5LMQ Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_5LMQ_001 | 1/A/12:22 | No text annotation | homologous HL_5J7L_001 NA | |
| HL_5LMQ_006 | 1/A/259:267 | GNRA related | homologous HL_4LFB_006 HL_36455.1 | |
| HL_5LMQ_007 | 1/A/296:301 | GNRA | homologous HL_4LFB_007 HL_34789.1 | |
| HL_5LMQ_008 | 1/A/320:333 | No text annotation | homologous HL_4LFB_008 HL_39665.1 | |
| HL_5LMQ_010 | 1/A/379:384 | GNRA | homologous HL_5J7L_010 NA | |
| HL_5LMQ_013 | 1/A/522:527 | No text annotation | geometric HL_4WF9_003 HL_75660.6 | |
| HL_5LMQ_014 | 1/A/617:623 | GNRA-like with tWH | homologous HL_4LFB_014 HL_92337.1 | |
| HL_5LMQ_016 | 1/A/726:731 | GNRA | homologous HL_4LFB_016 HL_34789.1 | |
| HL_5LMQ_017 | 1/A/786:796 | No text annotation | homologous HL_4LFB_017 HL_38491.1 | |
| HL_5LMQ_019 | 1/A/862:867 | GNRA | homologous HL_5J7L_019 NA | |
| HL_5LMQ_020 | 1/A/897:902 | GNRA | homologous HL_4LFB_020 HL_34789.1 | |
| HL_5LMQ_021 | 1/A/963:972 | No text annotation | homologous HL_4LFB_021 HL_97521.1 | |
| HL_5LMQ_025 | 1/A/1089:1096 | T-loop related | homologous HL_4LFB_025 HL_63894.1 | |
| HL_5LMQ_030 | 1/A/1356:1366 | No text annotation | homologous HL_4LFB_030 HL_86432.1 | |
| HL_5LMQ_032 | 1/A/1515:1520 | GNRA variation | geometric HL_4V88_222 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_5LMQ_002 | No text annotation | ||
| HL_5LMQ_003 | GNRA | ||
| HL_5LMQ_004 | No text annotation | ||
| HL_5LMQ_005 | Mini UNCG | ||
| HL_5LMQ_009 | UNCG | ||
| HL_5LMQ_011 | UNCG | ||
| HL_5LMQ_012 | GNRA | ||
| HL_5LMQ_015 | No text annotation | ||
| HL_5LMQ_018 | Mini UNCG | ||
| HL_5LMQ_022 | GNRA | ||
| HL_5LMQ_023 | No text annotation | ||
| HL_5LMQ_024 | GNRA | ||
| HL_5LMQ_026 | No text annotation | ||
| HL_5LMQ_027 | GNRA | ||
| HL_5LMQ_028 | GNRA | ||
| HL_5LMQ_029 | T-loop with 3 stacked bulged bases | ||
| HL_5LMQ_031 | UNCG | ||
| HL_5LMQ_033 | tRNA D-loop | ||
| HL_5LMQ_034 | tRNA anticodon loop | ||
| HL_5LMQ_035 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_5LMQ_001 | 1/A/30:32, 1/A/552:553 | Single bulged G | homologous IL_4LFB_001 IL_28408.1 | |
| IL_5LMQ_002 | 1/A/44:45, 1/A/396:398 | Single bulged A | homologous IL_4LFB_002 IL_14190.1 | |
| IL_5LMQ_003 | 1/A/47:52, 1/A/359:361 | No text annotation | geometric IL_4LFB_003 IL_68149.1 | |
| IL_5LMQ_005 | 1/A/63:66, 1/A/103:104 | Multiple bulged bases | homologous IL_4LFB_005 IL_71421.1 | |
| IL_5LMQ_007 | 1/A/129:131, 1/A/231:232 | Multiple bulged bases | homologous IL_6CZR_119 NA | |
| IL_5LMQ_008 | 1/A/132:136, 1/A/227:230 | No text annotation | homologous IL_4LFB_008 IL_60988.1 | |
| IL_5LMQ_009 | 1/A/148:153, 1/A/168:174 | tWH-tWH-tHW-tHW | homologous IL_4LFB_009 IL_00680.1 | |
| IL_5LMQ_011 | 1/A/242:247, 1/A/277:284 | Kink-turn with non-sequential stacking | homologous IL_4LFB_011 IL_46174.4 | |
| IL_5LMQ_012 | 1/A/249:252, 1/A/274:275 | No text annotation | homologous IL_4LFB_012 IL_22002.1 | |
| IL_5LMQ_013 | 1/A/292:293, 1/A/304:308 | C-loop | homologous IL_4LFB_013 IL_06671.1 | |
| IL_5LMQ_014 | 1/A/367:369, 1/A/392:393 | Single bulged U | homologous IL_4LFB_014 IL_97561.1 | |
| IL_5LMQ_015 | 1/A/371:375, 1/A/389:390 | C-loop | homologous IL_4LFB_015 IL_26900.1 | |
