5LMT Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_5LMT_001 | 1/A/12:22 | No text annotation | homologous HL_5J7L_001 HL_89881.5 | |
| HL_5LMT_004 | 1/A/189C:189H | No text annotation | homologous HL_4LFB_004 HL_48417.6 | |
| HL_5LMT_006 | 1/A/259:267 | GNRA related | homologous HL_4LFB_006 HL_84299.4 | |
| HL_5LMT_007 | 1/A/296:301 | GNRA | homologous HL_4LFB_007 HL_37824.8 | |
| HL_5LMT_008 | 1/A/320:333 | No text annotation | homologous HL_4LFB_008 HL_81205.3 | |
| HL_5LMT_013 | 1/A/522:527 | No text annotation | geometric HL_5J7L_143 HL_75660.5 | |
| HL_5LMT_014 | 1/A/617:623 | GNRA-like with tWH | homologous HL_4LFB_014 HL_10453.3 | |
| HL_5LMT_015 | 1/A/689:698 | No text annotation | homologous HL_4LFB_015 HL_75293.5 | |
| HL_5LMT_016 | 1/A/726:731 | GNRA | homologous HL_4LFB_016 HL_37824.8 | |
| HL_5LMT_017 | 1/A/786:796 | No text annotation | homologous HL_4LFB_017 HL_75293.5 | |
| HL_5LMT_019 | 1/A/862:867 | GNRA | homologous HL_5J7L_019 HL_37824.8 | |
| HL_5LMT_020 | 1/A/897:902 | GNRA | homologous HL_4LFB_020 HL_37824.8 | |
| HL_5LMT_021 | 1/A/963:972 | No text annotation | homologous HL_4LFB_021 HL_50779.4 | |
| HL_5LMT_024 | 1/A/1076:1081 | GNRA | homologous HL_4LFB_024 HL_37824.8 | |
| HL_5LMT_025 | 1/A/1089:1096 | T-loop related | homologous HL_4LFB_025 HL_77436.5 | |
| HL_5LMT_029 | 1/A/1314:1323 | T-loop with 3 stacked bulged bases | homologous HL_4LFB_029 HL_02887.3 | |
| HL_5LMT_030 | 1/A/1356:1366 | No text annotation | homologous HL_5J7L_029 HL_06226.4 | |
| HL_5LMT_032 | 1/A/1515:1520 | GNRA | homologous HL_4LFB_032 HL_37824.8 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_5LMT_002 | No text annotation | ||
| HL_5LMT_003 | GNRA | ||
| HL_5LMT_005 | Mini UNCG | ||
| HL_5LMT_009 | UNCG | ||
| HL_5LMT_010 | GNRA | ||
| HL_5LMT_011 | UNCG | ||
| HL_5LMT_012 | GNRA | ||
| HL_5LMT_018 | Mini UNCG | ||
| HL_5LMT_022 | GNRA | ||
| HL_5LMT_023 | No text annotation | ||
| HL_5LMT_026 | No text annotation | ||
| HL_5LMT_027 | GNRA | ||
| HL_5LMT_028 | GNRA | ||
| HL_5LMT_031 | UNCG | ||
| HL_5LMT_033 | tRNA D-loop | ||
| HL_5LMT_034 | tRNA anticodon loop | ||
| HL_5LMT_035 | T-loop with 2 stacked bulged bases |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_5LMT_001 | 1/A/30:32, 1/A/552:553 | Single bulged G | homologous IL_4LFB_001 IL_00225.14 | |
| IL_5LMT_003 | 1/A/47:52, 1/A/359:361 | No text annotation | homologous IL_4LFB_003 IL_14177.2 | |
| IL_5LMT_004 | 1/A/54:56, 1/A/356:357 | Minor groove platform | homologous IL_4LFB_004 IL_51454.3 | |
| IL_5LMT_005 | 1/A/63:66, 1/A/103:104 | Multiple bulged bases | homologous IL_4LFB_005 IL_82107.5 | |
| IL_5LMT_007 | 1/A/129:131, 1/A/231:232 | Multiple bulged bases | homologous IL_6CZR_119 NA | |
| IL_5LMT_008 | 1/A/132:136, 1/A/227:230 | Minor groove platform related | homologous IL_6CZR_120 NA | |
| IL_5LMT_011 | 1/A/242:247, 1/A/277:284 | Kink-turn with non-sequential stacking | homologous IL_4LFB_011 IL_46174.3 | |
| IL_5LMT_012 | 1/A/249:252, 1/A/274:275 | No text annotation | homologous IL_4LFB_012 IL_47074.2 | |
| IL_5LMT_013 | 1/A/292:293, 1/A/304:308 | C-loop | homologous IL_4LFB_013 IL_03109.3 | |
| IL_5LMT_014 | 1/A/367:369, 1/A/392:393 | No text annotation | ||
| IL_5LMT_015 | 1/A/371:375, 1/A/389:390 | C-loop | geometric IL_4LFB_015 IL_03109.3 | |
| IL_5LMT_016 | 1/A/375:376, 1/A/387:389 | Single bulged G | homologous IL_4LFB_016 IL_00225.14 | |
