RNA 3D Hub

JAR3D Query RF01407-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.

RF01407 STnc560 Hfq binding RNA

Input Summary

      0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111222222222222222222222
0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333444444444455555555556666666666777777777788888888889999999999000000000011111111112
1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890
............(((((((((.....((.(((.((....(((((((((.((........))))))))))).....))..)))))........................)))))))))...((((((.........))))))........(....(((((((((((((......)).))))))))))))....(((.(((.....))))))..........
>AE005174.2_1939628-1939841
CAUUCAUUGAGAAAACUGAUGCUACUGU-GUCAACGAUCCGUUAUCAGUGCAGGAAAAUGCCUGUUAGCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUCACCGCCGGUUUACUGGCGGU-UUUUUUUCGCCGUCAUAAAAAUC----AGGCCCCUUGUACACAACUGUAACAAGGGGCCGGUUAGGUGAGGGAUUAUCUCCGUUCAUUAGUCA
>AE014075.1_1805101-1804887
CAUUCAUUGAGAAAACUGAUGCUACUGU-GUCAACGAUCCGUUAUCAGUGCAGGAAAAUGCCUGUUAGCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUCACCGCCGGUUUACUGGCGGUUUUUUUUUCGCCGUCAUAAAAAUC----AGGCCCCUUGUACACAACUGUAACAAGGGGCCGGUUAGGUGAGGGAUUAUCUCCGUUCAUUAGUCA
>CP000034.1_1455774-1455986
CAUUCAUUGAGAAAACUGAUGCUACUGU-GUCAACGAUCCGUUAUCAGUGCAGGAAAAUGCCUGUUAGCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUCACCGCCGGUUUACUGGCGGU--UUUUUUCGCCGUCAUAAAAAUC----AGGCCCCUUGUACACAACUGUAACAAGGGGCCGGUUAGGUGAGGGAUUAUCUCCGUUCAUUAGUCA
>CP000266.1_1628757-1628544
CAUUCAUUGAGAAAACUGAUGCUACUGU-GUCAACGAUCCGUUAUCAGUGCAGGAAAAUGCCUGUUAGCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUCACCGCCGGUUUACUGGCGGU-UUUUUUUCGCCGUCAUAAAAAUC----AGGCCCCUUGUACACAACUGUAACAAGGGGCCGGUUAGGUGAGGGAUUAUCUCCGUUCAUUAGUCA
>CP000036.1_1598345-1598558
CAUUCAUUGAGAAAACUGAUGCUACUGU-GUCAACGAUUCGUUAUCAGUGCAGGAAAAUGCCUGUUAGCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUCACCGCCGGUUUACUGGCGGU-UUUUUUUCGCCGUCAUAAAAAUC----AGGCCCCUUGUACACAACUGUAACAAGGGGCCGGUUAGGUGAGGGAUUAUCUCCGUUCAUUAGUCA
