RNA 3D Hub

JAR3D Query RF01774-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam 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 1HL Column numbers: 15-21
  • Loop 2IL Column numbers: 42-48, 88-94
  • Loop 3IL Column numbers: 49-63, 84-87
  • Loop 4HL Column numbers: 70-77
  • Loop 5IL Column numbers: 103-106, 133-134
  • Loop 6HL Column numbers: 116-123

Loop 1 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 2 Internal loop

Column numbers: 42-48, 88-94 
    Scored sequences and counts

    
    UUAGUGU*AGAAAUG    4

    
    CUAGUGU*AGAAAUU    1

    
    UUAGUAU*AGAAAUG    1

    
    UUAGUGU*UAAAAUC    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_24254.1

Basepair signature:
cWW-cWW-tHH-cSH-tWH-tHS-cWW

85.71 3.14 5 2

7x6 Sarcin-Ricin with UU cWW pair; G-bulge

2

Motif group IL_26307.2

Basepair signature:
cWW-tSH-tHH-cSH-tWH-tHS-cWW

71.43 1.57 5 2

7x6 Sarcin-Ricin; G-bulge

3

Motif group IL_29198.2

Basepair signature:
cWW-cWW-L-R-cSH-R-tWH-tHS-cWW

14.29 -28.20 8 5

7x7 Sarcin-Ricin with intercalated A; G-bulge

Loop 3 Internal loop

Column numbers: 49-63, 84-87 
    Scored sequences and counts

    
    AAUU----------U*AUUU    4

    
    AAUUUAAUUUGACAG*UUUG    1

    
    AGUU----------U*AUUU    1

    
    AUUU----------U*AUUU    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_29223.1

Basepair signature:
cWW-L-R-L-cWW-cWW-cWW

85.71 -50.73 4 2

2

Motif group IL_68909.1

Basepair signature:
cWW-L-R-L-R-L-cWW

85.71 -114.00 5 2

3

Motif group IL_70096.1

Basepair signature:
cWW-L-cWW-cWW

85.71 -803.16 6 2

Kink-turn related

4

Motif group IL_26728.3

Basepair signature:
cWW-cSH-R-cSH-cWW-cWW

85.71 -807.60 7 3

5

Motif group IL_96236.1

Basepair signature:
cWW-tWW-cWW-L-cWW

85.71 -861.05 3 1

6

Motif group IL_51479.1

Basepair signature:
cWW-L-R-L-cWW

85.71 -1519.31 4 1

7

Motif group IL_74367.1

Basepair signature:
cWW-L-R-L-R-L-R-cWW

71.43 -925.15 5 2

8

Motif group IL_78800.1

Basepair signature:
cWW-cSH-L-cWW

57.14 -1204.37 4 2

9

Motif group IL_76758.2

Basepair signature:
cWW-L-R-L-cWW-L-L

14.29 -88.80 4 3

Intercalated tWH

10

Motif group IL_61242.1

Basepair signature:
cWW-cWW-L-R-L-R-cWW

14.29 -818.22 7 3

Loop 4 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 5 Internal loop

Column numbers: 103-106, 133-134 
    Scored sequences and counts

    
    U--A*UA    5

    
    UUCA*UA    1

    
    C--U*AG    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_84476.1

Basepair signature:
cWW-cWW

100.00 31.00 4 2

Multiple bulged bases

2

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

100.00 26.62 2 1

Intercalated cWS

3

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

100.00 25.36 4 1

4

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

100.00 21.15 3 1

Major groove intercalation

5

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

100.00 15.51 2 1

Single stack bend

6

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

100.00 8.10 4 1

7

Motif group IL_42771.1

Basepair signature:
cWW-cWW

85.71 16.88 2 1

Multiple bulged bases

8

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

85.71 16.10 2 1

Major groove platform

9

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

85.71 9.19 2 1

Single stack bend

10

Motif group IL_61258.15

Basepair signature:
cWW-L-cWW

85.71 2.59 1 1

Single bulged C

Loop 6 Hairpin loop

Column numbers: 116-123 
    Scored sequences and counts

    
    AGUA-UUU    4

    
    AGUGUUUU    1

    
    AGUA-GUU    1

    
    AGUA--UU    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

85.71 54.57 4 2

2

Motif group HL_48417.5

Basepair signature:
cWW-F-F

85.71 44.84 2 0

3

Motif group HL_57875.1

Basepair signature:
cWW-F-F

85.71 36.77 3 1

4

Motif group HL_80922.2

Basepair signature:
cWW-tSH-F

85.71 12.96 3 2

5

Motif group HL_66103.1

Basepair signature:
cWW-F-F

85.71 8.23 4 2

6

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

85.71 5.50 2 2

7

Motif group HL_42046.2

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

85.71 -1.62 4 2

8

Motif group HL_78347.4

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

71.43 18.08 3 1

9

Motif group HL_77436.5

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

71.43 12.13 3 1

T-loop related

10

Motif group HL_57176.2

Basepair signature:
cWW-F-F-F

71.43 -6.87 2 2

Pseudoknot geometry with 3' bulge

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