0  structures 33  species 33  sequences

Family: MicX (RF01808)

Description: MicX Vibrio cholerae sRNA

Summary

Wikipedia annotation Edit Wikipedia article

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

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

Sequences

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Table view (33 sequence regions)

Original order Download FASTA Accession Bit score Type Start End Description Species View context
0
CP000626.1 N/A seed 331,571 331,760 Vibrio cholerae O395 chromosome 1, complete genome. Vibrio cholerae O395 ENA graphic
1
ABCH01000001.1 N/A seed 19,775 19,585 Vibrio shilonii AK1 1103207002036, whole genome shotgun sequence. Vibrio shilonii AK1 ENA graphic
2
AAND01000001.1 N/A seed 379,408 379,215 Vibrio sp. MED222 1099517005441, whole genome shotgun sequence. Vibrio sp. MED222 ENA graphic
3
AAZW01000001.1 N/A seed 161,990 161,797 Vibrionales bacterium SWAT-3 1101732140681, whole genome shotgun sequence. Vibrionales bacterium SWAT-3 ENA graphic
4
AAMR01000001.1 N/A seed 281,169 280,976 Vibrio splendidus 12B01 1099451319047, whole genome shotgun sequence. Vibrio splendidus 12B01 ENA graphic
5
AAWP01000001.1 N/A seed 1,050 855 Vibrio harveyi HY01 gcontig_1104549817909, whole genome shotgun sequence. Vibrio harveyi HY01 ENA graphic
6
AAKK02000017.1 N/A seed 55,451 55,647 Vibrio sp. Ex25 gcontig_1102407882392, whole genome shotgun sequence. Vibrio sp. Ex25 ENA graphic
7
ACCV01000131.1 N/A seed 51,068 50,879 Vibrio parahaemolyticus 16 ctg_1108854221821, whole genome shotgun sequence. Vibrio parahaemolyticus 16 ENA graphic
8
BA000038.2 N/A seed 471,144 471,335 Vibrio vulnificus YJ016 DNA, chromosome II, complete sequence. Vibrio vulnificus YJ016 ENA graphic
9
AAWQ01000001.1 N/A seed 189,388 189,583 Vibrio parahaemolyticus AQ3810 gcontig_1104296536336, whole genome shotgun sequence. Vibrio parahaemolyticus AQ3810 ENA graphic
0
BA000032.2 211.40 full 1,469,059 1,468,864 Vibrio parahaemolyticus RIMD 2210633 DNA, chromosome 2, complete sequence. Vibrio parahaemolyticus RIMD 2210633 ENA graphic
1
LMXU01000032.1 190.20 full 504,290 504,482 LMXU01000032.1 Vibrio toranzoniae strain Vb 10.8 Contig_031, whole genome shotgun sequence Vibrio toranzoniae ENA graphic
2
LHPJ01000008.1 177.00 full 54,167 53,974 Vibrio nereis strain DSM 19584 contig0008, whole genome shotgun sequence. Vibrio nereis ENA graphic
3
JMCG01000001.1 175.40 full 2,861,426 2,861,234 JMCG01000001.1 Vibrio navarrensis strain ATCC 51183 contig1, whole genome shotgun sequence Vibrio navarrensis ENA graphic
4
FNDD01000011.1 172.80 full 59,094 59,286 FNDD01000011.1 Vibrio xiamenensis strain CGMCC 1.10228 genome assembly, contig: Ga0070553_111, whole genome shotgun sequence Vibrio sp. G21 ENA graphic
5
AE003853.1 171.70 full 893,460 893,271 Vibrio cholerae O1 biovar eltor str. N16961 chromosome II, complete sequence. Vibrio cholerae O1 biovar El Tor str. N16961 ENA graphic
6
BBMT01000003.1 171.10 full 13,140 13,329 Vibrio maritimus DNA, contig: contig00003, strain: JCM 19240. Vibrio sp. R-40493 ENA graphic
7
JXXV01000007.1 170.70 full 95,896 96,086 JXXV01000007.1 Vibrio galatheae strain S2757 contig0007, whole genome shotgun sequence Vibrio sp. S2757 ENA graphic
8
WXWF01000081.1 169.90 full 42,894 42,702 WXWF01000081.1 Vibrio sp. V28_P6S34P95 scaffold8_size56994, whole genome shotgun sequence Vibrio sp. V28_P6S34P95 ENA graphic
9
LKHS01000001.1 169.30 full 273,115 273,303 LKHS01000001.1 Vibrio furnissii strain S0821 contig0001, whole genome shotgun sequence Vibrio furnissii ENA graphic
10
BATJ01000005.1 169.20 full 230,379 230,183 Vibrio proteolyticus NBRC 13287 DNA, contig: VPR01S05. Vibrio proteolyticus NBRC 13287 ENA graphic
11
OANU01000028.1 162.50 full 73,190 73,379 OANU01000028.1 Vibrio thalassae strain CECT8203 genome assembly, contig: 0028, whole genome shotgun sequence Vibrio thalassae ENA graphic
12
AJYW02000178.1 157.30 full 15,481 15,668 Vibrio genomosp. F6 str. FF-238 FF-238_contig_382, whole genome shotgun sequence. Vibrio genomosp. F6 str. FF-238 ENA graphic
13
CP049332.1 155.90 full 690,922 691,112 CP049332.1 Vibrio ziniensis strain ZWAL4003 chromosome 2, complete sequence Vibrio ziniensis ENA graphic
14
JAKRRX010000165.1 152.90 full 3,213 3,017 JAKRRX010000165.1 Vibrio paucivorans strain DBSS07 165, whole genome shotgun sequence Vibrio paucivorans ENA graphic
15
BATL01000058.1 145.90 full 16,373 16,567 Vibrio azureus NBRC 104587 DNA, contig: VAZ01S058. Vibrio azureus NBRC 104587 ENA graphic
16
MAJZ01000488.1 143.00 full 313 119 Vibrio genomosp. F10 strain 9CSC122 9CSC122_contig_366, whole genome shotgun sequence. Vibrio sp. F10 ENA graphic
17
JAJNNZ010000003.1 142.20 full 196,623 196,807 JAJNNZ010000003.1 Vibrio gelatinilyticus strain ZSDZ34 3, whole genome shotgun sequence Vibrio gelatinilyticus ENA graphic
18
JTKH01000024.1 130.90 full 872,178 872,367 JTKH01000024.1 Vibrio renipiscarius strain DCR 1-4-2 Contig24, whole genome shotgun sequence Vibrio renipiscarius ENA graphic
19
MCUV01000024.1 125.00 full 116,292 116,484 MCUV01000024.1 Vibrio sp. 10N.286.49.B3 10N.286.49.B3_contig_3, whole genome shotgun sequence Vibrio sp. 10N.286.49.B3 ENA graphic
20
CP045351.1 123.00 full 1,155,020 1,155,211 CP045351.1 Vibrio aquimaris strain THAF100 plasmid pTHAF100_a, complete sequence Vibrio aquimaris ENA graphic
21
FO203527.1 96.60 full 1,661,322 1,661,124 Vibrio nigripulchritudo str. SFn1 chromosome, complete genome. Vibrio nigripulchritudo ENA graphic
22
CP047476.1 93.70 full 1,540,272 1,540,497 CP047476.1 Vibrio astriarenae strain HN897 chromosome 2, complete sequence Vibrio astriarenae ENA graphic

