52  structures 0  species 0  sequences

Motif: T-loop (RM00024)

Description: T-loop

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 T arm 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 52 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 1C04 42 - 49
2 1E8O 110 - 117
2 1GAX 952 - 960
2 1H3E 31 - 39
2 1J1U 532 - 540
2 1J2B 932 - 940
2 1J5E 259 - 267
2 1MJI 38 - 44
2 1MMS 1092 - 1099
2 1N78 531 - 539
2 1NBS 118 - 125
2 1QA6 142 - 149
2 1QTQ 953 - 961
2 1QU2 53 - 61
2 1S72 1196 - 1203
2 1U0B 31 - 39
2 1U9S 181 - 189
2 1VFG 53 - 61
2 1WZ2 965 - 973
2 1Y0Q 224 - 234
2 1Y69 1103 - 1110
2 2A2E 156 - 164
2 2A64 69 - 76
2 2AVY 259 - 267
2 2AW4 1092 - 1099
2 2AZX 531 - 539
2 2BH2 1949 - 1957
2 2BTE 53 - 61
2 2CT8 53 - 61
2 2D6F 953 - 961
2 2DER 31 - 39
2 2DET 31 - 39
2 2DEU 31 - 39
2 2DR2 31 - 39
2 2G9C 46 - 53
2 2HOP 65 - 74
2 2IL9 6118 - 6124
2 2IY5 31 - 39
2 2J01 1949 - 1957
2 2DU3 952 - 960
2 2FK6 53 - 61
2 2NQP 53 - 61
2 2NR0 53 - 61
2 2NRE 53 - 61
2 2R8S 166 - 174
2 387D 4 - 13
2 3B31 6184 - 6193
2 2i82 E 3 - 19
2 1ser T 67 - 83
2 2zzn C 48 - 64
2 1j4y A 1 - 17
2 2zue B 51 - 67

