10  structures 0  species 0  sequences

Motif: k-turn-1 (RM00010)

Description: Kink turn 1, 3' bulge

Summary

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam data in Wikipedia. This motif is described by a Wikipedia entry entitled Internal loop but we are unable to retrieve the article content at this time. More...

Alignments

You can either download the motif alignment or view it directly in your browser window. More...

Formatting options

You can view or download motif 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:
Download/view:

Structures

There are 10 PDB entires which have been used to build the motif model.

The table of results below may be sorted by clicking on the column titles, or restored to the original order here.

Original order PDB ID PDB chain ID PDB Residues
2 3BBO A 74 - 108
2 1s72 0 70 - 104
2 2j01 A 74 - 108
2 1t0k C -
2 2gis A 11 - 43
2 1rlg C 1 - 25
2 2hvy E 16 - 42
2 1u6b B -
2 3cc2 0 71 - 105
2 2wh1 A 230 - 289

Family matches

There are 89 Rfam families which match this motif.

This section shows the families which have been annotated with this motif. 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 Family Accession Family Description Number of Hits Fraction of Hits Sum of Bits Image
3 RF00009 Nuclear RNase P 23 0.198 242.4 Match Image
3 RF00010 Bacterial RNase P class A 84 0.183 1029.0 Match Image
3 RF00017 Metazoan signal recognition particle RNA 35 0.385 367.0 Match Image
3 RF00023 transfer-messenger RNA 42 0.088 546.1 Match Image
3 RF00024 Vertebrate telomerase RNA 27 0.730 350.4 Match Image
3 RF00045 Small nucleolar RNA SNORA73 family 27 0.409 293.2 Match Image
3 RF00058 HgcF RNA 4 1.000 54.5 Match Image
3 RF00060 HgcE RNA 3 0.750 53.8 Match Image
3 RF00064 HgcG RNA 5 1.000 196.3 Match Image
3 RF00065 Small nucleolar RNA snoR9 5 1.000 74.8 Match Image
3 RF00079 OmrA-B family 13 0.565 134.9 Match Image
3 RF00095 Pyrococcus C/D box small nucleolar RNA 4 0.160 39.1 Match Image
3 RF00100 7SK RNA 4 0.089 40.5 Match Image
3 RF00162 SAM riboswitch (S box leader) 256 0.591 3219.4 Match Image
3 RF00168 Lysine riboswitch 16 0.340 198.4 Match Image
3 RF00174 Cobalamin riboswitch 54 0.126 581.2 Match Image
3 RF00177 Bacterial small subunit ribosomal RNA 83 0.838 1976.8 Match Image
3 RF00222 Bag-1 internal ribosome entry site (IRES) 5 0.333 90.6 Match Image
3 RF00224 FGF-2 internal ribosome entry site (IRES) 2 0.333 38.3 Match Image
3 RF00261 L-myc internal ribosome entry site (IRES) 8 0.727 123.3 Match Image
3 RF00286 Small Cajal body specific RNA 8 5 0.227 48.3 Match Image
3 RF00373 Archaeal RNase P 16 0.229 254.8 Match Image
3 RF00408 Small nucleolar RNA SNORA1 3 0.103 31.4 Match Image
3 RF00449 HIF-1 alpha IRES 2 0.118 23.4 Match Image
3 RF00461 Vascular endothelial growth factor (VEGF) IRES A 4 0.571 39.0 Match Image
3 RF00504 Glycine riboswitch 5 0.114 47.6 Match Image
3 RF00512 Leucine operon leader 5 0.833 52.0 Match Image
3 RF00547 TrkB IRES 7 0.438 72.3 Match Image
3 RF00549 c-sis internal ribosome entry site (IRES) 10 1.000 165.4 Match Image
3 RF00564 Small Cajal body specific RNA 11 3 0.125 42.9 Match Image
3 RF00598 Small nucleolar RNA SNORA76 5 0.227 50.7 Match Image
3 RF00602 Small Cajal body specific RNA 21 3 0.125 33.3 Match Image
3 RF00603 Small nucleolar RNA SNORD23 5 0.333 66.0 Match Image
3 RF00604 Small nucleolar RNA SNORD88 12 0.343 122.6 Match Image
3 RF00613 Small nucleolar RNA SNORD94 6 0.286 58.3 Match Image
3 RF00625 Pseudomonas sRNA P11 3 0.200 28.2 Match Image
3 RF00629 Pseudomonas sRNA P24 4 0.286 37.6 Match Image
3 RF00634 S-adenosyl methionine (SAM) riboswitch, 6 0.150 68.1 Match Image
3 RF00674 microRNA mir-187 4 0.200 36.4 Match Image
3 RF00783 microRNA mir-484 6 0.400 54.9 Match Image
3 RF01010 microRNA mir-632 8 0.500 87.3 Match Image
3 RF01052 Arthropod 7SK RNA 6 0.316 77.9 Match Image
3 RF01069 purD RNA motif 2 0.095 18.3 Match Image
3 RF01071 Ornate Large Extremophilic RNA 4 0.200 42.5 Match Image
3 RF01073 Gag/pol translational readthrough site 3 0.429 30.5 Match Image
3 RF01219 Small nucleolar RNA snoR100 2 0.222 18.8 Match Image
3 RF01246 Small nucleolar RNA snR81 2 0.667 26.5 Match Image
3 RF01268 Small Cajal body-specific RNA 2 11 0.550 139.7 Match Image
3 RF01292 Small nucleolar RNA snoR2/U65 6 0.545 93.1 Match Image
3 RF01412 BsrG 2 0.333 21.2 Match Image
3 RF01497 ALIL pseudoknot 2 0.077 18.9 Match Image
3 RF01502 Fungal signal recognition particle RNA 9 0.180 98.9 Match Image
3 RF01643 Caenorhabditis sRNA ceN56 3 0.750 31.3 Match Image
3 RF01702 Cyano-2 RNA 7 0.123 69.6 Match Image
3 RF01722 Pyrobac-1 RNA 3 0.375 35.8 Match Image
3 RF01746 mraW RNA 6 0.133 68.5 Match Image
3 RF01752 psaA RNA 6 0.194 58.6 Match Image
3 RF01848 ACEA small nucleolar RNA U3 6 0.214 56.6 Match Image
3 RF01849 Alphaproteobacteria transfer-messenger RNA 10 0.090 105.6 Match Image
3 RF01855 Plant signal recognition particle RNA 12 0.190 126.3 Match Image
3 RF01857 Archaeal signal recognition particle RNA 14 0.264 185.6 Match Image
3 RF01867 caulobacter sRNA CC2171 5 0.385 53.0 Match Image
3 RF01946 KCNQ1 overlapping transcript 1 conserved region 1 3 0.375 29.2 Match Image
3 RF01959 Archaeal small subunit ribosomal RNA 66 0.767 1634.1 Match Image
3 RF01960 Eukaryotic small subunit ribosomal RNA 37 0.407 698.8 Match Image
3 RF02005 Group II catalytic intron D1-D4-6 30 0.172 321.6 Match Image
3 RF02042 HOXA transcript at the distal tip, conserved region 3 2 0.087 25.9 Match Image
3 RF02122 FTX transcript, XIST regulator conserved region 5 2 0.143 22.2 Match Image
3 RF02132 HOXB13 antisense RNA 1 conserved region 1 3 0.250 31.7 Match Image
3 RF02141 HOXA11 antisense RNA 1 conserved region 5 2 0.071 21.5 Match Image
3 RF02143 Hydatidiform mole associated and imprinted conserved region 1 2 0.125 21.0 Match Image
3 RF02164 Pvt1 oncogene conserved region 1 5 0.294 54.2 Match Image
3 RF02165 Pvt1 oncogene conserved region 2 2 0.118 21.2 Match Image
3 RF02196 TP53 target 1 conserved region 2 2 0.167 20.0 Match Image
3 RF02198 TTC28 antisense RNA 1 conserved region 1 2 0.143 20.3 Match Image
3 RF02205 WT1 antisense RNA conserved region 3 3 0.158 40.6 Match Image
3 RF02336 Giardia snoRNA GlsR1/miRNA miR6 2 1.000 28.6 Match Image
3 RF02347 Alphaproteobacterial sRNA ar45 11 0.306 102.5 Match Image
3 RF02355 Bradyrhizobiaceae sRNA BjrC174 2 0.133 20.0 Match Image
3 RF02357 RNaseP truncated form 7 0.778 73.2 Match Image
3 RF02462 Ascomycota telomerase RNA 3 0.750 31.8 Match Image
3 RF02471 Actinobacteria sRNA Ms_IGR-5 2 0.095 21.0 Match Image
3 RF02540 Archaeal large subunit ribosomal RNA 91 1.000 6958.4 Match Image
3 RF02541 Bacterial large subunit ribosomal RNA 99 0.971 3865.1 Match Image
3 RF02542 Microsporidia small subunit ribosomal RNA 25 0.543 420.7 Match Image
3 RF02543 Eukaryotic large subunit ribosomal RNA 46 0.523 914.8 Match Image
3 RF02605 Streptomyces sRNA scr5239 2 0.333 23.1 Match Image
3 RF02735 Saccharopolyspora sRNA 350 2 1.000 21.0 Match Image
3 RF02743 Saccharopolyspora sRNA 389 2 1.000 23.4 Match Image