>CP000038.1_1675303-1675516
CAUUCAUUGAGAAAACUGAUGCUACUGU-GUCAACGAUCCGUUAUCAGUGCAGGAAAAUGCCUGUUAGCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUCACCGCCGGUUUACUGGCGGU-UUUUUUUCGCCGUCAUAAAAAUC----AGGCCCCUUGUACACAACUGUAACAAGGGGCCGGUUAGGUGAGGGAUUAUCUCCGUUCAGGUGAUG
>ABAN01000003.1_243628-243410
GCUUCAUUGAUAUUGACGGUGCUACAGUCGUUAGCGAUCCGUUAUCCUCGCAAGAAUUUGCCCGGUAGCGUAUAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUUACCGCUGGUGAACCGGCGGU-UUUUUUUGCCUGCCAUCCAGACAAAAGCGGCCCCUUGCGCAACGAUGCAGCAAGGGGCCGGCUCUGCGAGGGAUUAUCUCCGUUCAUUAAUCA
>CP000468.1_1667136-1666923
CAUUCAUUGAGAAAACUGAUGCUACUGU-GUCAACGAUCCGUUAUCAGUGCAGGAAAAUGCCUGUUAGCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUCACCGCCGGUUUACUGGCGGU-UUUUUUUCGCCGUCAUAAAAAUC----AGGCCCCUUGUACACAACUGUAACAAGGGGCCGGUUAGGUGAGGGAUUAUCUCCGUUCAUUAGUCA
>CP000970.1_1619937-1620150
CAUUCAUUGAGAAAACUGAUGCUACUGU-GUCAACGAUCCGUUAUCAGUGCAGGAAAAUGCCUGUUAGCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUCACCGCCGGUUUACUGGCGGU-UUUUUUUCGCCGUCAUAAAAAUC----AGGCCCCUUGUACACAGUUGUAACAAGGGGCCGGUUAGGUGAGGGAUUAUCUCCGUUCAUUAGUCA
>AP009048.1_1624662-1624449
CAUUCAUUGAGAAAACUGAUGCUACUGU-GUCAACGAUUCGUUAUCAGUGCAGGAAAAUGCCUGUUAGCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUCACCGCCGGUUUACUGGCGGU-UUUUUUUCGCCGUCAUAAAAAUC----AGGCCCCUUGUACACAACUGUAACAAGGGGCCGGUUAGGUGAGGGAUUAUCUCCGUUCAUUAGUCA
>FM180568.1_1719664-1719451
CAUUCAUUGAGAAAACUGAUGCUACUGU-GUCAACGAUCCGUUAUCAGUGCAGGAAAAUGCCUGUUAGCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUCACCGCCGGUUUACUGGCGGU-UUUUUUUCGCCGUCAUAAAAAUC----AGGCCCCUUGUACACAACUGUAACAAGGGGCCGGUUAGGUGAGGGAUUAUCUCCGUUCAUUAGUCA
>AE005674.2_1592783-1592995
CUUUCAUUGAGAAAACUGAUGCUACUGU-GUCAACGAUCCGUUAUCAGUGCAGGAAAAUGCCUGUUAGCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUCACCGCCGGUUUACUGGCGGU--UUUUUUCGCCGUCAUAAAAAUC----AGGCCCCUUGUACACAACUGUAACAAGGGGCCGGUUAGGUGAGGGAUUAUCUCCGUUCAUUAGUCA