Family matches

There are 108 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 RF00004 U2 spliceosomal RNA 39 0.188 400.1 Match Image
3 RF00005 tRNA 567 0.594 8155.1 Match Image
3 RF00007 U12 minor spliceosomal RNA 33 0.532 395.4 Match Image
3 RF00009 Nuclear RNase P 15 0.129 170.9 Match Image
3 RF00010 Bacterial RNase P class A 393 0.858 6917.8 Match Image
3 RF00013 6S / SsrS RNA 15 0.101 158.8 Match Image
3 RF00017 Metazoan signal recognition particle RNA 11 0.121 109.1 Match Image
3 RF00022 GcvB RNA 3 0.111 29.9 Match Image
3 RF00023 transfer-messenger RNA 352 0.738 4368.9 Match Image
3 RF00030 RNase MRP 7 0.106 73.6 Match Image
3 RF00050 FMN riboswitch (RFN element) 16 0.111 173.2 Match Image
3 RF00066 U7 small nuclear RNA 7 0.143 71.7 Match Image
3 RF00078 MicA sRNA 2 0.118 19.3 Match Image
3 RF00079 OmrA-B family 10 0.435 93.0 Match Image
3 RF00102 VA RNA 9 0.167 100.4 Match Image
3 RF00113 Short Intergenic Abundant RNA 7 0.412 69.4 Match Image
3 RF00166 PrrB/RsmZ RNA family 34 0.919 427.3 Match Image
3 RF00174 Cobalamin riboswitch 95 0.221 1005.1 Match Image
3 RF00177 Bacterial small subunit ribosomal RNA 61 0.616 864.8 Match Image
3 RF00304 Small nucleolar RNA Z279/snoR105/snoR108 3 0.150 29.8 Match Image
3 RF00370 sroD RNA 4 0.800 42.9 Match Image
3 RF00373 Archaeal RNase P 16 0.229 181.6 Match Image
3 RF00386 Enterovirus 5' cloverleaf cis-acting replication element 24 0.150 237.8 Match Image
3 RF00391 RtT RNA 7 0.123 71.3 Match Image
3 RF00438 Small nucleolar RNA SNORA33 3 0.107 30.4 Match Image
3 RF00513 Tryptophan operon leader 9 0.409 102.3 Match Image
3 RF00547 TrkB IRES 3 0.188 31.5 Match Image
3 RF00553 Small Cajal body specific RNA 1 11 0.379 110.6 Match Image
3 RF00558 Ribosomal protein L20 leader 4 0.093 44.0 Match Image
3 RF00604 Small nucleolar RNA SNORD88 4 0.114 39.6 Match Image
3 RF00617 flavivirus capsid hairpin cHP 15 0.254 155.3 Match Image
3 RF00625 Pseudomonas sRNA P11 3 0.200 33.6 Match Image
3 RF00630 Pseudomonas sRNA P26 7 0.259 70.0 Match Image
3 RF00634 S-adenosyl methionine (SAM) riboswitch, 17 0.425 197.1 Match Image
3 RF00685 microRNA mir-36 8 0.174 86.9 Match Image
3 RF00717 microRNA mir-315 3 0.188 37.2 Match Image
3 RF00972 microRNA mir-651 2 0.500 21.0 Match Image
3 RF01050 Saccharomyces telomerase 3 0.231 27.9 Match Image
3 RF01067 ATPC RNA motif 8 0.089 77.6 Match Image
3 RF01071 Ornate Large Extremophilic RNA 12 0.600 135.6 Match Image
3 RF01085 Pseudoknot of tRNA-like structure 2 1.000 20.9 Match Image
3 RF01116 Cyanobacterial functional RNA 1 6 0.162 83.8 Match Image
3 RF01267 Small nucleolar RNA snR37 4 0.444 42.3 Match Image
3 RF01290 Small nucleolar RNA SNORD10 2 0.091 18.6 Match Image
3 RF01317 CRISPR RNA direct repeat element 5 0.152 47.6 Match Image
3 RF01322 CRISPR RNA direct repeat element 3 0.429 31.5 Match Image
3 RF01394 isrK Hfq binding RNA 14 0.269 165.9 Match Image
3 RF01401 rseX Hfq binding RNA 9 0.750 103.5 Match Image
3 RF01510 M. florum riboswitch 2 0.667 23.4 Match Image
3 RF01518 NoRC assoicated RNA, pRNA 6 0.261 57.8 Match Image
3 RF01583 small nucleolar RNA snoR01 2 0.667 21.1 Match Image
3 RF01684 MALAT1-associated small cytoplasmic RNA/MEN beta RNA 36 0.679 397.3 Match Image
3 RF01687 Acido-Lenti-1 RNA 20 0.230 212.6 Match Image
3 RF01700 Collinsella-1 RNA 4 0.667 42.1 Match Image
3 RF01721 Pseudomon-groES RNA 5 0.278 56.1 Match Image
3 RF01729 Termite-flg RNA 3 0.231 35.3 Match Image
3 RF01730 Termite-leu RNA 14 0.700 316.0 Match Image
3 RF01731 TwoAYGGAY RNA 80 0.381 1056.1 Match Image
3 RF01732 asd RNA 3 0.097 31.5 Match Image
3 RF01754 radC RNA 18 0.138 187.2 Match Image
3 RF01758 sucA-II RNA 15 0.882 210.6 Match Image
3 RF01766 cspA thermoregulator 2 0.133 31.1 Match Image
3 RF01770 Gammaprotebacteria rimP leader 14 0.304 134.2 Match Image
3 RF01776 RNA anti-toxin A 2 0.125 21.3 Match Image