| IL_5LMT_017 | 1/A/409:416, 1/A/427:433 | No text annotation | homologous IL_4LFB_017 IL_28026.3 | |
| IL_5LMT_018 | 1/A/446:450, 1/A/483:488 | 6x5 Sarcin-Ricin; G-bulge | geometric IL_4LFB_018 IL_88269.4 | |
| IL_5LMT_019 | 1/A/450:455, 1/A/476:483 | No text annotation | homologous IL_4LFB_019 IL_31561.1 | |
| IL_5LMT_020 | 1/A/504:511, 1/A/540:541 | SSU/LSU pseudoknot | homologous IL_5J7L_024 IL_41203.4 | |
| IL_5LMT_021 | 1/A/515:521, 1/A/528:536 | Kink-turn related | geometric IL_4V88_415 NA | |
| IL_5LMT_022 | 1/A/580:584, 1/A/757:761 | tSH-tHW-tHS | homologous IL_4LFB_023 IL_17136.7 | |
| IL_5LMT_023 | 1/A/594:596, 1/A/644:645 | Major groove platform | homologous IL_4LFB_024 IL_48076.6 | |
| IL_5LMT_025 | 1/A/605:612, 1/A/628:633 | No text annotation | homologous IL_4LFB_026 IL_78349.3 | |
| IL_5LMT_026 | 1/A/654:655, 1/A/751:754 | Major groove platform; stack outside cWW | geometric IL_5J7L_031 IL_50694.7 | |
| IL_5LMT_062 | 1/A/673:677, 1/A/713:717 | Triple non-canonical cWW pairs | homologous IL_4LFB_065 IL_49751.4 | |
| IL_5LMT_030 | 1/A/683:688, 1/A/699:707 | Kink-turn | homologous IL_4LFB_031 IL_95727.1 | |
| IL_5LMT_031 | 1/A/774:778, 1/A/804:805 | Left turn | homologous IL_4LFB_032 IL_29346.2 | |
| IL_5LMT_033 | 1/A/887:894, 1/A/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_4LFB_034 IL_41756.4 | |
| IL_5LMT_034 | 1/A/922:923, 1/A/1393:1395 | Single bulged A | homologous IL_5J7L_039 IL_31462.7 | |
| IL_5LMT_035 | 1/A/925:927, 1/A/1390:1391 | Single bulged G | homologous IL_4LFB_036 IL_00225.14 | |
| IL_5LMT_036 | 1/A/933:935, 1/A/1380:1384 | Minor groove platform | homologous IL_5J7L_041 IL_47078.3 | |
| IL_5LMT_037 | 1/A/953:954, 1/A/1226:1228 | Minor groove platform | homologous IL_4LFB_038 IL_51454.3 | |
| IL_5LMT_038 | 1/A/1048:1050, 1/A/1208:1209 | Single bulged U | homologous IL_4LFB_042 IL_89505.4 | |
| IL_5LMT_039 | 1/A/1052:1056, 1/A/1204:1206 | Isolated cWS basepair | homologous IL_4LFB_044 IL_76319.5 | |
| IL_5LMT_040 | 1/A/1057:1058, 1/A/1199:1203 | Minor groove platform | homologous IL_4LFB_045 IL_95583.2 | |
| IL_5LMT_041 | 1/A/1060:1061, 1/A/1195:1197 | Single bulged U | geometric IL_4LFB_046 IL_89505.4 | |
| IL_5LMT_042 | 1/A/1061:1063, 1/A/1193:1195 | Isolated non-canonical cWW pair | geometric IL_4LFB_047 IL_28037.2 | |
| IL_5LMT_043 | 1/A/1124:1127, 1/A/1145:1149 | No text annotation | ||
| IL_5LMT_064 | 1/A/1124:1128, 1/A/1143:1149 | No text annotation | homologous IL_4LFB_048 IL_85222.1 | |
| IL_5LMT_046 | 1/A/1158:1161, 1/A/1175:1181 | No text annotation | geometric IL_4LFB_050 IL_42032.1 | |
| IL_5LMT_047 | 1/A/1247:1253, 1/A/1284:1290 | No text annotation | homologous IL_4LFB_051 IL_09129.2 | |
| IL_5LMT_048 | 1/A/1255:1258, 1/A/1277:1282 | 180 degree turn | homologous IL_6CZR_161 NA | |
| IL_5LMT_065 | 1/A/1259:1262, 1/A/1273:1276 | Double sheared | homologous IL_4LFB_067 IL_09705.15 | |
| IL_5LMT_050 | 1/A/1260:1262, 1/A/1273:1274 | Minor groove platform | geometric IL_4LFB_054 IL_51454.3 | |
| IL_5LMT_052 | 1/A/1399:1401, 1/A/1501:1504 | No text annotation | homologous IL_4LFB_056 IL_61438.4 | |
| IL_5LMT_053 | 1/A/1401:1404, 1/A/1497:1501 | No text annotation | geometric IL_4V88_464 NA | |
| IL_5LMT_054 | 1/A/1405:1407, 1/A/1494:1496 | Isolated non-canonical cWW pair | geometric IL_4V88_465 NA | |