There are no chains in PDB that we map to Rfam family RF01407.

Jump to results for:

  • Loop 1IL Column numbers: 21-27, 84-109
  • Loop 2IL Column numbers: 28-30, 82-83
  • Loop 3IL Column numbers: 32-34, 77-80
  • Loop 4IL Column numbers: 35-40, 70-76
  • Loop 5IL Column numbers: 48-50, 61-62
  • Loop 6HL Column numbers: 51-60
  • Loop 7HL Column numbers: 126-136
  • Loop 8IL Column numbers: 150-155, 187-188
  • Loop 9IL Column numbers: 165-166, 175-177
  • Loop 10HL Column numbers: 167-174
  • Loop 11IL Column numbers: 195-197, 207-208
  • Loop 12HL Column numbers: 199-205

Loop 1 Internal loop

Column numbers: 21-27, 84-109 
    Scored sequences and counts

    
    GCUACUG*CAAAUCUAUCCAUGCAAGCAUUCACC   11

    
    GCUACAG*CAAAUCUAUCCAUGCAAGCAUUUACC    1
No Matches Found View All Results for this Loop

Loop 2 Internal loop

Column numbers: 28-30, 82-83 
    Scored sequences and counts

    
    U-G*CA   11

    
    UCG*CA    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_07039.3

Basepair signature:
cWW-L-cWW

100.00 27.79 2 1

Major groove platform

2

Motif group IL_42771.1

Basepair signature:
cWW-cWW

100.00 27.00 3 1

Multiple bulged bases

3

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

100.00 25.84 2 1

Intercalated cWS

4

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

100.00 25.14 3 1

5

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

100.00 24.11 1 1

Single stack bend

6

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

100.00 18.61 2 1

Major groove intercalation

7

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

100.00 18.38 2 1

Single stack bend

8

Motif group IL_61258.15

Basepair signature:
cWW-L-cWW

100.00 17.35 1 1

Single bulged C

9

Motif group IL_16386.4

Basepair signature:
cWW-L-cWW

100.00 15.99 3 1

10

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

100.00 10.14 4 1

Loop 3 Internal loop

Column numbers: 32-34, 77-80 
    Scored sequences and counts

    
    CAA*CAAA   11

    
    UAG*CAAA    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_41344.1

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

100.00 79.44 3 0

2

Motif group IL_55516.2

Basepair signature:
cWW-cWW-cSH-cWW

100.00 64.37 3 0

3

Motif group IL_31531.3

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

100.00 61.71 3 0

Decoding loop related

4

Motif group IL_31737.3

Basepair signature:
cWW-L-cWW

100.00 51.44 3 0

Stack and bulge

5

Motif group IL_08770.1

Basepair signature:
cWW-L-R-cWW

100.00 48.43 3 0

6

Motif group IL_57744.1

Basepair signature:
cWW-cWW-cWW

100.00 46.50 3 0

Isolated non-canonical cWW pair

7

Motif group IL_90351.1

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

100.00 39.49 3 0

8

Motif group IL_83389.2

Basepair signature:
cWW-cWW

100.00 24.74 4 1

9

Motif group IL_15698.3

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

100.00 12.38 4 1

10

Motif group IL_14688.1

Basepair signature:
cWW-cWW-cWW

100.00 10.52 5 1

Isolated non-canonical cWW pair

Loop 4 Internal loop

Column numbers: 35-40, 70-76 
    Scored sequences and counts

    
    CGAUCC*GUAAAAG    9

    
    CGAUUC*GUAAAAG    2

    
    CGAUCC*GUAUAAG    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_16458.4

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

83.33 1.05 7 3

Sarcin-Ricin target in LSU H95; G-bulge

2

Motif group IL_26307.2

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

83.33 -3.25 4 3

7x6 Sarcin-Ricin; G-bulge

3

Motif group IL_24254.1

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

16.67 -23.39 8 4

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

Loop 5 Internal loop

Column numbers: 48-50, 61-62 
    Scored sequences and counts

    
    GUG*CC   11

    
    UCG*CC    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_81831.1

Basepair signature:
cWW-L-cWW

100.00 93.89 2 0

Intercalated cWS

2

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

100.00 92.41 2 0

3

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

100.00 91.97 0 0

Single stack bend

4

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

100.00 78.05 1 0

Single stack bend

5

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

100.00 76.24 2 0

6

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

100.00 67.81 3 0

Major groove platform

7

Motif group IL_42771.1

Basepair signature:
cWW-cWW

100.00 61.06 3 1

Multiple bulged bases

8

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

100.00 60.86 1 1

Major groove intercalation

9

Motif group IL_48076.6

Basepair signature:
cWW-cSH-cWW

100.00 51.01 2 0

Major groove platform

10

Motif group IL_16386.4

Basepair signature:
cWW-L-cWW

100.00 40.79 3 1

Loop 6 Hairpin loop

Column numbers: 51-60 
    Scored sequences and counts

    
    CAGGAAAAUG   11

    
    CAAGAAUUUG    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_36335.1

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

100.00 22.78 3 3

2

Motif group HL_57863.1

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

100.00 13.89 5 3

G-quadruplex fragment

3

Motif group HL_93438.2

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

91.67 27.67 2 2

4

Motif group HL_75293.5

