5LMO Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_5LMO_001 | 1/A/12:22 | No text annotation | homologous HL_5J7L_001 NA | |
| HL_5LMO_004 | 1/A/189C:189H | No text annotation | homologous HL_6CZR_075 NA | |
| HL_5LMO_006 | 1/A/259:267 | GNRA related | homologous HL_4LFB_006 HL_36455.1 | |
| HL_5LMO_007 | 1/A/296:301 | GNRA | homologous HL_4LFB_007 HL_34789.1 | |
| HL_5LMO_008 | 1/A/320:333 | No text annotation | homologous HL_4LFB_008 HL_39665.1 | |
| HL_5LMO_013 | 1/A/522:527 | No text annotation | geometric HL_5J7L_143 NA | |
| HL_5LMO_014 | 1/A/617:623 | GNRA-like with tWH | homologous HL_4LFB_014 HL_92337.1 | |
| HL_5LMO_016 | 1/A/726:731 | GNRA | homologous HL_4LFB_016 HL_34789.1 | |
| HL_5LMO_017 | 1/A/786:796 | No text annotation | homologous HL_4LFB_017 HL_38491.1 | |
| HL_5LMO_019 | 1/A/862:867 | GNRA | homologous HL_4LFB_019 HL_34789.1 | |
| HL_5LMO_025 | 1/A/1089:1096 | T-loop related | homologous HL_4LFB_025 HL_63894.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_5LMO_002 | No text annotation | ||
| HL_5LMO_003 | GNRA | ||
| HL_5LMO_005 | Mini UNCG | ||
| HL_5LMO_009 | UNCG | ||
| HL_5LMO_010 | GNRA | ||
| HL_5LMO_011 | UNCG | ||
| HL_5LMO_012 | GNRA | ||
| HL_5LMO_015 | No text annotation | ||
| HL_5LMO_018 | Mini UNCG | ||
| HL_5LMO_020 | GNRA | ||
| HL_5LMO_021 | No text annotation | ||
| HL_5LMO_022 | GNRA | ||
| HL_5LMO_023 | No text annotation | ||
| HL_5LMO_024 | GNRA | ||
| HL_5LMO_026 | No text annotation | ||
| HL_5LMO_027 | GNRA | ||
| HL_5LMO_028 | GNRA | ||
| HL_5LMO_029 | T-loop with 3 stacked bulged bases | ||
| HL_5LMO_030 | No text annotation | ||
| HL_5LMO_031 | UNCG | ||
| HL_5LMO_032 | GNRA |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_5LMO_001 | 1/A/30:32, 1/A/552:553 | Single bulged G | homologous IL_5J7L_001 NA | |
| IL_5LMO_003 | 1/A/47:52, 1/A/359:361 | No text annotation | homologous IL_4LFB_003 IL_68149.1 | |
| IL_5LMO_005 | 1/A/63:66, 1/A/103:104 | Multiple bulged bases | homologous IL_4LFB_005 IL_71421.1 | |
| IL_5LMO_007 | 1/A/129:131, 1/A/231:232 | Multiple bulged bases | homologous IL_6CZR_119 NA | |
| IL_5LMO_008 | 1/A/132:136, 1/A/227:230 | Minor groove platform related | homologous IL_6CZR_120 NA | |
| IL_5LMO_009 | 1/A/148:153, 1/A/168:174 | tWH-tWH-tHW-tHW | homologous IL_4LFB_009 IL_00680.1 | |
| IL_5LMO_011 | 1/A/242:247, 1/A/277:284 | Kink-turn with non-sequential stacking | homologous IL_5J7L_014 NA | |
| IL_5LMO_013 | 1/A/292:293, 1/A/304:308 | C-loop | homologous IL_4LFB_013 IL_06671.1 | |
| IL_5LMO_016 | 1/A/375:376, 1/A/387:389 | Single bulged G | homologous IL_4LFB_016 IL_28408.1 | |
| IL_5LMO_018 | 1/A/446:450, 1/A/483:488 | 6x5 Sarcin-Ricin; G-bulge | geometric IL_4LFB_018 IL_82100.1 | |
| IL_5LMO_020 | 1/A/504:511, 1/A/540:541 | SSU/LSU pseudoknot | homologous IL_5J7L_024 NA | |
| IL_5LMO_021 | 1/A/515:521, 1/A/528:536 | Kink-turn related | geometric IL_4V88_415 NA | |
| IL_5LMO_022 | 1/A/580:584, 1/A/757:761 | tSH-tHW-tHS | homologous IL_4LFB_023 IL_05821.1 | |
| IL_5LMO_023 | 1/A/594:596, 1/A/644:645 | Major groove platform | homologous IL_4LFB_024 IL_48076.7 | |
| IL_5LMO_027 | 1/A/657:658, 1/A/747:749 | Major groove platform | homologous IL_4LFB_028 IL_48076.7 | |
| IL_5LMO_028 | 1/A/662:666, 1/A/740:743 | Tandem non-canonical cWW pairs | homologous IL_4LFB_029 IL_15225.1 | |
| IL_5LMO_031 | 1/A/774:778, 1/A/804:805 | Left turn | homologous IL_4LFB_032 IL_29346.3 | |
| IL_5LMO_033 | 1/A/887:894, 1/A/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_4LFB_034 IL_84044.1 | |
| IL_5LMO_036 | 1/A/933:935, 1/A/1380:1384 | Minor groove platform | homologous IL_5J7L_041 NA | |
| IL_5LMO_042 | 1/A/1061:1063, 1/A/1193:1195 | Isolated non-canonical cWW pair | geometric IL_4LFB_047 IL_68118.1 | |
