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 Pseudomonas 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 (47 sequence regions)
Original order | Download FASTA | Accession | Bit score | Type | Start | End | Description | Species | View context |
---|---|---|---|---|---|---|---|---|---|
0 | CP000438.1 | N/A | seed | 6,107,695 | 6,107,297 | Pseudomonas aeruginosa UCBPP-PA14, complete genome. | Pseudomonas aeruginosa UCBPP-PA14 | ||
1 | AE004091.2 | N/A | seed | 5,835,480 | 5,835,082 | Pseudomonas aeruginosa PAO1, complete genome. | Pseudomonas aeruginosa PAO1 | ||
2 | CP000744.1 | N/A | seed | 6,117,984 | 6,117,586 | Pseudomonas aeruginosa PA7, complete genome. | Pseudomonas aeruginosa PA7 | ||
3 | AEAZ01000003.1 | N/A | seed | 118,029 | 118,399 | Pseudomonas fluorescens WH6 WH6_3, whole genome shotgun sequence. | Pseudomonas fluorescens WH6 | ||
4 | CP002585.1 | N/A | seed | 372,972 | 373,256 | Pseudomonas brassicacearum subsp. brassicacearum NFM421, complete genome. | Pseudomonas brassicacearum subsp. brassicacearum NFM421 | ||
0 | BQMB01000699.1 | 235.00 | full | 3,060 | 2,689 | BQMB01000699.1 Closterium sp. NIES-67 DNA, Cpp_p_000134Fqp, whole genome shotgun sequence | Closterium sp. NIES-67 | ||
1 | RBRL01000307.1 | 218.20 | full | 4,168 | 4,587 | RBRL01000307.1 Pseudomonas salomonii strain ICMP 11288 PflICMP11288_Contig_406, whole genome shotgun sequence | Pseudomonas salomonii | ||
2 | RBOJ01000075.1 | 198.10 | full | 84,856 | 85,229 | RBOJ01000075.1 Pseudomonas corrugata strain NCPPB2445 PcoNCPPB2445_Contig_36, whole genome shotgun sequence | Pseudomonas corrugata | ||
3 | AM181176.4 | 193.70 | full | 301,885 | 302,252 | Pseudomonas fluorescens SBW25 complete genome | Pseudomonas fluorescens SBW25 | ||
4 | AP024341.1 | 187.20 | full | 339,549 | 339,921 | AP024341.1 Pseudomonas sp. Boi14 DNA, complete genome | Pseudomonas sp. Boi14 | ||
5 | WEIY01002464.1 | 176.30 | full | 1,754 | 2,126 | WEIY01002464.1 Pteruthius melanotis isolate B10K-IZ-033-77 scaffold_2460, whole genome shotgun sequence | Pteruthius melanotis | ||
6 | CP010892.1 | 173.40 | full | 345,974 | 346,336 | CP010892.1 Pseudomonas sp. MRSN12121, complete genome | Pseudomonas sp. MRSN 12121 | ||
7 | AFOY02000027.1 | 167.30 | full | 87,763 | 88,162 | Pseudomonas fluorescens HK44 Contig27, whole genome shotgun sequence. | Pseudomonas fluorescens HK44 | ||
8 | LLWI01000068.1 | 155.50 | full | 85,346 | 85,708 | LLWI01000068.1 Pseudomonas sp. TAD18 contig000068, whole genome shotgun sequence | Pseudomonas sp. TAD18 | ||
9 | NFSA01000049.1 | 130.60 | full | 72,119 | 72,496 | NFSA01000049.1 Pseudomonas sp. 1239 Contig49, whole genome shotgun sequence | Pseudomonas sp. 1239 | ||
10 | CP014135.1 | 117.80 | full | 3,508,393 | 3,508,107 | Pseudomonas agarici strain NCPPB 2472 genome. | Pseudomonas agarici | ||
11 | FNIJ01000003.1 | 115.20 | full | 44,407 | 44,028 | FNIJ01000003.1 Pseudomonas jinjuensis strain JCM 21621 genome assembly, contig: Ga0104665_103, whole genome shotgun sequence | Pseudomonas jinjuensis | ||
12 | CP024478.1 | 114.20 | full | 4,942,380 | 4,941,989 | CP024478.1 Pseudomonas sp. HLS-6 chromosome, complete genome | Pseudomonas sp. HLS-6 | ||
