RNA 3D Hub

JAR3D Query RF01774-3.98 completed
Run on Motif Atlas Version 3.98 using the Rfam secondary structure. Run with the CaCoFold secondary structure.

RF01774 Rickettsia rpsL leader

Input Summary

      00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000011111111111111111111111111111111111111111111111
00000000011111111112222222222333333333344444444445555555555666666666677777777778888888888999999999900000000001111111111222222222233333333334444444
12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456
...(((.((((((((.....)))))))).)))..............................((((((((......)))))))).....................((((((.(((((....))))).)))))).............
>AE006914.1/171220-171350
AACAUACUUGCUUUUAUGGAAAAAGUAAUUAUAAUUUAAAUUUAGUGUAAUU----------UACAAAUUCUU-AUAAUUUGUAUUUAGAAAUGAUUGAAAAU--AAAGGGUGGAAGUA-UUUUUCACCCUUUAAUUAUC-GUAUA
>CP001612.1/172039-172169
AACAUACUUGCUUUUAUGGAAAAAGUAAUUAUAAUUUAAAUUUAGUGUAGUU----------UACAAAUUCUU-AUAAUUUGUAUUUAGAAAUGAUUGAAAAU--AAAGGGUGGAAGUA-UUUUUCACCCUUUAAUUAUC-GUAUA
>CP000847.1/178030-178161
AACAUACUUGCUUUUAUGGAAAAAGUCAUUAUAAUCUGAAUCUAGUGUAUUU----------UACAAAUUCUU-AUAAUUUGUAUUUAGAAAUUAUUCAAAAU--AAAGGGUGGAAGUA-UUUUGCUCCCUUUAUUUAUCUGUAUA
>CP000849.1/284262-284404
AACAUACUUGCUUUUAUGGAAAAAGUAAUUAUAAUUUAAAUUUAGUGUAAUUUAAUUUGACAGUGUAAAUAUA-UUAUUUACAUUUGUAAAAUCAUUUAAAAUUCAAAGGGCAAAAGUA-GUUUUUGCCCUUUAAUCAUC-GUAUG
>CP000409.1/152235-152365
AACAUACUUGCUUUUAUAGAAAAAGUAAUUAUAAUUCAAGUUUAGUAUAAUU----------UACAAAUGCUU-AUAAUUUGUAUUUAGAAAUGAUUUAAAAC--UAAAGGGUGGAGUGUUUUUCACCCUUUAG-UUAUC-GUAUA
>CP000683.1/175879-176010
AACAUACUUGCUUUUAUGGAAAAAGUAAUUAUAAUUUAAAUUUAGUGUAAUU----------UACAAGUUCUUAAUAAUUUGUAUUUAGAAAUGAUUGAAAAU--AAAGGGUGGAAGUA-UUUUCCACCCUUUAAUUAUC-GUAUA
>CP000766.2/173657-173786
AACAUACUUGCUUUUAUGGAAAAAGUAAUUAUAAUUUAAAUUUAGUGUAAUU----------UACAAAUUAUA-AGAAUUUGUAUUUAGAAAUGAUUGAAAAU--AAAGGGUGGAAGUA--UUUUCACCCUUUAAUUAUC-GUAUA

There are no chains in PDB that we map to Rfam family RF01774.

Jump to results for:

  • Loop 1IL Column numbers: 6-8, 28-30
  • Loop 2HL Column numbers: 15-21
  • Loop 3HL Column numbers: 70-77
  • Loop 4IL Column numbers: 111-113, 126-128
  • Loop 5HL Column numbers: 117-122

Loop 1 Internal loop

Column numbers: 6-8, 28-30 
    Scored sequences and counts

    
    ACU*AUU    7
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group IL_14688.1

Basepair signature:
cWW-cWW-cWW

100.00 99.49 2 0

Isolated non-canonical cWW pair

2

Motif group IL_08770.1

Basepair signature:
cWW-L-R-cWW

100.00 94.74 2 0

3

Motif group IL_07785.1

Basepair signature:
cWW-cWW-cWW

100.00 89.08 1 0

Isolated non-canonical cWW pair

4

Motif group IL_87907.2

Basepair signature:
cWW-cWW-cWW

100.00 75.70 0 0

Isolated non-canonical cWW pair

5

Motif group IL_28037.2

Basepair signature:
cWW-cWW-cWW

100.00 58.37 0 0

Isolated non-canonical cWW pair

6

Motif group IL_10167.6

Basepair signature:
cWW-cHW-cWW

100.00 44.68 2 0

Isolated cWH basepair

7

Motif group IL_42771.1

Basepair signature:
cWW-cWW

100.00 40.95 3 1

Multiple bulged bases

8

Motif group IL_31737.3

Basepair signature:
cWW-L-cWW

100.00 40.78 3 1

Stack and bulge

9

Motif group IL_42997.3

Basepair signature:
cWW-L-R-cWW

100.00 34.11 3 1

Isolated cWS basepair

10

Motif group IL_83389.2

Basepair signature:
cWW-cWW

100.00 22.86 3 1

Loop 2 Hairpin loop

Column numbers: 15-21 
    Scored sequences and counts

    
    UAUGGAA    6

    
    UAUAGAA    1
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group HL_48417.5

