0  structures 47  species 47  sequences

Family: P34 (RF02405)

Description: Pseudomonas sRNA P34

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...

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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 ENA graphic
1
AE004091.2 N/A seed 5,835,480 5,835,082 Pseudomonas aeruginosa PAO1, complete genome. Pseudomonas aeruginosa PAO1 ENA graphic
2
CP000744.1 N/A seed 6,117,984 6,117,586 Pseudomonas aeruginosa PA7, complete genome. Pseudomonas aeruginosa PA7 ENA graphic
3
AEAZ01000003.1 N/A seed 118,029 118,399 Pseudomonas fluorescens WH6 WH6_3, whole genome shotgun sequence. Pseudomonas fluorescens WH6 ENA graphic
4
CP002585.1 N/A seed 372,972 373,256 Pseudomonas brassicacearum subsp. brassicacearum NFM421, complete genome. Pseudomonas brassicacearum subsp. brassicacearum NFM421 ENA graphic
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 ENA graphic
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 ENA graphic
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 ENA graphic
3
AM181176.4 193.70 full 301,885 302,252 Pseudomonas fluorescens SBW25 complete genome Pseudomonas fluorescens SBW25 ENA graphic
4
AP024341.1 187.20 full 339,549 339,921 AP024341.1 Pseudomonas sp. Boi14 DNA, complete genome Pseudomonas sp. Boi14 ENA graphic
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 ENA graphic
6
CP010892.1 173.40 full 345,974 346,336 CP010892.1 Pseudomonas sp. MRSN12121, complete genome Pseudomonas sp. MRSN 12121 ENA graphic
7
AFOY02000027.1 167.30 full 87,763 88,162 Pseudomonas fluorescens HK44 Contig27, whole genome shotgun sequence. Pseudomonas fluorescens HK44 ENA graphic
8
LLWI01000068.1 155.50 full 85,346 85,708 LLWI01000068.1 Pseudomonas sp. TAD18 contig000068, whole genome shotgun sequence Pseudomonas sp. TAD18 ENA graphic
9
NFSA01000049.1 130.60 full 72,119 72,496 NFSA01000049.1 Pseudomonas sp. 1239 Contig49, whole genome shotgun sequence Pseudomonas sp. 1239 ENA graphic
10
CP014135.1 117.80 full 3,508,393 3,508,107 Pseudomonas agarici strain NCPPB 2472 genome. Pseudomonas agarici ENA graphic
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 ENA graphic
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 ENA graphic
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 ENA graphic
14
HG322950.1 112.90 full 404,558 404,952 Pseudomonas knackmussii B13 complete genome Pseudomonas knackmussii B13 ENA graphic
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 ENA graphic
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 ENA graphic
17
AJWX01000023.1 107.20 full 64,565 64,933 Pseudomonas sp. M47T1 contig023, whole genome shotgun sequence. Pseudomonas sp. M47T1 ENA graphic
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 ENA graphic
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 ENA graphic
20
CP009455.1 83.90 full 1,637,037 1,637,415 Pseudomonas cremoricolorata strain ND07, complete genome. Pseudomonas cremoricolorata ENA graphic
21
CP032419.1 81.60 full 4,626,346 4,625,993 CP032419.1 Pseudomonas cavernae strain K2W31S-8 chromosome, complete genome Pseudomonas cavernae ENA graphic
22
AE015451.2 81.40 full 309,730 310,021 Pseudomonas putida KT2440 complete genome. Pseudomonas putida KT2440 ENA graphic
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 ENA graphic
24
CP053746.1 78.00 full 1,901,641 1,902,024 CP053746.1 Pseudomonas graminis strain PgKB30 chromosome, complete genome Pseudomonas graminis ENA graphic
25
AP014637.1 76.80 full 2,116,378 2,116,816 Pseudomonas sp. StFLB209 DNA, complete genome. Pseudomonas sp. StFLB209 ENA graphic
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 ENA graphic
27
CCSF01000001.1 70.80 full 2,336,277 2,335,976 Pseudomonas sp. 20_BN genome assembly, contig: CONTIG000001 Pseudomonas saudiphocaensis ENA graphic
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 ENA graphic
29
CP010415.1 62.40 full 3,941,631 3,941,256 CP010415.1 Azotobacter chroococcum NCIMB 8003, complete genome Azotobacter chroococcum NCIMB 8003 ENA graphic
30
AP013068.1 60.70 full 6,008,076 6,007,764 Pseudomonas resinovorans NBRC 106553 DNA, complete geonome. Pseudomonas resinovorans NBRC 106553 ENA graphic
31
CP009533.1 60.70 full 3,877,372 3,877,727 Pseudomonas rhizosphaerae strain DSM 16299, complete genome. Pseudomonas rhizosphaerae ENA graphic
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 ENA graphic
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 ENA graphic
34
QAOJ01000005.1 55.40 full 308,427 308,099 QAOJ01000005.1 Pseudomonas sp. GV071 Ga0189753_105, whole genome shotgun sequence Pseudomonas sp. GV071 ENA graphic
35
QLAG01000007.1 54.90 full 78,138 78,371 QLAG01000007.1 Stutzerimonas nosocomialis strain SD129 contig00007, whole genome shotgun sequence Stutzerimonas nosocomialis ENA graphic
36
CP000304.1 53.60 full 369,086 369,401 Pseudomonas stutzeri A1501, complete genome. Pseudomonas stutzeri A1501 ENA graphic
37
CP020892.1 53.40 full 4,529,481 4,529,105 Pseudomonas sp. M30-35, complete genome. Pseudomonas sp. M30-35 ENA graphic
38
AZSV01000093.1 50.00 full 16,859 16,569 Pseudomonas sp. BAY1663 contig000093, whole genome shotgun sequence. Pseudomonas sp. BAY1663 ENA graphic
39
JYFT01000036.1 50.00 full 45,992 46,288 Pseudomonas sp. FeS53a scaffold11.1, whole genome shotgun sequence. Pseudomonas sp. FeS53a ENA graphic
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 ENA graphic
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 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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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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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.

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 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
7 RM00005 CsrA/RsmA binding motif 9 1.800 83.5 Match Image
7 RM00008 GNRA tetraloop 6 1.200 57.3 Match Image
7 RM00022 Rho independent terminator 1 5 1.000 88.2 Match Image
7 RM00023 Rho independent terminator 2 5 1.000 99.9 Match Image
7 RM00029 UNCG tetraloop 2 0.400 31.2 Match Image

References

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

Literature references

  1. 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

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 RORCID logo
Alignment details
Alignment Number of
sequences
full 42
seed 5

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 22.27 -Z 2958934 CM SEQDB
Gathering cutoff 44.0
Trusted cutoff 44.3
Noise cutoff 42.8
Covariance model Download
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