| IL_5LMQ_016 | 1/A/375:376, 1/A/387:389 | Single bulged G | geometric IL_4LFB_016 IL_28408.1 | |
| IL_5LMQ_020 | 1/A/504:511, 1/A/540:541 | SSU/LSU pseudoknot | homologous IL_5J7L_024 NA | |
| IL_5LMQ_021 | 1/A/515:521, 1/A/528:536 | Kink-turn related | geometric IL_4V88_415 NA | |
| IL_5LMQ_022 | 1/A/569:575, 1/A/880:881 | No text annotation | homologous IL_5J7L_026 NA | |
| IL_5LMQ_023 | 1/A/580:584, 1/A/757:761 | tSH-tHW-tHS | homologous IL_4LFB_023 IL_05821.1 | |
| IL_5LMQ_024 | 1/A/594:596, 1/A/644:645 | Major groove platform | homologous IL_4LFB_024 IL_48076.7 | |
| IL_5LMQ_026 | 1/A/605:612, 1/A/628:633 | No text annotation | homologous IL_4LFB_026 IL_04211.1 | |
| IL_5LMQ_027 | 1/A/654:655, 1/A/751:754 | Major groove platform; stack outside cWW | geometric IL_4LFB_027 IL_74641.1 | |
| IL_5LMQ_029 | 1/A/662:666, 1/A/740:743 | Tandem non-canonical cWW pairs | homologous IL_4LFB_029 IL_15225.1 | |
| IL_5LMQ_064 | 1/A/673:677, 1/A/713:717 | Triple non-canonical cWW pairs | homologous IL_4LFB_065 IL_71154.1 | |
| IL_5LMQ_032 | 1/A/774:778, 1/A/804:805 | Left turn | homologous IL_4LFB_032 IL_29346.3 | |
| IL_5LMQ_034 | 1/A/887:894, 1/A/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_4LFB_034 IL_84044.1 | |
| IL_5LMQ_035 | 1/A/922:923, 1/A/1393:1395 | Single bulged A | homologous IL_5J7L_039 NA | |
| IL_5LMQ_036 | 1/A/925:927, 1/A/1390:1391 | Single bulged G | homologous IL_4LFB_036 IL_28408.1 | |
| IL_5LMQ_037 | 1/A/933:935, 1/A/1380:1384 | Minor groove platform | homologous IL_5J7L_041 NA | |
| IL_5LMQ_039 | 1/A/993:997, 1/A/1044:1045 | Minor groove platform | geometric IL_4LFB_039 IL_61370.1 | |
| IL_5LMQ_042 | 1/A/1057:1058, 1/A/1199:1203 | Minor groove platform | homologous IL_4LFB_045 IL_24264.1 | |
| IL_5LMQ_044 | 1/A/1061:1063, 1/A/1193:1195 | Isolated non-canonical cWW pair | homologous IL_4LFB_047 IL_68118.1 | |
| IL_5LMQ_045 | 1/A/1124:1128, 1/A/1143:1149 | No text annotation | geometric IL_4LFB_048 IL_89862.1 | |
| IL_5LMQ_048 | 1/A/1247:1253, 1/A/1284:1290 | No text annotation | homologous IL_4LFB_051 IL_12056.1 | |
| IL_5LMQ_049 | 1/A/1255:1258, 1/A/1277:1282 | 180 degree turn | homologous IL_4LFB_052 IL_08849.1 | |
| IL_5LMQ_053 | 1/A/1399:1401, 1/A/1501:1504 | No text annotation | homologous IL_4LFB_056 IL_18228.1 | |
| IL_5LMQ_054 | 1/A/1401:1404, 1/A/1497:1501 | No text annotation | geometric IL_4V88_464 NA | |
| IL_5LMQ_055 | 1/A/1405:1407, 1/A/1494:1496 | Isolated non-canonical cWW pair | geometric IL_4V88_465 NA | |
| IL_5LMQ_060 | 1/A/1435:1437, 1/A/1464:1466 | Isolated non-canonical cWW pair | geometric IL_4V9F_017 IL_01003.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_5LMQ_004 | Minor groove platform | ||
| IL_5LMQ_006 | Isolated non-canonical cWW pair | ||
| IL_5LMQ_010 | Isolated non-canonical cWW pair | ||
| IL_5LMQ_063 | No text annotation | ||
| IL_5LMQ_017 | No text annotation | ||
| IL_5LMQ_018 | 6x5 Sarcin-Ricin; G-bulge | ||
| IL_5LMQ_019 | No text annotation | ||
| IL_5LMQ_025 | Major groove minor groove platform; mini C-loop | ||
| IL_5LMQ_028 | Major groove platform | ||
| IL_5LMQ_030 | No text annotation | ||
