0.10 | 0.11

Changes in PDB files used for clustering

Release 0.10 has 195 PDB files, release 0.11 has 196 PDB files, 194 of them are identical.

No equivalence class representatives have been replaced.

2 new structures in release 0.11: 3ZD3, 4E59.

No equivalence class representatives have been obsoleted.

Help Every Motif Atlas release is based on a representative set of PDB files. When comparing two releases, it's important to know how the input data changed.

Representative sets are quite stable in time, but PDB files from the older releases can be replaced by newer PDB files or removed from the set altogether if the structure is obsoleted by PDB without replacement.

PDB files from the newer release either replace representatives in the existing equivalence classes or come from new equivalence classes.

Redistribution of motif instances

Loading the Sankey diagram...

Changes in motif groups

Release 0.10 has 266 motif groups, release 0.11 has 266 motif groups, 252 of them are identical.

6 motif groups were updated, 8 groups are present only in release 0.10, 8 groups are only in release 0.11.

Help The Sankey diagram shows redistribution of motif instances (loops) between two releases. The rectangles represent the motif groups and are colored as follows:

Added motif groups: green
Removed motif groups: grey
Updated motif groups: orange
Added motif instances: green
Removed motif instances: grey

Hover over the links connecting the motif groups to see which motif instances were exchanged.

Identical motif groups

#	Motif id	Instances	Description
1	IL_97217.4	235	1-3 bulged nucleotides, same chain
2	IL_39199.2	55	Hoogsteen-edge Platform, Single bulged base
3	IL_41766.2	49	Tandem cWW pairs (Not AU or GC)
4	IL_56465.2	45	Single, unpaired intercalated base, consensus A
5	IL_44540.2	43	Sugar-edge, 1-base platform, consensus tHS
6	IL_87904.3	31	Triple sheared (tSH-tHS-tHS) no inserted bases
7	IL_06390.1	25	cWH basepair with syn base
8	IL_13959.2	24	Double Sheared (tSH-tHS)
9	IL_93424.2	22	tSH-inserted-tHW
10	IL_65553.4	22	Kink-turn
11	IL_32390.2	21	16S h19 IL and 23S H41 IL
12	IL_73276.1	20	C-loop
13	IL_55938.2	19	LSU Helix 89 (H89) IL2. cSH Platform.
14	IL_92027.2	17	16S h21 S8 binding site
15	IL_06429.2	16	cWW-bulge-cWW
16	IL_85647.2	16	Sarcin-ricin parent motif with 15 Nts
17	IL_94430.3	15	16S h32-h33-h34 3WJ
18	IL_31555.3	15	Tandem sheared with inserted, unpaired purine.
19	IL_24982.3	15	SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
20	IL_49493.2	14	Sarcin-ricin Parent Motif - bacterial LSU H95 IL
21	IL_21304.1	11	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
22	IL_40090.2	11	16S h34 ILa : Part of larger motif
23	IL_46648.1	11	23S H91 IL \| Single-Base Intercalation Site
24	IL_27618.2	11	23S H73 ILa : Part of larger Motif
25	IL_24546.2	10	23S H41 IL and 16S h18 IL : Has large bulge on one side
26	IL_58291.2	9	Recurrent Sub-motif found in junctions
27	IL_92114.3	9	GAAA loop receptor "platform" motif
28	IL_47444.3	9	SRP Loop E-like motif
29	IL_02809.1	8	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
30	IL_90459.2	8	cWW AG or UU
31	IL_92321.2	8	Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
32	IL_86357.2	7	LSU Helix 61 IL2
33	IL_83451.2	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
34	IL_73000.2	7	cHS-cWS
35	IL_08926.1	6	23S H91 IL
36	IL_44067.2	6	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
37	IL_72158.2	6	LSU Helix 62 (H62) IL
38	IL_25230.2	6	Bacterial 5S rRNA Loop E
39	IL_53635.2	6	LSU Helix 32 (H32) IL
40	IL_70237.3	6
41	IL_13069.2	6	LSU 3WJ H32-H33-H35A
42	IL_24022.2	6
43	IL_10007.1	6	Single sheared with bulged bases
44	IL_54420.1	6
45	IL_89088.1	6	16S h19 IL and 23S H41 IL
46	IL_97057.2	6
47	IL_45262.2	5
48	IL_79083.2	5
49	IL_82188.1	5	LSU H68 IL from H.m.
50	IL_90133.1	5
51	IL_01239.1	5
52	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
53	IL_77263.1	5	Kink-turn from U4
54	IL_02359.2	5
55	IL_78732.3	5	Double S-turn motif
56	IL_92484.1	5
57	IL_22732.1	4	tSH-inserted-tHS
58	IL_28572.1	4	16S h18 kink-turn like motif
59	IL_47758.1	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
60	IL_93568.1	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
61	IL_38807.2	4
62	IL_31066.2	4	SSU Helix 44 (h44) extension
63	IL_62661.2	4	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
64	IL_10005.1	4
65	IL_21333.1	4	tSH-tHW-bulge
66	IL_39526.3	4
67	IL_98591.2	4
68	IL_16166.2	3
69	IL_23262.3	3
70	IL_34363.1	3	Kink-turn from 23S H42
71	IL_09348.3	3	cWW-L-cWW-cWW
72	IL_16252.2	3	23S H91 IL
73	IL_30840.1	3
74	IL_34628.2	3	Kink-turn
75	IL_36254.1	3
76	IL_79955.2	3	SSU Helix (23) h23 IL1
77	IL_37053.1	3	Kink-turn from 23S H58
78	IL_53774.1	3	Single sheared with bulged bases
79	IL_82563.1	3	Thi-box riboswitch T-loop
80	IL_52173.1	3
81	IL_58586.2	3
82	IL_80494.2	3	LSU H58 IL2 H.m.
83	IL_95150.3	3
84	IL_98421.2	3	SSU Helix 12 (h12) IL
85	IL_71565.1	3
86	IL_75447.1	3
87	IL_95652.2	3	SSU Helix 27 (h27) IL Sarcin-Ricin motif
88	IL_43946.1	3
89	IL_15840.2	2	Triple Sheared with unpaired, inserted A
90	IL_25174.1	2
91	IL_76095.3	2	Motif from Hairpin Ribozyme
92	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
93	IL_89231.1	2	LSU H77
94	IL_12211.1	2
95	IL_28942.1	2
96	IL_40892.1	2
97	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
98	IL_81441.1	2
99	IL_91132.1	2
100	IL_23414.1	2
101	IL_54965.1	2	Leadzyme Motif. SSU Decoding site motif, extended.
102	IL_69901.1	2
103	IL_87336.1	2	LSU Eukaryal Helix 96 (H96) IL1
104	IL_90057.1	2
105	IL_00998.1	2
106	IL_09882.1	2
107	IL_16330.1	2
108	IL_25271.1	2	SSU Helix 8 (h8) IL E.c. and Yeast
109	IL_41397.2	2	LSU Helix 96 (H96) IL2
110	IL_45794.1	2
111	IL_55287.1	2
112	IL_77076.1	2
113	IL_87548.1	2
114	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
115	IL_97833.1	2
116	IL_01054.1	2
117	IL_16377.1	2
118	IL_50521.1	2
119	IL_70280.1	2	Double sheared with wobble cWW.
120	IL_74876.1	2
121	IL_80093.1	2
122	IL_16415.1	2	SSU Helix 23 (h23) Kink-turn T. thermophilus
123	IL_37197.1	2
124	IL_46435.1	2
125	IL_65137.1	2	Kink-turn like motif in Group I Intron
126	IL_21495.1	2
127	IL_31707.1	2	Vitamin B12 aptamer
128	IL_98566.1	2
129	IL_07300.1	2
130	IL_11751.1	2
131	IL_37406.1	2
132	IL_52940.1	2
133	IL_82831.2	2	Kink-turn from 16S H23
134	IL_06306.1	1
135	IL_11869.1	1
136	IL_18755.1	1
137	IL_37715.1	1
138	IL_40845.1	1
139	IL_47687.1	1
140	IL_52958.1	1
141	IL_54576.1	1
142	IL_56513.1	1
143	IL_60649.1	1	Kink-turn
144	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
145	IL_71942.1	1
146	IL_81398.1	1
147	IL_83250.1	1	16S h40 3WJ T.th.
148	IL_91089.1	1
149	IL_97073.1	1
150	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
151	IL_02835.1	1
152	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
153	IL_20775.1	1	tSH-inserted
154	IL_25181.1	1
155	IL_37990.1	1
156	IL_53323.1	1
157	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
158	IL_61730.1	1
159	IL_67735.1	1
160	IL_76256.1	1
161	IL_78809.1	1
162	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
163	IL_89794.1	1
164	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
165	IL_98688.1	1
166	IL_02957.1	1
167	IL_12486.1	1
168	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
169	IL_41139.1	1
170	IL_47968.1	1
171	IL_53423.1	1
172	IL_57977.1	1
173	IL_61991.1	1
174	IL_76486.1	1	Sarcin-ricin motif with syn G
175	IL_82113.1	1
176	IL_83856.1	1
177	IL_91904.1	1
178	IL_98924.1	1
179	IL_03110.1	1
180	IL_06468.1	1	16S h40 3WJ E.c.
181	IL_12507.1	1
182	IL_23639.1	1	tWH-tHS-L-cWW
183	IL_83920.1	1
184	IL_03282.1	1
185	IL_06471.1	1
186	IL_25307.1	1
187	IL_31241.1	1
188	IL_39324.1	1
189	IL_46306.1	1
190	IL_55649.1	1
191	IL_58454.1	1
192	IL_63952.1	1
193	IL_77195.1	1
194	IL_85510.1	1
195	IL_94973.1	1	Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
196	IL_97842.1	1
197	IL_03741.1	1
198	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
199	IL_13682.1	1
200	IL_21421.1	1
201	IL_26868.1	1
202	IL_41791.1	1
203	IL_53988.1	1
204	IL_55934.1	1	kink-turn-like
205	IL_75415.1	1	Pseudo-knot forming internal loop
206	IL_82601.1	1	Tandem cWW water-inserted CU pairs
207	IL_88367.1	1
208	IL_90880.1	1
209	IL_92280.1	1
210	IL_05221.1	1
211	IL_06847.1	1	Group II Intron IL
212	IL_11302.1	1
213	IL_17603.1	1
214	IL_26971.1	1
215	IL_37347.1	1
216	IL_43316.1	1
217	IL_52509.1	1
218	IL_59529.1	1
219	IL_77296.1	1
220	IL_80505.1	1
221	IL_82650.1	1
222	IL_85805.1	1
223	IL_88403.1	1
224	IL_91044.1	1
225	IL_02690.1	1
226	IL_05462.1	1
227	IL_15205.1	1
228	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
229	IL_22579.1	1
230	IL_25082.1	1
231	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
232	IL_40527.1	1	Kink-turn
233	IL_54450.1	1
234	IL_60643.1	1
235	IL_65788.1	1
236	IL_71685.1	1	Sarcin-like with an intercalated basepair
237	IL_75688.1	1	Part of Helix 71 (H71) junction in 23S of D.r.
238	IL_80652.1	1
239	IL_86059.1	1
240	IL_91078.1	1

Updated motif groups

#	Motif id	Instances	Description
1	IL_47174.5	203	cWW AG or water inserted cWW Y-Y.
2	IL_98556.3	4
3	IL_40387.4	4	LSU Helix 89 (H89) IL2
4	IL_34156.4	3	cWW AG or UU
5	IL_62499.4	3
6	IL_89028.3	3	Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena

Removed motif groups

#	Motif id	Instances	Description
1	IL_86826.1	3	tHS tHH bulge with S-turn
2	IL_73816.1	2	tHS tHH bulge with S-turn
3	IL_93782.1	2
4	IL_37737.1	2
5	IL_06780.1	1
6	IL_17268.1	1
7	IL_62017.1	1	Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
8	IL_70550.1	1

Added motif groups

#	Motif id	Instances	Description
1	IL_91547.1	3	tHS tHH bulge with S-turn
2	IL_33965.1	2	tHS tHH bulge with S-turn
3	IL_58811.1	2
4	IL_96031.1	1	tHS tHH bulge with S-turn
5	IL_97961.1	1
6	IL_37150.1	1	tHS tHH bulge with S-turn
7	IL_41864.1	1	Part of H71 junction in 23S rRNA from T.th.
8	IL_87544.1	1