0.10 | 0.9

Changes in PDB files used for clustering

Release 0.10 has 196 PDB files, release 0.9 has 196 PDB files, 194 of them are identical.

1 equivalence classes changed representatives: 3UMY → 3U4M.

1 new structures in release 0.9: 3G78.

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 0.9 has 264 motif groups, 244 of them are identical.

8 motif groups were updated, 12 groups are present only in release 0.10, 14 groups are only in release 0.9.

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_39199.2	55	Hoogsteen-edge Platform, Single bulged base
2	IL_41766.2	49	Tandem cWW pairs (Not AU or GC)
3	IL_56465.2	45	Single, unpaired intercalated base, consensus A
4	IL_44540.2	43	Sugar-edge, 1-base platform, consensus tHS
5	IL_06390.1	25	cWH basepair with syn base
6	IL_13959.2	24	Double Sheared (tSH-tHS)
7	IL_93424.2	22	tSH-inserted-tHW
8	IL_32390.2	21	16S h19 IL and 23S H41 IL
9	IL_73276.1	20	C-loop
10	IL_55938.2	19	LSU Helix 89 (H89) IL2. cSH Platform.
11	IL_92027.2	17	16S h21 S8 binding site
12	IL_85647.2	16	Sarcin-ricin parent motif with 15 Nts
13	IL_24982.3	15	SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
14	IL_94430.3	15	16S h32-h33-h34 3WJ
15	IL_49493.2	14	Sarcin-ricin Parent Motif - bacterial LSU H95 IL
16	IL_40090.2	11	16S h34 ILa : Part of larger motif
17	IL_21304.1	11	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
18	IL_46648.1	11	23S H91 IL \| Single-Base Intercalation Site
19	IL_27618.2	11	23S H73 ILa : Part of larger Motif
20	IL_24546.2	10	23S H41 IL and 16S h18 IL : Has large bulge on one side
21	IL_58291.2	9	Recurrent Sub-motif found in junctions
22	IL_90459.2	8	cWW AG or UU
23	IL_02809.1	8	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
24	IL_92321.2	8	Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
25	IL_83451.2	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
26	IL_73000.2	7	cHS-cWS
27	IL_86357.2	7	LSU Helix 61 IL2
28	IL_97057.2	6
29	IL_89088.1	6	16S h19 IL and 23S H41 IL
30	IL_44067.2	6	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
31	IL_53635.2	6	LSU Helix 32 (H32) IL
32	IL_72158.2	6	LSU Helix 62 (H62) IL
33	IL_54420.1	6
34	IL_13069.2	6	LSU 3WJ H32-H33-H35A
35	IL_24022.2	6
36	IL_25230.2	6	Bacterial 5S rRNA Loop E
37	IL_70237.3	6
38	IL_10007.1	6	Single sheared with bulged bases
39	IL_08926.1	6	23S H91 IL
40	IL_90133.1	5
41	IL_79083.2	5
42	IL_92484.1	5
43	IL_82188.1	5	LSU H68 IL from H.m.
44	IL_78732.3	5	Double S-turn motif
45	IL_02359.2	5
46	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
47	IL_45262.2	5
48	IL_77263.1	5	Kink-turn from U4
49	IL_01239.1	5
50	IL_98556.2	4
51	IL_93568.1	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
52	IL_22732.1	4	tSH-inserted-tHS
53	IL_62661.2	4	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
54	IL_47758.1	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
55	IL_21333.1	4	tSH-tHW-bulge
56	IL_98591.2	4
57	IL_39526.3	4
58	IL_28572.1	4	16S h18 kink-turn like motif
59	IL_31066.2	4	SSU Helix 44 (h44) extension
60	IL_38807.2	4
61	IL_40387.3	4
62	IL_98421.2	3	SSU Helix 12 (h12) IL
63	IL_36254.1	3
64	IL_16166.2	3
65	IL_75447.1	3
66	IL_23262.3	3
67	IL_86826.1	3	tHS tHH bulge with S-turn
68	IL_09348.3	3	cWW-L-cWW-cWW
69	IL_16252.2	3	23S H91 IL
70	IL_95150.3	3
71	IL_79955.2	3	SSU Helix (23) h23 IL1
72	IL_71565.1	3
73	IL_82563.1	3	Thi-box riboswitch T-loop
74	IL_89028.2	3	Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
75	IL_62499.3	3
76	IL_58586.2	3
77	IL_80494.2	3	LSU H58 IL2 H.m.
78	IL_53774.1	3	Single sheared with bulged bases
79	IL_34628.2	3	Kink-turn
80	IL_95652.2	3	SSU Helix 27 (h27) IL Sarcin-Ricin motif
81	IL_52173.1	3
82	IL_37053.1	3	Kink-turn from 23S H58
83	IL_30840.1	3
84	IL_43946.1	3
85	IL_34363.1	3	Kink-turn from 23S H42
86	IL_31707.1	2	Vitamin B12 aptamer
87	IL_09882.1	2
88	IL_98566.1	2
89	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
90	IL_37737.1	2