| IL_5LMT_059 | 1/A/1435:1437, 1/A/1464:1466 | Isolated non-canonical cWW pair | geometric IL_4V9F_017 IL_87907.2 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_5LMT_002 | Single bulged A | ||
| IL_5LMT_006 | Isolated non-canonical cWW pair | ||
| IL_5LMT_009 | No text annotation | ||
| IL_5LMT_010 | Isolated non-canonical cWW pair | ||
| IL_5LMT_024 | Major groove minor groove platform; mini C-loop | ||
| IL_5LMT_027 | Major groove platform | ||
| IL_5LMT_028 | Tandem non-canonical cWW pairs | ||
| IL_5LMT_029 | No text annotation | ||
| IL_5LMT_032 | tSH-tHW-tHS | ||
| IL_5LMT_063 | No text annotation | ||
| IL_5LMT_044 | Single stack bend | ||
| IL_5LMT_045 | Minor groove platform | ||
| IL_5LMT_049 | Not an internal loop | ||
| IL_5LMT_051 | No text annotation | ||
| IL_5LMT_055 | Decoding loop related | ||
| IL_5LMT_056 | Isolated non-canonical cWW pair | ||
| IL_5LMT_057 | Double sheared | ||
| IL_5LMT_058 | UAA/GAN variation | ||
| IL_5LMT_060 | No text annotation | ||
| IL_5LMT_061 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_5LMT_001 | 1/A/46:47, 1/A/361:367, 1/A/393:395 | No text annotation | ||
| J3_5LMT_014 | 1/A/46:47, 1/A/361:369, 1/A/392:395 | No text annotation | ||
| J3_5LMT_015 | 1/A/46:52, 1/A/359:369, 1/A/392:395 | No text annotation | ||
| J3_5LMT_002 | 1/A/586:588, 1/A/651:654, 1/A/754:755 | No text annotation | homologous J3_5J7L_002 J3_56052.5 | |
| J3_5LMT_016 | 1/A/586:588, 1/A/651:655, 1/A/751:755 | No text annotation | homologous J3_4LFB_015 J3_17385.4 | |
| J3_5LMT_003 | 1/A/672:673, 1/A/717:725, 1/A/732:734 | No text annotation | homologous J3_6CZR_017 NA | |
| J3_5LMT_004 | 1/A/826:829, 1/A/857:861, 1/A/868:874 | No text annotation | homologous J3_4LFB_001 J3_85054.4 | |
| J3_5LMT_005 | 1/A/936:939, 1/A/1344:1350, 1/A/1372:1379 | No text annotation | homologous J3_4LFB_002 J3_25303.4 | |
| J3_5LMT_006 | 1/A/943:946, 1/A/1235:1237, 1/A/1337:1340 | No text annotation | homologous J3_5J7L_005 J3_52655.4 | |
| J3_5LMT_007 | 1/A/955:962, 1/A/973:984, 1/A/1221:1225 | No text annotation | homologous J3_4LFB_004 J3_83516.4 | |
| J3_5LMT_010 | 1/A/1063:1068, 1/A/1107:1113, 1/A/1187:1193 | No text annotation | homologous J3_4LFB_007 J3_08394.3 | |
| J3_5LMT_019 | 1/A/1073:1074, 1/A/1083:1086, 1/A/1099:1102 | No text annotation | homologous J3_4LFB_017 J3_79369.1 | |
| J3_5LMT_020 | 1/A/1116:1118, 1/A/1155:1161, 1/A/1175:1184 | No text annotation | homologous J3_4LFB_018 J3_17791.2 | |
| J3_5LMT_013 | 1/A/1237:1241, 1/A/1296:1303, 1/A/1334:1337 | No text annotation | homologous J3_4LFB_009 J3_37047.6 | |
| J4_5LMT_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_35578.3 | |
| J4_5LMT_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_5LMT_003 | 1/A/569:577, 1/A/764:769, 1/A/810:821, 1/A/879:881 | No text annotation | ||
| J5_5LMT_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_5LMT_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_59910.6 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_5LMT_017 | No text annotation | ||
| J3_5LMT_008 | No text annotation | ||
| J3_5LMT_018 | No text annotation | ||
| J3_5LMT_009 | No text annotation | ||
| J3_5LMT_011 | No text annotation | ||
| J3_5LMT_012 | No text annotation | ||
| J4_5LMT_004 | tRNA junction | ||
| J5_5LMT_002 | No text annotation |
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