References

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

Literature references

  1. Sarver M, Zirbel CL, Stombaugh J, Mokdad A, Leontis NB J Math Biol. 2008;56:215-52. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. PUBMED:17694311

  2. Klosterman PS, Hendrix DK, Tamura M, Holbrook SR, Brenner SE Nucleic Acids Res. 2004;32:2342-52. Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns. PUBMED:15121895

  3. Zirbel CL, Sponer JE, Sponer J, Stombaugh J, Leontis NB Nucleic Acids Res. 2009;37:4898-918. Classification and energetics of the base-phosphate interactions in RNA. PUBMED:19528080

  4. Schroeder KT, McPhee SA, Ouellet J, Lilley DM RNA. 2010;16:1463-8. A structural database for k-turn motifs in RNA. PUBMED:20562215

  5. Blouin S, Chinnappan R, Lafontaine DA Nucleic Acids Res. 2010 Folding of the lysine riboswitch: importance of peripheral elements for transcriptional regulation. PUBMED:21169337

  6. Meyer M, Westhof E, Masquida B RNA Biol. 2012;9:[Epub ahead of print]. A structural module in RNase P expands the variety of RNA kinks. PUBMED:22336704

  7. Lescoute A, Leontis NB, Massire C, Westhof E Nucleic Acids Res. 2005;33:2395-409. Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments. PUBMED:15860776

External database links

Curation and motif details

This section shows the detailed information about the Rfam motif. 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 Published; PMID:19528080
Structure source N/A
Type Internal Loop
Author Gardner PP
Alignment details
Alignment Number of
sequences
Average length Sequence
identity (%)
seed 15 38.33 41

Model information

Build commands
cmbuild -F k-turn-CM k-turn-SEED
cmcalibrate --mpi --seed 1 k-turn-CM
Gathering cutoff 9.0
Covariance model Download the Infernal CM for the motif here