91	IL_93782.1	2
92	IL_73816.1	2	tHS tHH bulge with S-turn
93	IL_37197.1	2
94	IL_50521.1	2
95	IL_81441.1	2
96	IL_55287.1	2
97	IL_45794.1	2
98	IL_87548.1	2
99	IL_16415.1	2	SSU Helix 23 (h23) Kink-turn T. thermophilus
100	IL_52940.1	2
101	IL_65137.1	2	Kink-turn like motif in Group I Intron
102	IL_97833.1	2
103	IL_80093.1	2
104	IL_46435.1	2
105	IL_82831.2	2	Kink-turn from 16S H23
106	IL_28942.1	2
107	IL_07300.1	2
108	IL_16330.1	2
109	IL_96446.1	2
110	IL_11751.1	2
111	IL_76095.3	2	Motif from Hairpin Ribozyme
112	IL_12211.1	2
113	IL_25271.1	2	SSU Helix 8 (h8) IL E.c. and Yeast
114	IL_00998.1	2
115	IL_23414.1	2
116	IL_40892.1	2
117	IL_54965.1	2	Leadzyme Motif. SSU Decoding site motif, extended.
118	IL_34156.3	2	cWW AG or UU
119	IL_21495.1	2
120	IL_74876.1	2
121	IL_87336.1	2	LSU Eukaryal Helix 96 (H96) IL1
122	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
123	IL_25174.1	2
124	IL_90057.1	2
125	IL_91132.1	2
126	IL_01054.1	2
127	IL_15840.2	2	Triple Sheared with unpaired, inserted A
128	IL_37406.1	2
129	IL_41397.2	2	LSU Helix 96 (H96) IL2
130	IL_70280.1	2	Double sheared with wobble cWW.
131	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
132	IL_91379.1	1
133	IL_26868.1	1
134	IL_31006.1	1	tSH-tHW-L-bif-cWW
135	IL_55649.1	1
136	IL_52509.1	1
137	IL_37715.1	1
138	IL_55934.1	1	kink-turn-like
139	IL_27243.1	1
140	IL_71942.1	1
141	IL_25082.1	1
142	IL_71685.1	1	Sarcin-like with an intercalated basepair
143	IL_25181.1	1
144	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
145	IL_23448.1	1
146	IL_85805.1	1
147	IL_68827.1	1	Reverse Kink-Turn
148	IL_11302.1	1
149	IL_61730.1	1
150	IL_75328.1	1
151	IL_53423.1	1
152	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
153	IL_23639.1	1	tWH-tHS-L-cWW
154	IL_90880.1	1
155	IL_15205.1	1
156	IL_60643.1	1
157	IL_83250.1	1	16S h40 3WJ T.th.
158	IL_88865.1	1
159	IL_02835.1	1
160	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
161	IL_98688.1	1
162	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
163	IL_89794.1	1
164	IL_65788.1	1
165	IL_75688.1	1	Part of Helix 71 (H71) junction in 23S of D.r.
166	IL_78809.1	1
167	IL_67735.1	1
168	IL_76486.1	1	Sarcin-ricin motif with syn G
169	IL_37990.1	1
170	IL_17603.1	1
171	IL_85510.1	1
172	IL_57285.1	1
173	IL_43316.1	1
174	IL_83920.1	1
175	IL_53988.1	1
176	IL_20775.1	1	tSH-inserted
177	IL_11869.1	1
178	IL_54576.1	1
179	IL_13682.1	1
180	IL_97842.1	1
181	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
182	IL_56513.1	1
183	IL_88367.1	1
184	IL_63952.1	1
185	IL_03110.1	1
186	IL_41791.1	1
187	IL_62017.1	1	Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
188	IL_12507.1	1
189	IL_88403.1	1
190	IL_05462.1	1
191	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
192	IL_02690.1	1
193	IL_06306.1	1
194	IL_37347.1	1
195	IL_46306.1	1
196	IL_21421.1	1
197	IL_40527.1	1	Kink-turn
198	IL_27668.1	1
199	IL_92280.1	1
200	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
201	IL_86059.1	1
202	IL_80505.1	1
203	IL_06468.1	1	16S h40 3WJ E.c.
204	IL_80652.1	1
205	IL_12486.1	1
206	IL_31241.1	1
207	IL_75415.1	1	Pseudo-knot forming internal loop
208	IL_83856.1	1
209	IL_05221.1	1
210	IL_06471.1	1
211	IL_58454.1	1
212	IL_41139.1	1
213	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
214	IL_40845.1	1
215	IL_39324.1	1
216	IL_82650.1	1
217	IL_61991.1	1
218	IL_47687.1	1
219	IL_52958.1	1
220	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
221	IL_97073.1	1
222	IL_54450.1	1
223	IL_76256.1	1
224	IL_03741.1	1
225	IL_81398.1	1
226	IL_53323.1	1
227	IL_26971.1	1
228	IL_91904.1	1
229	IL_18755.1	1
230	IL_70550.1	1
231	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
232	IL_57977.1	1
233	IL_76263.1	1
234	IL_25307.1	1
235	IL_06780.1	1
236	IL_22579.1	1
237	IL_77014.1	1
238	IL_91078.1	1
239	IL_82113.1	1
240	IL_98924.1	1
241	IL_59529.1	1
242	IL_02957.1	1
243	IL_82601.1	1	Tandem cWW water-inserted CU pairs
244	IL_91089.1	1

