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0  structures 501  species 1027  sequences

Family: suhB (RF00519)

Description: Makes More Granules Regulator RNA (mmgR)

Summary

Clan

This family is a member of clan (CL00108), which contains the following 2 members:

ar15 suhB

Wikipedia annotation Edit Wikipedia article

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

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Motif matches

There are 4 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 35 0.402 388.2 Match Image
7 RM00022 Rho independent terminator 1 72 0.828 1153.1 Match Image
7 RM00023 Rho independent terminator 2 81 0.931 1185.2 Match Image
7 RM00029 UNCG tetraloop 38 0.437 474.1 Match Image

References

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

Literature references

  1. Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M, Rudnick ND, Breaker RR; Genome Biol. 2005;6:R70. Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria. PUBMED:16086852

  2. Valverde C, Livny J, Schluter JP, Reinkensmeier J, Becker A, Parisi G BMC Genomics. 2008;9:416. Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011. PUBMED:18793445

  3. Schluter JP, Reinkensmeier J, Daschkey S, Evguenieva-Hackenberg E, Janssen S, Janicke S, Becker JD, Giegerich R, Becker A BMC Genomics. 2010;11:245. A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti. PUBMED:20398411

  4. Lagares A Jr, Ceizel Borella G, Linne U, Becker A, Valverde C J Bacteriol. 2017; [Epub ahead of print] Regulation of Polyhydroxybutyrate Accumulation in Sinorhizobium meliloti by the Trans-Encoded Small RNA MmgR. PUBMED:28167519

  5. Lagares A Jr, Roux I, Valverde C Mol Phylogenet Evol. 2016;99:182-193. Phylogenetic distribution and evolutionary pattern of an alpha-proteobacterial small RNA gene that controls polyhydroxybutyrate accumulation in Sinorhizobium meliloti. PUBMED:27033949

  6. Torres-Quesada O, Reinkensmeier J, Schluter JP, Robledo M, Peregrina A, Giegerich R, Toro N, Becker A, Jimenez-Zurdo JI RNA Biol. 2014;11:563-579. Genome-wide profiling of Hfq-binding RNAs uncovers extensive post-transcriptional rewiring of major stress response and symbiotic regulons in Sinorhizobium meliloti. PUBMED:24786641

  7. Sobrero P, Valverde C Arch Microbiol. 2011;193:629-639. Evidences of autoregulation of hfq expression in Sinorhizobium meliloti strain 2011. PUBMED:21484295

  8. Ceizel Borella G, Lagares A Jr, Valverde C FEMS Microbiol Lett. 2016; [Epub ahead of print] Expression of the Sinorhizobium meliloti small RNA gene mmgR is controlled by the nitrogen source. PUBMED:27010014

  9. Ceizel Borella G, Lagares A Jr, Valverde C Microbiology. 2018;164:88-98. Expression of the small regulatory RNA gene mmgR is regulated negatively by AniA and positively by NtrC in Sinorhizobium meliloti 2011. PUBMED:29214973

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 Barrick JE
Structure source Predicted; Barrick JE
Type Gene; sRNA;
Author Barrick JE
Alignment details
Alignment Number of
sequences
full 940
seed 87

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 19.00 -Z 549862.597050 CM SEQDB
Gathering cutoff 41.0
Trusted cutoff 41.0
Noise cutoff 40.7
Covariance model Download