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

91.67 0.30 3 3

5

Motif group HL_73255.1

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

8.33 -9.42 4 4

Loop 7 Hairpin loop

Column numbers: 126-136 
    Scored sequences and counts

    
    U-UUUUUUUCG    8

    
    U--UUUUUUCG    2

    
    UUUUUUUUUCG    1

    
    U-UUUUUUUGC    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_69139.1

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

75.00 6.75 3 3

2

Motif group HL_25061.1

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

16.67 -13.61 4 3

3

Motif group HL_98252.1

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

8.33 -10.87 5 3

Loop 8 Internal loop

Column numbers: 150-155, 187-188 
    Scored sequences and counts

    
    C----A*GG   11

    
    AAAAGC*GG    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

91.67 -11.20 2 2

Multiple bulged bases

Loop 9 Internal loop

Column numbers: 165-166, 175-177 
    Scored sequences and counts

    
    UA*UAA   11

    
    CG*CAG    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_42771.1

Basepair signature:
cWW-cWW

100.00 99.83 2 0

Multiple bulged bases

2

Motif group IL_10569.1

Basepair signature:
cWW-L-cWW

100.00 96.68 2 0

3

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

100.00 96.03 2 0

Single stack bend

4

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

100.00 90.65 2 0

Single stack bend

5

Motif group IL_48076.6

Basepair signature:
cWW-cSH-cWW

100.00 89.98 1 0

Major groove platform

6

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

100.00 87.31 4 0

7

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

100.00 84.96 2 0

Major groove intercalation

8

Motif group IL_31462.6

Basepair signature:
cWW-L-cWW

100.00 83.33 0 0

Single bulged A

9

Motif group IL_31737.3

Basepair signature:
cWW-L-cWW

100.00 82.72 3 0

Stack and bulge

10

Motif group IL_51454.3

Basepair signature:
cWW-cSH-cWW

100.00 81.18 0 0

Minor groove platform

Loop 10 Hairpin loop

Column numbers: 167-174 
    Scored sequences and counts

    
    CACAACUG   10

    
    CAACGAUG    1

    
    CACAGUUG    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_39243.1

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

91.67 18.81 4 2

2

Motif group HL_20535.2

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

91.67 5.73 5 3

3

Motif group HL_13529.1

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

83.33 -3.08 3 2

4

Motif group HL_04259.3

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

83.33 -3.40 4 2

GNRA with extra cWW

5

Motif group HL_22622.1

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

16.67 -28.75 4 4

6

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

8.33 -14.99 2 2

7

Motif group HL_47854.1

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

8.33 -16.73 5 3

8

Motif group HL_99748.1

Basepair signature:
cWW-F-F-cSH

8.33 -30.79 4 4

Other HL

9

Motif group HL_04641.1

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

8.33 -57.01 5 5

10

Motif group HL_50006.2

Basepair signature:
cWW-F-F

8.33 -60.36 4 4

Loop 11 Internal loop

Column numbers: 195-197, 207-208 
    Scored sequences and counts

    
    GAG*CC   12
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_26793.1

Basepair signature:
cWW-L-cWW

100.00 100.00 0 0

Single stack bend

2

Motif group IL_31462.6

Basepair signature:
cWW-L-cWW

100.00 100.00 0 0

Single bulged A

3

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

100.00 100.00 0 0

Single stack bend

4

Motif group IL_10569.1

Basepair signature:
cWW-L-cWW

100.00 99.41 2 0

5

Motif group IL_42771.1

Basepair signature:
cWW-cWW

100.00 96.85 2 0

Multiple bulged bases

6

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

100.00 93.80 1 0

Major groove intercalation

7

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

100.00 87.35 3 0

8

Motif group IL_31737.3

Basepair signature:
cWW-L-cWW

100.00 86.52 1 0

Stack and bulge

9

Motif group IL_48076.6

Basepair signature:
cWW-cSH-cWW

100.00 80.96 2 0

Major groove platform

10

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

100.00 75.28 3 0

Major groove platform

Loop 12 Hairpin loop

Column numbers: 199-205 
    Scored sequences and counts

    
    GAUUAUC   12
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_57875.1

Basepair signature:
cWW-F-F

100.00 83.87 2 0

2

Motif group HL_50318.1

Basepair signature:
cWW-cSH-F-F

100.00 83.14 4 2

3

Motif group HL_48417.5

Basepair signature:
cWW-F-F

100.00 80.27 1 0

4

Motif group HL_80922.2

Basepair signature:
cWW-tSH-F

100.00 68.42 1 1

5

Motif group HL_25967.2

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

100.00 62.14 1 1

6

Motif group HL_56131.2

Basepair signature:
cWW-F-F

100.00 56.44 3 1

7

Motif group HL_20535.2

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

100.00 54.68 2 2

8

Motif group HL_43517.1

Basepair signature:
cWW-F-F-F

100.00 36.89 1 1

9

Motif group HL_77436.5

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

100.00 25.93 2 2

T-loop related

10

Motif group HL_28075.1

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

100.00 24.88 2 2

Coloring options: