5GAF Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_5GAF_001 | 1/1/52:57 | No text annotation | homologous HL_4XCO_004 HL_34789.1 | |
| HL_5GAF_002 | 1/A/59:68 | No text annotation | homologous HL_5J7L_134 NA | |
| HL_5GAF_004 | 1/A/123:128 | No text annotation | homologous HL_5J7L_136 NA | |
| HL_5GAF_007 | 1/A/194:201 | No text annotation | homologous HL_5J7L_139 NA | |
| HL_5GAF_073 | 1/A/382:392 | No text annotation | homologous HL_5J7L_145 NA | |
| HL_5GAF_014 | 1/A/410:417 | Pseudoknot geometry | homologous HL_5J7L_146 NA | |
| HL_5GAF_017 | 1/A/566:575 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_150 NA | |
| HL_5GAF_022 | 1/A/744:753 | No text annotation | homologous HL_7A0S_022 HL_50204.1 | |
| HL_5GAF_023 | 1/A/779:785 | No text annotation | homologous HL_5J7L_156 NA | |
| HL_5GAF_024 | 1/A/826:831 | No text annotation | homologous HL_4WF9_025 HL_27530.1 | |
| HL_5GAF_025 | 1/A/955:962 | GNRA | homologous HL_4WF9_027 HL_34789.1 | |
| HL_5GAF_026 | 1/A/978:985 | No text annotation | homologous HL_5J7L_160 NA | |
| HL_5GAF_033 | 1/A/1363:1368 | GNRA | homologous HL_5J7L_167 NA | |
| HL_5GAF_039 | 1/A/1612:1619 | No text annotation | homologous HL_7RQB_040 NA | |
| HL_5GAF_044 | 1/A/1777:1787 | No text annotation | homologous HL_5J7L_178 NA | |
| HL_5GAF_049 | 1/A/2027:2036 | No text annotation | homologous HL_4WF9_047 HL_78372.1 | |
| HL_5GAF_052 | 1/A/2248:2256 | No text annotation | geometric HL_7A0S_052 HL_11974.1 | |
| HL_5GAF_059 | 1/A/2471:2479 | No text annotation | homologous HL_4WF9_056 HL_52011.1 | |
| HL_5GAF_060 | 1/A/2528:2535 | GNRA variation | homologous HL_5J7L_194 NA | |
| HL_5GAF_061 | 1/A/2551:2557 | No text annotation | homologous HL_4WF9_058 HL_48677.1 | |
| HL_5GAF_062 | 1/A/2594:2599 | GNRA | homologous HL_7RQB_063 NA | |
| HL_5GAF_065 | 1/A/2745:2759 | No text annotation | homologous HL_5J7L_199 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_5GAF_003 | No text annotation | ||
| HL_5GAF_071 | No text annotation | ||
| HL_5GAF_005 | No text annotation | ||
| HL_5GAF_006 | No text annotation | ||
| HL_5GAF_008 | No text annotation | ||
| HL_5GAF_009 | No text annotation | ||
| HL_5GAF_010 | T-loop with 2 stacked bulged bases | ||
| HL_5GAF_011 | No text annotation | ||
| HL_5GAF_012 | T-loop with unstacked turn | ||
| HL_5GAF_013 | No text annotation | ||
| HL_5GAF_015 | GNRA | ||
| HL_5GAF_016 | GNRA | ||
| HL_5GAF_018 | No text annotation | ||
| HL_5GAF_019 | GNRA | ||
| HL_5GAF_020 | No text annotation | ||
| HL_5GAF_021 | GNRA wlth tandem sheared | ||
| HL_5GAF_027 | No text annotation | ||
| HL_5GAF_028 | GNRA wlth tandem sheared | ||
| HL_5GAF_029 | No text annotation | ||
| HL_5GAF_030 | GNRA | ||
| HL_5GAF_031 | T-loop with 2 stacked bulged bases | ||
| HL_5GAF_032 | Pseudoknot geometry with 3' bulge | ||
| HL_5GAF_034 | No text annotation | ||
| HL_5GAF_035 | Mini UNCG with extended bulge | ||
| HL_5GAF_036 | Pseudoknot geometry with 3' bulge | ||
| HL_5GAF_037 | UNCG | ||
| HL_5GAF_038 | No text annotation | ||
| HL_5GAF_040 | GNRA | ||
| HL_5GAF_041 | No text annotation | ||
| HL_5GAF_042 | No text annotation | ||
| HL_5GAF_043 | No text annotation | ||
| HL_5GAF_045 | GNRA related | ||
| HL_5GAF_046 | GNRA variation | ||
| HL_5GAF_047 | No text annotation | ||
| HL_5GAF_048 | No text annotation | ||
| HL_5GAF_050 | No text annotation | ||
| HL_5GAF_051 | No text annotation | ||
| HL_5GAF_053 | No text annotation | ||
| HL_5GAF_054 | No text annotation | ||
| HL_5GAF_074 | No text annotation | ||
| HL_5GAF_055 | Pseudoknot geometry | ||
| HL_5GAF_056 | GNRA | ||
| HL_5GAF_057 | GNRA | ||
| HL_5GAF_058 | No text annotation | ||
| HL_5GAF_063 | GNRA | ||
| HL_5GAF_064 | Ribsomal LSU H95 | ||
| HL_5GAF_066 | No text annotation | ||
| HL_5GAF_067 | No text annotation | ||
| HL_5GAF_068 | GNRA | ||
| HL_5GAF_072 | No text annotation | ||
| HL_5GAF_069 | No text annotation | ||
| HL_5GAF_070 | Mini UNCG |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_5GAF_003 | 1/A/24:30, 1/A/510:516 | Triple sheared with non-canonical cWW | homologous IL_5J7L_245 NA | |
| IL_5GAF_004 | 1/A/36:37, 1/A/442:444 | Single bulged A | homologous IL_7RQB_002 NA | |
| IL_5GAF_005 | 1/A/43:44, 1/A/434:436 | Minor groove platform | homologous IL_5J7L_247 NA | |
| IL_5GAF_008 | 1/A/183:184, 1/A/212:214 | Single stack bend | homologous IL_4WF9_007 IL_15011.1 | |
| IL_5GAF_009 | 1/A/188:194, 1/A/201:208 | 8x7 Sarcin-Ricin; G-bulge | geometric IL_5J7L_250 NA | |
| IL_5GAF_010 | 1/A/239:245, 1/A/253:258 | 7x6 Sarcin-Ricin; G-bulge | homologous IL_5J7L_251 NA | |
| IL_5GAF_011 | 1/A/269:271, 1/A/366:370 | No text annotation | homologous IL_5J7L_252 NA | |
| IL_5GAF_018 | 1/A/606:610, 1/A/618:622 | AAA cross-strand stack | homologous IL_5J7L_258 NA | |
| IL_5GAF_019 | 1/A/672:674, 1/A/806:808 | Isolated non-canonical cWW pair | homologous IL_4WF9_020 IL_01003.1 | |
| IL_5GAF_020 | 1/A/674:678, 1/A/799:806 | tHW-tHW cross-strand stack | geometric IL_7RQB_018 NA | |
| IL_5GAF_021 | 1/A/697:698, 1/A/763:765 | Single bulged A | geometric IL_5J7L_261 NA | |
| IL_5GAF_025 | 1/A/775:777, 1/A/787:791 | Multiple bulged bases | geometric IL_5J7L_265 NA | |
| IL_5GAF_026 | 1/A/837:838, 1/A/940:942 | Single stack bend | homologous IL_5J7L_266 NA | |
| IL_5GAF_027 | 1/A/844:847, 1/A/933:934 | 90 degree turn | homologous IL_5J7L_267 NA | |
| IL_5GAF_122 | 1/A/844:848, 1/A/930:934 | No text annotation | homologous IL_5J7L_399 NA | |
| IL_5GAF_032 | 1/A/864:868, 1/A/909:912 | C-loop with bulged stacked A's | homologous IL_5J7L_272 NA | |
| IL_5GAF_038 | 1/A/1004:1011, 1/A/1150:1151 | SSU/LSU pseudoknot | geometric IL_5J7L_278 NA | |
| IL_5GAF_041 | 1/A/1024:1030, 1/A/1124:1140 | No text annotation | geometric IL_5J7L_281 NA | |
| IL_5GAF_042 | 1/A/1031:1034, 1/A/1121:1123 | Isolated non-canonical cWW pair | homologous IL_5J7L_282 NA | |
| IL_5GAF_047 | 1/A/1196:1198, 1/A/1247:1250 | Isolated cWS basepair | homologous IL_5J7L_286 NA | |
| IL_5GAF_050 | 1/A/1262:1269, 1/A/2011:2017 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_5J7L_289 NA | |
| IL_5GAF_066 | 1/A/1663:1665, 1/A/1995:1997 | Isolated tWW turn | homologous IL_5J7L_305 NA | |
| IL_5GAF_125 | 1/A/1666:1674, 1/A/1990:1994 | No text annotation | homologous IL_5J7L_386 NA | |
| IL_5GAF_068 | 1/A/1669:1674, 1/A/1990:1993 | Intercalated tWH | homologous IL_5J7L_307 NA | |
| IL_5GAF_069 | 1/A/1686:1691, 1/A/1696:1702 | tSH-tSH-tHH-tHS | homologous IL_5J7L_308 NA | |
| IL_5GAF_073 | 1/A/1798:1804, 1/A/1813:1821 | Kink-turn related | homologous IL_5J7L_313 NA | |
| IL_5GAF_077 | 1/A/1864:1867, 1/A/1874:1878 | UAA/GAN related | homologous IL_5J7L_317 NA | |
| IL_5GAF_078 | 1/A/1933:1934, 1/A/1964:1967 | Bulged stacked bases | geometric IL_7RQB_076 NA | |
| IL_5GAF_079 | 1/A/1934:1945, 1/A/1961:1964 | No text annotation | homologous IL_7A0S_072 IL_04332.3 | |
| IL_5GAF_081 | 1/A/2054:2056, 1/A/2612:2615 | No text annotation | homologous IL_5J7L_321 NA | |
| IL_5GAF_082 | 1/A/2067:2069, 1/A/2442:2443 | Single bulged U | homologous IL_7A0S_075 IL_97561.1 | |
| IL_5GAF_083 | 1/A/2070:2071, 1/A/2438:2441 | Minor groove platform | homologous IL_7RQB_081 NA | |
| IL_5GAF_084 | 1/A/2081:2083, 1/A/2236:2239 | Isolated tHS basepair with bulges | homologous IL_5J7L_325 NA | |
| IL_5GAF_085 | 1/A/2085:2087, 1/A/2232:2234 | No text annotation | homologous IL_7RQB_083 NA | |
| IL_5GAF_096 | 1/A/2453:2454, 1/A/2498:2500 | Single stack bend | geometric IL_4WF9_089 IL_15011.1 | |
| IL_5GAF_097 | 1/A/2454:2455, 1/A/2496:2498 | Major groove platform | homologous IL_7RQB_092 NA | |
| IL_5GAF_098 | 1/A/2457:2459, 1/A/2493:2494 | Major groove platform | geometric IL_7A0S_085 IL_48076.7 | |
| IL_5GAF_130 | 1/A/2459:2461, 1/A/2489:2493 | No text annotation | homologous IL_9DFE_094 IL_36931.1 | |
| IL_5GAF_101 | 1/A/2507:2508, 1/A/2580:2582 | Major groove platform | homologous IL_4WF9_094 IL_46637.1 | |
| IL_5GAF_102 | 1/A/2510:2512, 1/A/2574:2578 | Isolated non-canonical cWW with bulges | geometric IL_5J7L_340 NA | |
| IL_5GAF_103 | 1/A/2512:2513, 1/A/2571:2574 | No text annotation | homologous IL_5J7L_341 NA | |
| IL_5GAF_104 | 1/A/2522:2523, 1/A/2540:2543 | Major groove platform with intercalation | homologous IL_5J7L_342 NA | |
| IL_5GAF_111 | 1/A/2737:2742, 1/A/2762:2767 | UAA/GAN with extra cWW | homologous IL_5J7L_350 NA | |
| IL_5GAF_115 | 1/A/2843:2846, 1/A/2870:2874 | Multiple bulged bases with non-canonical cWW | homologous IL_5J7L_353 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_5GAF_001 | No text annotation | ||
| IL_5GAF_002 | tSH-tHW-tHS-cWW | ||
| IL_5GAF_006 | No text annotation | ||
| IL_5GAF_007 | No text annotation | ||
| IL_5GAF_012 | No text annotation | ||
| IL_5GAF_013 | No text annotation | ||
| IL_5GAF_014 | No text annotation | ||
| IL_5GAF_015 | No text annotation | ||
| IL_5GAF_016 | Double sheared | ||
| IL_5GAF_017 | Isolated non-canonical cWW pair | ||
| IL_5GAF_022 | Single bulged G | ||
| IL_5GAF_023 | Triple sheared | ||
| IL_5GAF_024 | Major groove platform | ||
| IL_5GAF_028 | Stack outside cWW | ||
| IL_5GAF_123 | No text annotation | ||
| IL_5GAF_029 | Single stack bend | ||
| IL_5GAF_030 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | ||
| IL_5GAF_031 | Single bulged G | ||
| IL_5GAF_033 | Isolated non-canonical cWW pair | ||
| IL_5GAF_034 | Double sheared with non-canonical cWW | ||
| IL_5GAF_124 | No text annotation | ||
| IL_5GAF_035 | Tandem non-canonical cWW pairs | ||
| IL_5GAF_036 | Single bulged C | ||
| IL_5GAF_037 | UAA/GAN | ||
| IL_5GAF_039 | Single bulged U | ||
| IL_5GAF_040 | Kink-turn related | ||
| IL_5GAF_043 | Tandem non-canonical cWW pairs | ||
| IL_5GAF_044 | Kink-turn | ||
| IL_5GAF_045 | No text annotation | ||
| IL_5GAF_046 | Major groove platform | ||
| IL_5GAF_048 | No text annotation | ||
| IL_5GAF_049 | Kink-turn | ||
| IL_5GAF_051 | Major groove platform; stack outside cWW | ||
| IL_5GAF_052 | C-loop | ||
| IL_5GAF_053 | UAA/GAN | ||
| IL_5GAF_054 | tSH-tHW-tHS | ||
| IL_5GAF_055 | No text annotation | ||
| IL_5GAF_056 | UAA/GAN | ||
| IL_5GAF_057 | Tandem non-canonical cWW pairs | ||
| IL_5GAF_058 | tSH-tHW | ||
| IL_5GAF_059 | Single bulged U | ||
| IL_5GAF_060 | No text annotation | ||
| IL_5GAF_061 | tSH-tHW-tHS | ||
| IL_5GAF_062 | 180 degree turn | ||
| IL_5GAF_063 | Major groove platform | ||
| IL_5GAF_064 | UAA/GAN variation | ||
| IL_5GAF_065 | No text annotation | ||
| IL_5GAF_067 | Major groove platform; stack outside cWW | ||
| IL_5GAF_070 | 6x5 Sarcin-Ricin; G-bulge | ||
| IL_5GAF_071 | Triple sheared | ||
| IL_5GAF_072 | Single bulged A | ||
| IL_5GAF_074 | Minor groove platform, major groove intercalation | ||
| IL_5GAF_075 | Major groove intercalation | ||
| IL_5GAF_076 | Major groove minor groove platform; mini C-loop | ||
| IL_5GAF_126 | No text annotation | ||
| IL_5GAF_080 | Major groove platform | ||
| IL_5GAF_086 | No text annotation | ||
| IL_5GAF_127 | No text annotation | ||
| IL_5GAF_131 | No text annotation | ||
| IL_5GAF_087 | No text annotation | ||
| IL_5GAF_128 | Kink-turn | ||
| IL_5GAF_088 | Kink-turn related | ||
| IL_5GAF_089 | Kink-turn | ||
| IL_5GAF_129 | No text annotation | ||
| IL_5GAF_090 | Isolated cWH basepair | ||
| IL_5GAF_091 | Single bulged U | ||
| IL_5GAF_092 | No text annotation | ||
| IL_5GAF_093 | No text annotation | ||
| IL_5GAF_094 | Double sheared | ||
| IL_5GAF_095 | Single bulged U | ||
| IL_5GAF_099 | No text annotation | ||
| IL_5GAF_100 | Double sheared with non-canonical cWW | ||
| IL_5GAF_105 | Single bulged A | ||
| IL_5GAF_106 | tSH-tHS-tHW | ||
| IL_5GAF_107 | Sarcin-Ricin target in LSU H95; G-bulge | ||
| IL_5GAF_108 | C-loop | ||
| IL_5GAF_109 | UAA/GAN related, with intercalation | ||
| IL_5GAF_110 | Multiple bulged bases | ||
| IL_5GAF_112 | Single bulged A | ||
| IL_5GAF_113 | No text annotation | ||
| IL_5GAF_114 | Major groove intercalation | ||
| IL_5GAF_116 | tHS double platform | ||
| IL_5GAF_117 | Major groove intercalation | ||
| IL_5GAF_118 | No text annotation | ||
| IL_5GAF_119 | Major groove minor groove platform; mini C-loop | ||
| IL_5GAF_120 | Symmetric double minor groove platform | ||
| IL_5GAF_121 | Bacterial 5S Loop E |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_5GAF_013 | 1/A/32:35, 1/A/445:461, 1/A/468:473 | No text annotation | homologous J3_5J7L_067 NA | |
| J3_5GAF_014 | 1/A/56:57, 1/A/70:76, 1/A/110:114 | No text annotation | homologous J3_5J7L_037 NA | |