| IL_5LMO_051 | 1/A/1399:1401, 1/A/1501:1504 | No text annotation | geometric IL_4V88_463 NA | |
| IL_5LMO_052 | 1/A/1401:1404, 1/A/1497:1501 | No text annotation | geometric IL_4V88_464 NA | |
| IL_5LMO_054 | 1/A/1407:1409, 1/A/1491:1494 | Not an internal loop | geometric IL_5VCI_005 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_5LMO_002 | Single bulged A | ||
| IL_5LMO_004 | Minor groove platform | ||
| IL_5LMO_006 | Isolated non-canonical cWW pair | ||
| IL_5LMO_010 | Isolated non-canonical cWW pair | ||
| IL_5LMO_012 | No text annotation | ||
| IL_5LMO_014 | Single bulged U | ||
| IL_5LMO_015 | C-loop | ||
| IL_5LMO_017 | No text annotation | ||
| IL_5LMO_019 | No text annotation | ||
| IL_5LMO_024 | Major groove minor groove platform; mini C-loop | ||
| IL_5LMO_025 | No text annotation | ||
| IL_5LMO_026 | Major groove platform; stack outside cWW | ||
| IL_5LMO_060 | Triple non-canonical cWW pairs | ||
| IL_5LMO_029 | No text annotation | ||
| IL_5LMO_030 | Kink-turn | ||
| IL_5LMO_032 | tSH-tHW-tHS | ||
| IL_5LMO_034 | Single bulged A | ||
| IL_5LMO_035 | Single bulged G | ||
| IL_5LMO_037 | Minor groove platform | ||
| IL_5LMO_038 | Single bulged U | ||
| IL_5LMO_039 | Isolated cWS basepair | ||
| IL_5LMO_040 | Minor groove platform | ||
| IL_5LMO_041 | Single bulged U | ||
| IL_5LMO_043 | No text annotation | ||
| IL_5LMO_061 | No text annotation | ||
| IL_5LMO_044 | Single stack bend | ||
| IL_5LMO_045 | Minor groove platform | ||
| IL_5LMO_046 | No text annotation | ||
| IL_5LMO_047 | No text annotation | ||
| IL_5LMO_048 | 180 degree turn | ||
| IL_5LMO_049 | Double sheared | ||
| IL_5LMO_050 | No text annotation | ||
| IL_5LMO_053 | Isolated non-canonical cWW pair | ||
| IL_5LMO_055 | Isolated non-canonical cWW pair | ||
| IL_5LMO_056 | Double sheared | ||
| IL_5LMO_057 | UAA/GAN variation | ||
| IL_5LMO_058 | Isolated non-canonical cWW pair | ||
| IL_5LMO_059 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_5LMO_001 | 1/A/46:47, 1/A/361:367, 1/A/393:395 | No text annotation | homologous J3_5J7L_001 NA | |
| J3_5LMO_014 | 1/A/46:52, 1/A/359:367, 1/A/393:395 | No text annotation | homologous J3_4LFB_014 J3_63856.1 | |
| J3_5LMO_002 | 1/A/586:588, 1/A/651:654, 1/A/754:755 | No text annotation | homologous J3_5J7L_002 NA | |
| J3_5LMO_015 | 1/A/586:588, 1/A/651:655, 1/A/751:755 | No text annotation | homologous J3_4LFB_015 J3_17385.5 | |
| J3_5LMO_004 | 1/A/826:829, 1/A/857:861, 1/A/868:874 | No text annotation | homologous J3_6CZR_018 NA | |
| J3_5LMO_010 | 1/A/1063:1068, 1/A/1107:1113, 1/A/1187:1193 | No text annotation | homologous J3_4LFB_007 J3_01343.1 | |
| J3_5LMO_011 | 1/A/1073:1074, 1/A/1083:1087, 1/A/1098:1102 | No text annotation | homologous J3_5J7L_009 NA | |
| J4_5LMO_001 | 1/A/115:122, 1/A/239:240, 1/A/286:289, 1/A/311:312 | No text annotation | homologous J4_4LFB_001 J4_90044.1 | |
| J4_5LMO_003 | 1/A/569:577, 1/A/764:769, 1/A/810:821, 1/A/879:881 | No text annotation | ||
| J5_5LMO_001 | 1/A/36:39, 1/A/403:406, 1/A/436:442, 1/A/492:500, 1/A/545:548 | No text annotation | homologous J5_4LFB_001 J5_70703.1 | |
| J5_5LMO_003 | 1/A/58:61, 1/A/106:113, 1/A/314:316, 1/A/337:339, 1/A/350:354 | No text annotation | homologous J5_4LFB_002 J5_58574.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_5LMO_003 | No text annotation | ||
| J3_5LMO_017 | No text annotation | ||
| J3_5LMO_005 | No text annotation | ||
| J3_5LMO_006 | No text annotation | ||
| J3_5LMO_007 | No text annotation | ||
| J3_5LMO_008 | No text annotation | ||
| J3_5LMO_009 | No text annotation | ||
| J3_5LMO_012 | No text annotation | ||
| J3_5LMO_016 | No text annotation | ||
| J3_5LMO_013 | No text annotation | ||
| J4_5LMO_002 | No text annotation | ||
| J5_5LMO_002 | No text annotation |
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