Basepair signature:
cWW-F-F

100.00 35.30 3 1

2

Motif group HL_97917.2

Basepair signature:
cWW-F-F-F-F

100.00 22.91 4 2

3

Motif group HL_50318.1

Basepair signature:
cWW-cSH-F-F

100.00 8.83 6 4

4

Motif group HL_30680.3

Basepair signature:
cWW-F-F-F-F-F

85.71 29.32 3 1

Pseudoknot geometry

5

Motif group HL_50006.2

Basepair signature:
cWW-F-F

85.71 13.64 4 2

6

Motif group HL_22622.1

Basepair signature:
cWW-F-F-F-F-F

85.71 5.50 3 1

7

Motif group HL_89893.1

Basepair signature:
cWW-F-F-F-F

14.29 4.09 5 3

8

Motif group HL_20535.2

Basepair signature:
cWW-F-F-F-F

14.29 -0.72 5 3

9

Motif group HL_47854.1

Basepair signature:
cWW-F-F-F-F

14.29 -7.44 5 3

10

Motif group HL_93535.1

Basepair signature:
cWW-F-F-F-F

14.29 -7.52 3 2

Loop 3 Hairpin loop

Column numbers: 70-77 
    Scored sequences and counts

    
    UCUU-AUA    3

    
    UCUUAAUA    1

    
    GCUU-AUA    1

    
    UAUA-AGA    1

    
    UAUA-UUA    1
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group HL_50318.1

Basepair signature:
cWW-cSH-F-F

100.00 64.11 4 2

2

Motif group HL_20535.2

Basepair signature:
cWW-F-F-F-F

85.71 21.57 4 3

3

Motif group HL_57875.1

Basepair signature:
cWW-F-F

85.71 12.42 3 1

4

Motif group HL_48417.5

Basepair signature:
cWW-F-F

71.43 21.74 3 1

5

Motif group HL_25967.2

Basepair signature:
cWW-cWW-F-F-F

71.43 21.14 3 1

6

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

71.43 16.61 3 1

7

Motif group HL_77436.5

Basepair signature:
cWW-F-F-F-F-F

71.43 7.88 3 2

T-loop related

8

Motif group HL_57176.2

Basepair signature:
cWW-F-F-F

57.14 3.85 3 1

Pseudoknot geometry with 3' bulge

9

Motif group HL_08100.1

Basepair signature:
cWW-F-F-F

57.14 3.09 3 1

10

Motif group HL_10453.3

Basepair signature:
cWW-F-F-F-F-F

57.14 2.98 4 2

tRNA anticodon loop

Loop 4 Internal loop

Column numbers: 111-113, 126-128 
    Scored sequences and counts

    
    GUG*CAC    4

    
    GCA*UGC    1

    
    GGU*ACC    1

    
    GUG*CUC    1
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group IL_08770.1

Basepair signature:
cWW-L-R-cWW

100.00 75.30 2 0

2

Motif group IL_31737.3

Basepair signature:
cWW-L-cWW

100.00 54.18 2 1

Stack and bulge

3

Motif group IL_42997.3

Basepair signature:
cWW-L-R-cWW

100.00 49.40 3 1

Isolated cWS basepair

4

Motif group IL_14688.1

Basepair signature:
cWW-cWW-cWW

100.00 47.31 3 1

Isolated non-canonical cWW pair

5

Motif group IL_07785.1

Basepair signature:
cWW-cWW-cWW

100.00 47.05 2 1

Isolated non-canonical cWW pair

6

Motif group IL_87907.2

Basepair signature:
cWW-cWW-cWW

100.00 39.67 1 1

Isolated non-canonical cWW pair

7

Motif group IL_44465.1

Basepair signature:
cWW-L-R-cWW

100.00 39.44 3 1

Isolated non-canonical cWW contact

8

Motif group IL_28037.2

Basepair signature:
cWW-cWW-cWW

100.00 33.49 1 1

Isolated non-canonical cWW pair

9

Motif group IL_57744.1

Basepair signature:
cWW-cWW-cWW

85.71 27.72 2 1

Isolated non-canonical cWW pair

10

Motif group IL_67095.2

Basepair signature:
cWW-tWW-cWW

85.71 27.65 3 1

Isolated tWW turn

Loop 5 Hairpin loop

Column numbers: 117-122 
    Scored sequences and counts

    
    GUA-UU    4

    
    GUGUUU    1

    
    GUA-GU    1

    
    GUA--U    1
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group HL_56334.1

Basepair signature:
cWW-F

100.00 56.10 1 0

Mini UNCG

2

Motif group HL_69752.2

Basepair signature:
cWW-F

100.00 16.82 3 2

3

Motif group HL_32346.4

Basepair signature:
cWW-F

85.71 21.58 3 1

4

Motif group HL_75660.5

Basepair signature:
cWW-F

85.71 20.33 2 1

5

Motif group HL_70782.2

Basepair signature:
cWW-F

85.71 14.25 3 2

6

Motif group HL_46501.1

Basepair signature:
cWW-cWS

85.71 7.66 4 2

7

Motif group HL_86870.2

Basepair signature:
cWW-F-F-F

71.43 25.87 2 1

8

Motif group HL_48778.2

Basepair signature:
cWW-F

71.43 18.70 2 1

Mini UNCG

9

Motif group HL_56131.2

Basepair signature:
cWW-F-F

71.43 8.09 3 2

10

Motif group HL_38168.1

Basepair signature:
cWW-F

57.14 -0.62 4 2

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