genome shotgun sequence.	Buttiauxella agrestis ATCC 33320
21		LMLK01000012.1	75.60	full	424,561	424,639	Erwinia sp. Leaf53 contig_2, whole genome shotgun sequence.	Erwinia sp. Leaf53
22		CP003938.1	74.70	full	4,006,549	4,006,472	CP003938.1 Enterobacteriaceae bacterium strain FGI 57, complete genome	Enterobacteriaceae bacterium strain FGI 57
23		BAFF01000002.1	73.80	full	318,066	318,142	Escherichia hermannii NBRC 105704 DNA, contig: EH10570402.	Atlantibacter hermannii NBRC 105704
24		FP236843.1	73.40	full	813,863	813,941	Erwinia billingiae strain Eb661 complete chromosome.	Erwinia billingiae
25		MNCH01000025.1	72.10	full	121,966	122,043	MNCH01000025.1 Erwinia sp. OLSSP12 NODE_3_length_179035_cov_33.675_ID_5, whole genome shotgun sequence	Erwinia sp. OLSSP12
26		JRXE01000023.1	70.60	full	40,614	40,691	Erwinia iniecta strain B120 contig000023, whole genome shotgun sequence.	Erwinia iniecta
27		CP046509.1	70.40	full	3,914,336	3,914,259	CP046509.1 Erwinia sorbitola strain J780 chromosome, complete genome	Erwinia sorbitola
28		CP011427.1	69.70	full	3,344,716	3,344,637	CP011427.1 Pantoea vagans strain ND02 chromosome, complete genome	Pantoea vagans
29		VWUI01000070.1	67.20	full	11,451	11,371	VWUI01000070.1 Pantoea sp. M_5 Scaffold_69, whole genome shotgun sequence	Pantoea sp. M_5
30		CP054212.1	66.60	full	842,894	842,971	CP054212.1 Erwiniaceae bacterium PD-1 chromosome, complete genome	Erwiniaceae bacterium PD-1
31		LT906479.1	66.10	full	787,515	787,591	LT906479.1 Serratia ficaria strain NCTC12148 genome assembly, chromosome: 1	Serratia ficaria
32		LJAM02000106.1	66.00	full	5,062	4,986	LJAM02000106.1 Candidatus Erwinia dacicola strain Oroville edac.contig.100_1, whole genome shotgun sequence	Candidatus Erwinia dacicola
33		KZ478063.1	65.70	full	187,654	187,732	KZ478063.1 Enterobacterales bacterium CwR94 genomic scaffold scf_19201_5, whole genome shotgun sequence	Enterobacterales bacterium CwR94
34		LDZF01000016.1	64.60	full	5,074	4,996	Pluralibacter gergoviae strain JS81F13 contig_16, whole genome shotgun sequence.	Enterobacter gergoviae
35		LN907827.1	63.40	full	763,471	763,546	Erwinia sp. EM595 isolate E_g_EM595 genome assembly, chromosome: 1	Erwinia gerundensis
36		CP001560.1	63.30	full	3,431,843	3,431,767	Shimwellia blattae DSM 4481 = NBRC 105725, complete genome.	Escherichia blattae DSM 4481
37		UGSO01000001.1	62.70	full	3,369,078	3,368,998	UGSO01000001.1 Pantoea agglomerans strain NCTC9381 genome assembly, contig: ERS513136SCcontig000001, whole genome shotgun sequence	Pantoea agglomerans
38		JJMI01000019.1	61.90	full	168,409	168,332	Mangrovibacter sp. MFB070 Contig-019, whole genome shotgun sequence.	Mangrovibacter sp. MFB070
39		KB630006.1	60.70	full	137,333	137,258	KB630006.1 Dendroctonus ponderosae unplaced genomic scaffold Seq_968625, whole genome shotgun sequence	Dendroctonus ponderosae (mountain pine beetle)
40		CP001875.2	60.30	full	781,175	781,254	Pantoea ananatis LMG 20103, complete genome.	Pantoea ananatis LMG 20103
41		CP014136.1	59.30	full	1,929,262	1,929,186	CP014136.1 Gibbsiella quercinecans strain FRB97 chromosome, complete genome	Gibbsiella quercinecans
42		CP011254.1	56.40	full	2,649,434	2,649,510	Serratia fonticola strain DSM 4576, complete genome.	Serratia fonticola

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 2 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	RM00022	Rho independent terminator 1	4	0.667	58.9
7	RM00023	Rho independent terminator 2	6	1.000	98.3