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 |
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0 | CP000626.1 | N/A | seed | 331,571 | 331,760 | Vibrio cholerae O395 chromosome 1, complete genome. | Vibrio cholerae O395 |
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1 | ABCH01000001.1 | N/A | seed | 19,775 | 19,585 | Vibrio shilonii AK1 1103207002036, whole genome shotgun sequence. | Vibrio shilonii AK1 |
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2 | AAND01000001.1 | N/A | seed | 379,408 | 379,215 | Vibrio sp. MED222 1099517005441, whole genome shotgun sequence. | Vibrio sp. MED222 |
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3 | AAZW01000001.1 | N/A | seed | 161,990 | 161,797 | Vibrionales bacterium SWAT-3 1101732140681, whole genome shotgun sequence. | Vibrionales bacterium SWAT-3 |
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4 | AAMR01000001.1 | N/A | seed | 281,169 | 280,976 | Vibrio splendidus 12B01 1099451319047, whole genome shotgun sequence. | Vibrio splendidus 12B01 |
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5 | AAWP01000001.1 | N/A | seed | 1,050 | 855 | Vibrio harveyi HY01 gcontig_1104549817909, whole genome shotgun sequence. | Vibrio harveyi HY01 |
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6 | AAKK02000017.1 | N/A | seed | 55,451 | 55,647 | Vibrio sp. Ex25 gcontig_1102407882392, whole genome shotgun sequence. | Vibrio sp. Ex25 |
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7 | ACCV01000131.1 | N/A | seed | 51,068 | 50,879 | Vibrio parahaemolyticus 16 ctg_1108854221821, whole genome shotgun sequence. | Vibrio parahaemolyticus 16 |
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8 | BA000038.2 | N/A | seed | 471,144 | 471,335 | Vibrio vulnificus YJ016 DNA, chromosome II, complete sequence. | Vibrio vulnificus YJ016 |
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9 | AAWQ01000001.1 | N/A | seed | 189,388 | 189,583 | Vibrio parahaemolyticus AQ3810 gcontig_1104296536336, whole genome shotgun sequence. | Vibrio parahaemolyticus AQ3810 |
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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 |
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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 |
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2 | LHPJ01000008.1 | 177.00 | full | 54,167 | 53,974 | Vibrio nereis strain DSM 19584 contig0008, whole genome shotgun sequence. | Vibrio nereis |
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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 |
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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 |
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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 |
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6 | BBMT01000003.1 | 171.10 | full | 13,140 | 13,329 | Vibrio maritimus DNA, contig: contig00003, strain: JCM 19240. | Vibrio sp. R-40493 |
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7 | JXXV01000007.1 | 170.70 | full | 95,896 | 96,086 | JXXV01000007.1 Vibrio galatheae strain S2757 contig0007, whole genome shotgun sequence | Vibrio sp. S2757 |
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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 |
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9 | LKHS01000001.1 | 169.30 | full | 273,115 | 273,303 | LKHS01000001.1 Vibrio furnissii strain S0821 contig0001, whole genome shotgun sequence | Vibrio furnissii |
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10 | BATJ01000005.1 | 169.20 | full | 230,379 | 230,183 | Vibrio proteolyticus NBRC 13287 DNA, contig: VPR01S05. | Vibrio proteolyticus NBRC 13287 |
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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 |
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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 |
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13 | CP049332.1 | 155.90 | full | 690,922 | 691,112 | CP049332.1 Vibrio ziniensis strain ZWAL4003 chromosome 2, complete sequence | Vibrio ziniensis |
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14 | JAKRRX010000165.1 | 152.90 | full | 3,213 | 3,017 | JAKRRX010000165.1 Vibrio paucivorans strain DBSS07 165, whole genome shotgun sequence | Vibrio paucivorans |
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15 | BATL01000058.1 | 145.90 | full | 16,373 | 16,567 | Vibrio azureus NBRC 104587 DNA, contig: VAZ01S058. | Vibrio azureus NBRC 104587 |
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16 | MAJZ01000488.1 | 143.00 | full | 313 | 119 | Vibrio genomosp. F10 strain 9CSC122 9CSC122_contig_366, whole genome shotgun sequence. | Vibrio sp. F10 |
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17 | JAJNNZ010000003.1 | 142.20 | full | 196,623 | 196,807 | JAJNNZ010000003.1 Vibrio gelatinilyticus strain ZSDZ34 3, whole genome shotgun sequence | Vibrio gelatinilyticus |
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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 |
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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 |
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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 |
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21 | FO203527.1 | 96.60 | full | 1,661,322 | 1,661,124 | Vibrio nigripulchritudo str. SFn1 chromosome, complete genome. | Vibrio nigripulchritudo |
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22 | CP047476.1 | 93.70 | full | 1,540,272 | 1,540,497 | CP047476.1 Vibrio astriarenae strain HN897 chromosome 2, complete sequence | Vibrio astriarenae |
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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...
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.
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

R-scape optimised structure

- 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
Sunburst controls
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Move your mouse over the main tree to show the lineage of a particular node.
You can move this pane by dragging it.
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Colour assignments
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Selections
Click on a node to select that node and its sub-tree.
Clear selection
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...
Tree controls
HideThe tree shows the occurrence of this RNA across different species. More...
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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
Trees
This page displays the predicted phylogenetic tree for the alignment. More...
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 |
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7 | RM00004 | CRC binding motif | 6 | 0.600 | 97.2 |
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7 | RM00008 | GNRA tetraloop | 7 | 0.700 | 93.3 |
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7 | RM00022 | Rho independent terminator 1 | 10 | 1.000 | 256.9 |
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7 | RM00023 | Rho independent terminator 2 | 10 | 1.000 | 279.2 |
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7 | RM00024 | T-loop | 4 | 0.400 | 39.3 |
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7 | RM00030 | U-turn motif | 5 | 0.500 | 61.9 |
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References
This section shows the database cross-references that we have for this Rfam family.
Literature references
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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
Sequence Ontology: | SO:0000370 (small_regulatory_ncRNA); |
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 PP |
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Alignment details |
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Model information
Build commands |
cmbuild -F CM SEED
cmcalibrate --mpi CM
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Search command |
cmsearch --cpu 4 --verbose --nohmmonly -T 25.27 -Z 2958934 CM SEQDB
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Gathering cutoff | 75.0 |
Trusted cutoff | 93.7 |
Noise cutoff | 71.1 |
Covariance model | Download |