13 | QETK01000017.1 | 114.00 | full | 59,619 | 59,273 | QETK01000017.1 Pseudomonas sp. SDI CONTIG_17_length_112720_cov_27.8163, whole genome shotgun sequence | Pseudomonas sp. SDI | ||
14 | HG322950.1 | 112.90 | full | 404,558 | 404,952 | Pseudomonas knackmussii B13 complete genome | Pseudomonas knackmussii B13 | ||
15 | FZOL01000002.1 | 112.70 | full | 362,098 | 362,489 | FZOL01000002.1 Pseudomonas japonica strain DSM 22348 genome assembly, contig: Ga0131112_102, whole genome shotgun sequence | Pseudomonas japonica | ||
16 | RHQN01000012.1 | 109.00 | full | 57,168 | 57,552 | RHQN01000012.1 Pseudomonas sp. v388 NODE_12_length_148770_cov_50.479653, whole genome shotgun sequence | Pseudomonas sp. v388 | ||
17 | AJWX01000023.1 | 107.20 | full | 64,565 | 64,933 | Pseudomonas sp. M47T1 contig023, whole genome shotgun sequence. | Pseudomonas sp. M47T1 | ||
18 | AE016853.1 | 100.80 | full | 6,141,312 | 6,140,919 | Pseudomonas syringae pv. tomato str. DC3000, complete genome. | Pseudomonas syringae pv. tomato str. DC3000 | ||
19 | LT629777.1 | 95.90 | full | 1,307,350 | 1,307,064 | LT629777.1 Pseudomonas asplenii strain ATCC 23835 genome assembly, chromosome: I | Pseudomonas asplenii | ||
20 | CP009455.1 | 83.90 | full | 1,637,037 | 1,637,415 | Pseudomonas cremoricolorata strain ND07, complete genome. | Pseudomonas cremoricolorata | ||
21 | CP032419.1 | 81.60 | full | 4,626,346 | 4,625,993 | CP032419.1 Pseudomonas cavernae strain K2W31S-8 chromosome, complete genome | Pseudomonas cavernae | ||
22 | AE015451.2 | 81.40 | full | 309,730 | 310,021 | Pseudomonas putida KT2440 complete genome. | Pseudomonas putida KT2440 | ||
23 | FNDS01000007.1 | 79.30 | full | 164,136 | 164,490 | FNDS01000007.1 Pseudomonas panipatensis strain CCM 7469 genome assembly, contig: Ga0104674_107, whole genome shotgun sequence | Pseudomonas panipatensis | ||
24 | CP053746.1 | 78.00 | full | 1,901,641 | 1,902,024 | CP053746.1 Pseudomonas graminis strain PgKB30 chromosome, complete genome | Pseudomonas graminis | ||
25 | AP014637.1 | 76.80 | full | 2,116,378 | 2,116,816 | Pseudomonas sp. StFLB209 DNA, complete genome. | Pseudomonas sp. StFLB209 | ||
26 | FNFD01000017.1 | 72.00 | full | 72,749 | 72,441 | FNFD01000017.1 Pseudomonas indica strain JCM 21544 genome assembly, contig: Ga0104664_117, whole genome shotgun sequence | Pseudomonas indica | ||
27 | CCSF01000001.1 | 70.80 | full | 2,336,277 | 2,335,976 | Pseudomonas sp. 20_BN genome assembly, contig: CONTIG000001 | Pseudomonas saudiphocaensis | ||
28 | FNCT01000005.1 | 64.60 | full | 179,005 | 178,705 | FNCT01000005.1 Pseudomonas benzenivorans strain DSM 8628 genome assembly, contig: Ga0104648_105, whole genome shotgun sequence | Pseudomonas benzenivorans | ||
29 | CP010415.1 | 62.40 | full | 3,941,631 | 3,941,256 | CP010415.1 Azotobacter chroococcum NCIMB 8003, complete genome | Azotobacter chroococcum NCIMB 8003 | ||
30 | AP013068.1 | 60.70 | full | 6,008,076 | 6,007,764 | Pseudomonas resinovorans NBRC 106553 DNA, complete geonome. | Pseudomonas resinovorans NBRC 106553 | ||
