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0  structures 196  species 292  sequences

Family: CsrB (RF00018)

Description: CsrB/RsmB RNA family

Summary

Clan

This family is a member of clan (CL00106), which contains the following 9 members:

CsrB CsrC McaS PrrB_RsmZ RsmW rsmX RsmY TwoAYGGAY Ysr186_sR026_CsrC

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry CsrB/RsmB RNA family. 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...

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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.

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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:
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Download

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

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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...

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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.

Motif matches

There are 7 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 RM00005 CsrA/RsmA binding motif 38 1.000 4480.4 Match Image
7 RM00007 Splicing domain V 19 0.500 202.5 Match Image
7 RM00008 GNRA tetraloop 23 0.605 261.7 Match Image
7 RM00022 Rho independent terminator 1 31 0.816 440.7 Match Image
7 RM00023 Rho independent terminator 2 35 0.921 660.3 Match Image
7 RM00029 UNCG tetraloop 19 0.500 157.5 Match Image
7 RM00030 U-turn motif 8 0.211 80.8 Match Image

References

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

Literature references

  1. Liu MY, Gui G, Wei B, Preston JF 3rd, Oakford L, Yuksel U, Giedroc DP, Romeo T J Biol Chem 1997;272:17502-17510. The RNA molecule CsrB binds to the global regulatory protein CsrA and antagonizes its activity in Escherichia coli. PUBMED:97362239

  2. Cui Y, Chatterjee A, Liu Y, Dumenyo CK, Chatterjee AK J Bacteriol 1995;177:5108-5115. Identification of a global repressor gene, rsmA, of Erwinia carotovora subsp. carotovora that controls extracellular enzymes, N-(3-oxohexanoyl)-L-homoserine lactone, and pathogenicity in soft-rotting Erwinia spp. PUBMED:7665490

  3. Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH, Stadler PF, Dersch P, Narberhaus F Proc Natl Acad Sci U S A. 2016;113:7237-7242. Temperature-responsive in vitro RNA structurome of Yersinia pseudotuberculosis. PUBMED:27298343

  4. Heroven AK, Sest M, Pisano F, Scheb-Wetzel M, Steinmann R, Bohme K, Klein J, Munch R, Schomburg D, Dersch P Front Cell Infect Microbiol. 2012;2:158. Crp induces switching of the CsrB and CsrC RNAs in Yersinia pseudotuberculosis and links nutritional status to virulence. PUBMED:23251905

  5. Mei L, Xu S, Lu P, Lin H, Guo Y, Wang Y PLoS One. 2017;12:e0187492. CsrB, a noncoding regulatory RNA, is required for BarA-dependent expression of biocontrol traits in Rahnella aquatilis HX2. PUBMED:29091941

  6. Yang S, Peng Q, Zhang Q, Yi X, Choi CJ, Reedy RM, Charkowski AO, Yang CH Mol Plant Microbe Interact. 2008;21:133-142. Dynamic regulation of GacA in type III secretion, pectinase gene expression, pellicle formation, and pathogenicity of Dickeya dadantii (Erwinia chrysanthemi 3937). PUBMED:18052890

  7. Cui Y, Chatterjee A, Yang H, Chatterjee AK J Bacteriol. 2008;190:4610-4623. Regulatory network controlling extracellular proteins in Erwinia carotovora subsp. carotovora: FlhDC, the master regulator of flagellar genes, activates rsmB regulatory RNA production by affecting gacA and hexA (lrhA) expression. PUBMED:18441056

  8. Yuan X, Khokhani D, Wu X, Yang F, Biener G, Koestler BJ, Raicu V, He C, Waters CM, Sundin GW, Tian F, Yang CH Environ Microbiol. 2015;17:4745-4763. Cross-talk between a regulatory small RNA, cyclic-di-GMP signalling and flagellar regulator FlhDC for virulence and bacterial behaviours. PUBMED:26462993

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 Bateman A
Structure source Predicted; PFOLD; Bateman A; Gardner PP;
Type Gene; sRNA;
Author Bateman AORCID logo, Gardner PPORCID logo
Alignment details
Alignment Number of
sequences
full 254
seed 38

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 71.0
Trusted cutoff 71.4
Noise cutoff 70.9
Covariance model Download