5LMP Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_5LMP_008 | 1/A/320:333 | No text annotation | homologous HL_4LFB_008 HL_39665.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_5LMP_001 | No text annotation | ||
| HL_5LMP_002 | No text annotation | ||
| HL_5LMP_003 | GNRA | ||
| HL_5LMP_004 | No text annotation | ||
| HL_5LMP_005 | Mini UNCG | ||
| HL_5LMP_006 | GNRA related | ||
| HL_5LMP_007 | GNRA | ||
| HL_5LMP_009 | UNCG | ||
| HL_5LMP_010 | GNRA | ||
| HL_5LMP_011 | UNCG | ||
| HL_5LMP_012 | GNRA | ||
| HL_5LMP_013 | No text annotation | ||
| HL_5LMP_014 | GNRA-like with tWH | ||
| HL_5LMP_015 | No text annotation | ||
| HL_5LMP_016 | GNRA | ||
| HL_5LMP_017 | No text annotation | ||
| HL_5LMP_018 | Mini UNCG | ||
| HL_5LMP_019 | GNRA | ||
| HL_5LMP_020 | GNRA | ||
| HL_5LMP_021 | No text annotation | ||
| HL_5LMP_022 | GNRA | ||
| HL_5LMP_023 | No text annotation | ||
| HL_5LMP_024 | GNRA | ||
| HL_5LMP_025 | T-loop related | ||
| HL_5LMP_026 | No text annotation | ||
| HL_5LMP_027 | GNRA | ||
| HL_5LMP_028 | GNRA | ||
| HL_5LMP_029 | T-loop with 3 stacked bulged bases | ||
| HL_5LMP_030 | No text annotation | ||
| HL_5LMP_031 | UNCG | ||
| HL_5LMP_032 | GNRA |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_5LMP_003 | 1/A/47:52, 1/A/359:361 | No text annotation | geometric IL_4LFB_003 IL_68149.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_5LMP_001 | Single bulged G | ||
| IL_5LMP_002 | Single bulged A | ||
| IL_5LMP_004 | Minor groove platform | ||
| IL_5LMP_005 | Multiple bulged bases | ||
| IL_5LMP_006 | Isolated non-canonical cWW pair | ||
| IL_5LMP_007 | Multiple bulged bases | ||
| IL_5LMP_008 | No text annotation | ||
| IL_5LMP_009 | tWH-tWH-tHW-tHW | ||
| IL_5LMP_010 | Isolated non-canonical cWW pair | ||
| IL_5LMP_011 | Kink-turn with non-sequential stacking | ||
| IL_5LMP_012 | No text annotation | ||
| IL_5LMP_013 | C-loop | ||
| IL_5LMP_014 | Single bulged U | ||
| IL_5LMP_015 | C-loop | ||
| IL_5LMP_016 | Single bulged G | ||
| IL_5LMP_017 | No text annotation | ||
| IL_5LMP_018 | 6x5 Sarcin-Ricin; G-bulge | ||
| IL_5LMP_019 | No text annotation | ||
| IL_5LMP_020 | SSU/LSU pseudoknot | ||
| IL_5LMP_021 | Kink-turn related | ||
| IL_5LMP_022 | No text annotation | ||
| IL_5LMP_023 | tSH-tHW-tHS | ||
| IL_5LMP_024 | Major groove platform | ||
| IL_5LMP_025 | Major groove minor groove platform; mini C-loop | ||
| IL_5LMP_026 | No text annotation | ||
| IL_5LMP_027 | Major groove platform; stack outside cWW | ||
| IL_5LMP_028 | Major groove platform | ||
| IL_5LMP_029 | Tandem non-canonical cWW pairs | ||
| IL_5LMP_061 | Triple non-canonical cWW pairs | ||
| IL_5LMP_030 | No text annotation | ||
| IL_5LMP_031 | Kink-turn | ||
| IL_5LMP_032 | Left turn | ||
| IL_5LMP_033 | tSH-tHW-tHS | ||
| IL_5LMP_034 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | ||
| IL_5LMP_035 | Single bulged A | ||
| IL_5LMP_036 | Single bulged G | ||
| IL_5LMP_037 | Minor groove platform | ||
| IL_5LMP_038 | Minor groove platform | ||
| IL_5LMP_039 | Single bulged U | ||
| IL_5LMP_040 | Isolated cWS basepair | ||
| IL_5LMP_041 | Minor groove platform | ||
| IL_5LMP_042 | Single bulged U | ||
| IL_5LMP_043 | Isolated non-canonical cWW pair | ||
| IL_5LMP_044 | No text annotation | ||
| IL_5LMP_062 | No text annotation | ||
| IL_5LMP_045 | Single stack bend | ||
| IL_5LMP_046 | Minor groove platform | ||
| IL_5LMP_047 | No text annotation | ||
| IL_5LMP_048 | No text annotation | ||
| IL_5LMP_049 | 180 degree turn | ||
| IL_5LMP_050 | Double sheared | ||
| IL_5LMP_051 | No text annotation | ||
| IL_5LMP_052 | No text annotation | ||
| IL_5LMP_053 | No text annotation | ||
| IL_5LMP_054 | Isolated non-canonical cWW pair | ||
| IL_5LMP_055 | Not an internal loop | ||
| IL_5LMP_056 | Isolated non-canonical cWW pair | ||
| IL_5LMP_057 | Double sheared | ||
| IL_5LMP_058 | UAA/GAN variation | ||
| IL_5LMP_059 | Isolated non-canonical cWW pair | ||
| IL_5LMP_060 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_5LMP_001 | 1/A/46:47, 1/A/361:367, 1/A/393:395 | No text annotation | homologous J3_5J7L_001 NA | |
| J3_5LMP_014 | 1/A/46:52, 1/A/359:367, 1/A/393:395 | No text annotation | homologous J3_4LFB_014 J3_63856.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_5LMP_002 | No text annotation | ||
| J3_5LMP_015 | No text annotation | ||
| J3_5LMP_003 | No text annotation | ||
| J3_5LMP_004 | No text annotation | ||
| J3_5LMP_005 | No text annotation | ||
| J3_5LMP_006 | No text annotation | ||
| J3_5LMP_007 | No text annotation | ||
| J3_5LMP_008 | No text annotation | ||
| J3_5LMP_009 | No text annotation | ||
| J3_5LMP_010 | No text annotation | ||
| J3_5LMP_017 | No text annotation | ||
| J3_5LMP_011 | No text annotation | ||
| J3_5LMP_012 | No text annotation | ||
| J3_5LMP_016 | No text annotation | ||
| J3_5LMP_013 | No text annotation | ||
| J4_5LMP_001 | No text annotation | ||
| J4_5LMP_002 | No text annotation | ||
| J4_5LMP_003 | No text annotation | ||
| J5_5LMP_001 | No text annotation | ||
| J5_5LMP_002 | No text annotation |
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