Updated motif groups

#	Motif id	Instances	Description
1	IL_97217.4	235	1-3 bulged nucleotides, same chain
2	IL_47174.4	202	16S h34 ILa : Part of larger motif
3	IL_87904.3	31	Triple sheared (tSH-tHS-tHS) no inserted bases
4	IL_65553.4	22	Kink-turn
5	IL_06429.2	16	cWW-bulge-cWW
6	IL_31555.3	15	Tandem sheared with inserted, unpaired purine.
7	IL_47444.3	9	SRP Loop E-like motif
8	IL_92114.3	9	GAAA loop receptor "platform" motif

Removed motif groups

#	Motif id	Instances
1	IL_80179.2	5
2	IL_12269.1	2
3	IL_80755.1	2
4	IL_14023.1	2
5	IL_99575.1	2
6	IL_12068.1	2
7	IL_26241.1	1
8	IL_29949.1	1
9	IL_41009.1	1
10	IL_41849.1	1
11	IL_61723.1	1
12	IL_12233.1	1

Added motif groups

#	Motif id	Instances	Description
1	IL_10005.1	4
2	IL_16377.1	2
3	IL_89231.1	2	LSU H77
4	IL_69901.1	2
5	IL_77076.1	2
6	IL_77296.1	1
7	IL_17268.1	1
8	IL_91044.1	1
9	IL_47968.1	1
10	IL_94973.1	1	Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
11	IL_60649.1	1	Kink-turn
12	IL_03282.1	1
13	IL_06847.1	1	Group II Intron IL
14	IL_77195.1	1