| IL_5LMQ_031 | Kink-turn | ||
| IL_5LMQ_033 | tSH-tHW-tHS | ||
| IL_5LMQ_038 | Minor groove platform | ||
| IL_5LMQ_040 | Single bulged U | ||
| IL_5LMQ_065 | No text annotation | ||
| IL_5LMQ_041 | Isolated cWS basepair | ||
| IL_5LMQ_043 | Single bulged U | ||
| IL_5LMQ_046 | Minor groove platform | ||
| IL_5LMQ_047 | No text annotation | ||
| IL_5LMQ_050 | Not an internal loop | ||
| IL_5LMQ_051 | Minor groove platform | ||
| IL_5LMQ_052 | No text annotation | ||
| IL_5LMQ_056 | Not an internal loop | ||
| IL_5LMQ_057 | Isolated non-canonical cWW pair | ||
| IL_5LMQ_066 | Tandem non-canonical cWW pairs | ||
| IL_5LMQ_058 | Double sheared | ||
| IL_5LMQ_059 | UAA/GAN variation | ||
| IL_5LMQ_061 | No text annotation | ||
| IL_5LMQ_062 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_5LMQ_001 | 1/A/46:47, 1/A/361:367, 1/A/393:395 | No text annotation | homologous J3_5J7L_001 NA | |
| J3_5LMQ_014 | 1/A/46:52, 1/A/359:367, 1/A/393:395 | No text annotation | homologous J3_4LFB_014 J3_63856.1 | |
| J3_5LMQ_002 | 1/A/586:588, 1/A/651:654, 1/A/754:755 | No text annotation | geometric J3_4LFB_011 J3_01633.1 | |
| J3_5LMQ_015 | 1/A/586:588, 1/A/651:655, 1/A/751:755 | No text annotation | homologous J3_4LFB_015 J3_17385.5 | |
| J3_5LMQ_003 | 1/A/672:673, 1/A/717:725, 1/A/732:734 | No text annotation | homologous J3_6CZR_017 NA | |
| J3_5LMQ_004 | 1/A/826:829, 1/A/857:861, 1/A/868:874 | No text annotation | homologous J3_6CZR_018 NA | |
| J3_5LMQ_019 | 1/A/936:939, 1/A/1344:1350, 1/A/1372:1379 | No text annotation | homologous J3_4LFB_002 J3_85722.1 | |
| J3_5LMQ_007 | 1/A/955:962, 1/A/973:984, 1/A/1221:1225 | No text annotation | homologous J3_4LFB_004 J3_88451.1 | |
| J3_5LMQ_016 | 1/A/990:997, 1/A/1044:1047, 1/A/1210:1215 | No text annotation | homologous J3_4LFB_016 J3_28881.1 | |
| J3_5LMQ_010 | 1/A/1063:1068, 1/A/1107:1113, 1/A/1187:1193 | No text annotation | homologous J3_4LFB_007 J3_01343.1 | |
| J3_5LMQ_020 | 1/A/1073:1074, 1/A/1083:1086, 1/A/1099:1102 | No text annotation | homologous J3_4LFB_017 J3_11018.1 | |
| J3_5LMQ_012 | 1/A/1116:1118, 1/A/1155:1158, 1/A/1181:1184 | No text annotation | homologous J3_5J7L_010 NA | |
| J3_5LMQ_018 | 1/A/1116:1118, 1/A/1155:1161, 1/A/1175:1184 | No text annotation | homologous J3_4LFB_018 J3_40706.1 | |
| J3_5LMQ_013 | 1/A/1237:1241, 1/A/1296:1303, 1/A/1334:1337 | No text annotation | homologous J3_4LFB_009 J3_03192.1 | |
| J4_5LMQ_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_5LMQ_002 | 1/A/142:144, 1/A/178:183, 1/A/194:198, 1/A/219:221 | No text annotation | homologous J4_4LFB_002 J4_88771.1 | |
| J4_5LMQ_003 | 1/A/575:577, 1/A/764:769, 1/A/810:821, 1/A/879:880 | No text annotation | homologous J4_4LFB_003 J4_14595.1 | |
| J5_5LMQ_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_5LMQ_002 | 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_5LMQ_005 | No text annotation | ||
| J3_5LMQ_006 | No text annotation | ||
| J3_5LMQ_008 | No text annotation | ||
| J3_5LMQ_017 | No text annotation | ||
| J3_5LMQ_009 | No text annotation | ||
| J3_5LMQ_011 | No text annotation | ||
| J4_5LMQ_004 | tRNA junction |
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