3 RF01796 Fumarate/nitrate reductase regulator sRNA 5 0.312 49.4 Match Image
3 RF01808 MicX Vibrio cholerae sRNA 4 0.400 39.3 Match Image
3 RF01815 rpsB sRNA 2 0.500 18.9 Match Image
3 RF01820 RNA Staph. aureus E 2 0.133 19.1 Match Image
3 RF01849 Alphaproteobacteria transfer-messenger RNA 23 0.207 224.4 Match Image
3 RF01850 Betaproteobacteria transfer-messenger RNA 4 0.571 39.4 Match Image
3 RF01851 Cyanobacteria transfer-messenger RNA 3 0.111 31.0 Match Image
3 RF01852 Selenocysteine transfer RNA 96 0.881 1312.9 Match Image
3 RF01871 Metastasis associated lung adenocarcinoma transcript 1 15 0.882 138.6 Match Image
3 RF01877 Myocardial infarction associated transcript exon 5 conserved region 3 9 0.562 88.5 Match Image
3 RF01959 Archaeal small subunit ribosomal RNA 77 0.895 2180.0 Match Image
3 RF01960 Eukaryotic small subunit ribosomal RNA 33 0.363 414.8 Match Image
3 RF01973 H19 conserved region 2 12 0.522 110.4 Match Image
3 RF02003 Group II catalytic intron D1-D4-4 15 0.167 155.5 Match Image
3 RF02029 sraA 17 0.850 213.1 Match Image
3 RF02032 Giant, ornate, lake- and Lactobacillales-derived (GOLLD) RNA 6 0.171 76.1 Match Image
3 RF02033 HNH endonuclease-associated RNA and ORF (HEARO) RNA 28 0.255 310.0 Match Image
3 RF02089 CLRN1 antisense RNA 1 conserved region 2 0.105 19.4 Match Image
3 RF02164 Pvt1 oncogene conserved region 1 2 0.118 20.6 Match Image
3 RF02165 Pvt1 oncogene conserved region 2 2 0.118 21.1 Match Image
3 RF02205 WT1 antisense RNA conserved region 3 6 0.316 58.8 Match Image
3 RF02223 Proteobacterial sRNA sX4 12 2.400 138.0 Match Image
3 RF02276 Hammerhead ribozyme (type II) 9 0.375 95.7 Match Image
3 RF02354 Bradyrhizobiaceae sRNA BjrC80 5 0.333 48.3 Match Image
3 RF02356 Alphaproteobacterial sRNA BjrC1505 8 0.320 80.4 Match Image
3 RF02373 PyrD leader 23 0.852 236.7 Match Image
3 RF02376 SR1 sRNA 2 0.333 22.8 Match Image
3 RF02399 Nitrogen stress-induced RNA 1 3 0.176 31.9 Match Image
3 RF02401 ClpQY promoter 6 0.154 65.7 Match Image
3 RF02423 Burkholderia sRNA Bp1_Cand871_SIPHT 12 0.800 138.9 Match Image
3 RF02428 Streptococcus sRNA SpF11 3 1.000 34.7 Match Image
3 RF02431 Streptococcus sRNA SpF22 5 0.227 48.4 Match Image
3 RF02435 Streptococcus sRNA SpF41 3 0.333 33.2 Match Image
3 RF02464 Actinobacteria sRNA Ms_AS-4 2 0.222 22.1 Match Image
3 RF02496 Rhizobiales sRNA Atu_At1 8 0.242 109.7 Match Image
3 RF02502 Rhizobiales sRNA Atu_C8 2 0.074 21.3 Match Image
3 RF02540 Archaeal large subunit ribosomal RNA 88 0.967 3648.2 Match Image
3 RF02541 Bacterial large subunit ribosomal RNA 101 0.990 3137.1 Match Image
3 RF02542 Microsporidia small subunit ribosomal RNA 22 0.478 242.8 Match Image
3 RF02543 Eukaryotic large subunit ribosomal RNA 39 0.443 526.0 Match Image
3 RF02553 Y RNA-like 3 0.600 31.2 Match Image
3 RF02630 Hfq-regulated sRNA 12 2 1.000 19.8 Match Image
3 RF02657 Sense overlapping transcript RNA 2652 (sot) 2 1.000 21.1 Match Image
3 RF02728 Haemophilus regulatory RNA responsive to iron 5 0.714 46.1 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. 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

  3. Nagaswamy U, Fox GE RNA. 2002;8:1112-9. Frequent occurrence of the T-loop RNA folding motif in ribosomal RNAs. PUBMED:12358430

  4. Krasilnikov AS, Mondragón A RNA. 2003;9:640-3. On the occurrence of the T-loop RNA folding motif in large RNA molecules. PUBMED:12756321

  5. Zhuang Z, Jaeger L, Shea JE Nucleic Acids Res. 2007;35:6995-7002. Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin. PUBMED:17940098

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 Stem Loop
Author Gardner PP
Alignment details
Alignment Number of
sequences
Average length Sequence
identity (%)
seed 90 17.49 36

Model information

Build commands
cmbuild -F T-CM T-SEED
cmcalibrate --mpi --seed 1 T-CM
Gathering cutoff 9.2
Covariance model Download the Infernal CM for the motif here