31 | CP009533.1 | 60.70 | full | 3,877,372 | 3,877,727 | Pseudomonas rhizosphaerae strain DSM 16299, complete genome. | Pseudomonas rhizosphaerae | ||
32 | AWSQ01000001.1 | 59.50 | full | 1,071,826 | 1,072,148 | Pseudomonas taeanensis MS-3 contig_01, whole genome shotgun sequence. | Pseudomonas taeanensis MS-3 | ||
33 | CAJFCI010000012.1 | 58.10 | full | 114,879 | 115,245 | CAJFCI010000012.1 Pseudomonas sp. Wesi-4 isolate CIP111764 genome assembly, contig: scfd_6, whole genome shotgun sequence | Pseudomonas carbonaria | ||
34 | QAOJ01000005.1 | 55.40 | full | 308,427 | 308,099 | QAOJ01000005.1 Pseudomonas sp. GV071 Ga0189753_105, whole genome shotgun sequence | Pseudomonas sp. GV071 | ||
35 | QLAG01000007.1 | 54.90 | full | 78,138 | 78,371 | QLAG01000007.1 Stutzerimonas nosocomialis strain SD129 contig00007, whole genome shotgun sequence | Stutzerimonas nosocomialis | ||
36 | CP000304.1 | 53.60 | full | 369,086 | 369,401 | Pseudomonas stutzeri A1501, complete genome. | Pseudomonas stutzeri A1501 | ||
37 | CP020892.1 | 53.40 | full | 4,529,481 | 4,529,105 | Pseudomonas sp. M30-35, complete genome. | Pseudomonas sp. M30-35 | ||
38 | AZSV01000093.1 | 50.00 | full | 16,859 | 16,569 | Pseudomonas sp. BAY1663 contig000093, whole genome shotgun sequence. | Pseudomonas sp. BAY1663 | ||
39 | JYFT01000036.1 | 50.00 | full | 45,992 | 46,288 | Pseudomonas sp. FeS53a scaffold11.1, whole genome shotgun sequence. | Pseudomonas sp. FeS53a | ||
40 | LT629751.1 | 45.00 | full | 3,343,210 | 3,342,966 | LT629751.1 Pseudomonas oryzae strain KCTC 32247 genome assembly, chromosome: I | Pseudomonas oryzae | ||
41 | CM028698.1 | 44.30 | full | 45,534,932 | 45,535,073 | CM028698.1 Brassica carinata isolate sxm20200214 chromosome C4, whole genome shotgun sequence | Brassica carinata |
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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Change the size of the sunburst
Colour assignments
Archea | Eukaryota |
Bacteria | Other sequences |
Viruses | Unclassified |
Viroids | Unclassified sequence |
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 5 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 | RM00005 | CsrA/RsmA binding motif | 9 | 1.800 | 83.5 | |
7 | RM00008 | GNRA tetraloop | 6 | 1.200 | 57.3 | |
7 | RM00022 | Rho independent terminator 1 | 5 | 1.000 | 88.2 | |
7 | RM00023 | Rho independent terminator 2 | 5 | 1.000 | 99.9 | |
7 | RM00029 | UNCG tetraloop | 2 | 0.400 | 31.2 |
References
This section shows the database cross-references that we have for this Rfam family.
Literature references
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Livny J, Brencic A, Lory S, Waldor MK; Nucleic Acids Res. 2006;34:3484-3493. Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2. PUBMED:16870723
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 | INFERNAL | ||||||
Structure source | Predicted; WAR; cmfinder; | ||||||
Type | Gene; sRNA; | ||||||
Author | Osuch I, Eberhardt R | ||||||
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 22.27 -Z 2958934 CM SEQDB
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Gathering cutoff | 44.0 |
Trusted cutoff | 44.3 |
Noise cutoff | 42.8 |
Covariance model | Download |