| J3_5GAF_001 | 1/A/683:689, 1/A/773:775, 1/A/791:794 | No text annotation | homologous J3_5J7L_038 NA | |
| J3_5GAF_006 | 1/A/2091:2093, 1/A/2196:2200, 1/A/2223:2228 | Kink-turn 3-way junction | homologous J3_5J7L_044 NA | |
| J3_5GAF_017 | 1/A/2282:2284, 1/A/2384:2395, 1/A/2421:2427 | No text annotation | homologous J3_5J7L_070 NA | |
| J3_5GAF_008 | 1/A/2517:2520, 1/A/2545:2547, 1/A/2561:2567 | No text annotation | homologous J3_5J7L_046 NA | |
| J3_5GAF_010 | 1/B/10:16, 1/B/68:70, 1/B/106:110 | No text annotation | homologous J3_5J7L_049 NA | |
| J4_5GAF_001 | 1/A/268:269, 1/A/370:375, 1/A/399:406, 1/A/421:424 | No text annotation | homologous J4_5J7L_018 NA | |
| J4_5GAF_003 | 1/A/601:604, 1/A/624:628, 1/A/635:638, 1/A/650:656 | No text annotation | homologous J4_5J7L_020 NA | |
| J4_5GAF_004 | 1/A/1270:1276, 1/A/1294:1295, 1/A/1645:1648, 1/A/2009:2010 | No text annotation | homologous J4_5J7L_021 NA | |
| J4_5GAF_011 | 1/A/2643:2646, 1/A/2674:2676, 1/A/2731:2735, 1/A/2769:2771 | No text annotation | homologous J4_5J7L_028 NA | |
| J5_5GAF_007 | 1/A/47:54, 1/A/116:121, 1/A/130:131, 1/A/148:150, 1/A/176:178 | No text annotation | homologous J5_5J7L_013 NA | |
| J5_5GAF_002 | 1/A/531:533, 1/A/560:564, 1/A/577:579, 1/A/1261:1262, 1/A/2017:2018 | No text annotation | homologous J5_5J7L_014 NA | |
| J5_5GAF_003 | 1/A/584:589, 1/A/668:671, 1/A/809:812, 1/A/1195:1196, 1/A/1250:1256 | No text annotation | homologous J5_5J7L_015 NA | |
| J5_5GAF_008 | 1/A/2057:2064, 1/A/2446:2453, 1/A/2500:2506, 1/A/2583:2588, 1/A/2606:2611 | No text annotation | ||
| J5_5GAF_006 | 1/A/2074:2077, 1/A/2243:2246, 1/A/2258:2259, 1/A/2281:2282, 1/A/2427:2435 | No text annotation | homologous J5_4WF9_007 J5_39529.2 | |
| J6_5GAF_001 | 1/A/45:46, 1/A/179:183, 1/A/214:224, 1/A/231:235, 1/A/262:266, 1/A/426:433 | No text annotation | ||
| J7_5GAF_001 | 1/A/8:15, 1/A/525:531, 1/A/2018:2023, 1/A/2040:2043, 1/A/2625:2630, 1/A/2788:2789, 1/A/2894:2895 | No text annotation | ||
| J7_5GAF_002 | 1/A/817:822, 1/A/835:837, 1/A/942:946, 1/A/971:976, 1/A/987:991, 1/A/1163:1164, 1/A/1185:1190 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_5GAF_011 | No text annotation | ||
| J3_5GAF_012 | No text annotation | ||
| J3_5GAF_002 | No text annotation | ||
| J3_5GAF_003 | No text annotation | ||
| J3_5GAF_004 | No text annotation | ||
| J3_5GAF_005 | No text annotation | ||
| J3_5GAF_015 | No text annotation | ||
| J3_5GAF_016 | No text annotation | ||
| J3_5GAF_007 | No text annotation | ||
| J3_5GAF_018 | No text annotation | ||
| J3_5GAF_019 | No text annotation | ||
| J3_5GAF_009 | No text annotation | ||
| J4_5GAF_002 | No text annotation | ||
| J4_5GAF_005 | No text annotation | ||
| J4_5GAF_006 | No text annotation | ||
| J4_5GAF_007 | No text annotation | ||
| J4_5GAF_008 | No text annotation | ||
| J4_5GAF_009 | No text annotation | ||
| J4_5GAF_010 | No text annotation | ||
| J5_5GAF_001 | No text annotation | ||
| J5_5GAF_004 | No text annotation | ||
| J5_5GAF_005 | No text annotation |
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