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 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.

Current Rfam structure

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R-scape optimised structure

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  • Colours
  •  Statistically significant basepair with covariation
  •  97% conserved nucleotide
  •  90% conserved nucleotide
  •  75% conserved nucleotide
  •  50% conserved nucleotide
  • Nucleotides
  • R: A or G
  • Y: C or U

Tip: The diagrams are interactive:
you can pan and zoom to see more details
or hover over nucleotides and basepairs.

R-scape is a method for testing whether covariation analysis supports the presence of a conserved RNA secondary structure. This page shows R-scape analysis of the secondary structure from the Rfam seed alignment and a new structure with covariation support that is compatible with the same alignment.

To find out more about the method, see the R-scape paper by Rivas et al., 2016. The structures are visualised using R2R.

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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The tree shows the occurrence of this RNA across different species. 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 6 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 RM00004 CRC binding motif 6 0.600 97.2 Match Image
7 RM00008 GNRA tetraloop 7 0.700 93.3 Match Image
7 RM00022 Rho independent terminator 1 10 1.000 256.9 Match Image
7 RM00023 Rho independent terminator 2 10 1.000 279.2 Match Image
7 RM00024 T-loop 4 0.400 39.3 Match Image
7 RM00030 U-turn motif 5 0.500 61.9 Match Image

References

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

Literature references

  1. Davis BM, Waldor MK Mol Microbiol. 2007;65:373-385. RNase E-dependent processing stabilizes MicX, a Vibrio cholerae sRNA. PUBMED:17590231

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 Gardner PP
Structure source Predicted; CMfinder
Type Gene; sRNA;
Author Gardner PPORCID logo, Moore BORCID logo
Alignment details
Alignment Number of
sequences
full 23
seed 10

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 25.27 -Z 2958934 CM SEQDB
Gathering cutoff 75.0
Trusted cutoff 93.7
Noise cutoff 71.1
Covariance model Download
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