0.8 | 0.9

Changes in PDB files used for clustering

Release 0.8 has 192 PDB files, release 0.9 has 196 PDB files, 192 of them are identical.

No equivalence class representatives have been replaced.

4 new structures in release 0.9: 4FNJ, 4FRG, 4GMA, 4GXY.

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 0.8 has 263 motif groups, release 0.9 has 264 motif groups, 224 of them are identical.

15 motif groups were updated, 24 groups are present only in release 0.8, 25 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_87904.2	31	Triple sheared
6	IL_06390.1	25	cWH basepair with syn base
7	IL_13959.2	24	Double Sheared (tSH-tHS)
8	IL_93424.2	22	tSH-inserted-tHW
9	IL_32390.2	21	16S h19 IL and 23S H41 IL
10	IL_73276.1	20	C-loop
11	IL_55938.2	19	LSU Helix 89 (H89) IL2. cSH Platform.
12	IL_92027.2	17	16S h21 S8 binding site
13	IL_06429.1	16	16S h19 IL and 23S H41 IL \| 1 or 2 bulged bases
14	IL_85647.2	16	Sarcin-ricin parent motif with 15 Nts
15	IL_31555.2	15	16S decoding site
16	IL_24982.3	15	SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
17	IL_49493.2	14	Sarcin-ricin Parent Motif - bacterial LSU H95 IL
18	IL_27618.2	11	23S H73 ILa : Part of larger Motif
19	IL_21304.1	11	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
20	IL_46648.1	11	23S H91 IL \| Single-Base Intercalation Site
21	IL_40090.2	11	16S h34 ILa : Part of larger motif
22	IL_24546.2	10	23S H41 IL and 16S h18 IL : Has large bulge on one side
23	IL_92114.2	9	GAAA loop receptor "platform" motif
24	IL_58291.2	9	Recurrent Sub-motif found in junctions
25	IL_47444.2	9	SRP Loop E-like motif
26	IL_02809.1	8	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
27	IL_92321.2	8	Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
28	IL_90459.2	8	cWW AG or UU
29	IL_86357.2	7	LSU Helix 61 IL2
30	IL_73000.2	7	cHS-cWS
31	IL_83451.2	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
32	IL_89088.1	6	16S h19 IL and 23S H41 IL
33	IL_13069.2	6	LSU 3WJ H32-H33-H35A
34	IL_24022.2	6
35	IL_10007.1	6	Single sheared with bulged bases
36	IL_08926.1	6	23S H91 IL
37	IL_70237.3	6
38	IL_97057.2	6
39	IL_72158.2	6	LSU Helix 62 (H62) IL
40	IL_25230.2	6	Bacterial 5S rRNA Loop E
41	IL_44067.2	6	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
42	IL_53635.2	6	LSU Helix 32 (H32) IL
43	IL_82188.1	5	LSU H68 IL from H.m.
44	IL_92484.1	5
45	IL_02359.2	5
46	IL_77263.1	5	Kink-turn from U4
47	IL_80179.2	5
48	IL_78732.3	5	Double S-turn motif
49	IL_45262.2	5
50	IL_79083.2	5
51	IL_01239.1	5
52	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
53	IL_28572.1	4	16S h18 kink-turn like motif
54	IL_21333.1	4	tSH-tHW-bulge
55	IL_62661.2	4	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
56	IL_47758.1	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
57	IL_31066.2	4	SSU Helix 44 (h44) extension
58	IL_38807.2	4
59	IL_22732.1	4	tSH-inserted-tHS
60	IL_98591.2	4
61	IL_75447.1	3
62	IL_80494.2	3	LSU H58 IL2 H.m.
63	IL_82563.1	3	Thi-box riboswitch T-loop
64	IL_37053.1	3	Kink-turn from 23S H58
65	IL_43946.1	3
66	IL_79955.2	3	SSU Helix (23) h23 IL1
67	IL_16252.2	3	23S H91 IL
68	IL_52173.1	3
69	IL_58586.2	3
70	IL_34628.2	3	Kink-turn
71	IL_95652.2	3	SSU Helix 27 (h27) IL Sarcin-Ricin motif
72	IL_34363.1	3	Kink-turn from 23S H42
73	IL_23262.3	3
74	IL_30840.1	3
75	IL_53774.1	3	Single sheared with bulged bases
76	IL_71565.1	3
77	IL_90057.1	2
78	IL_80093.1	2
79	IL_00998.1	2
80	IL_12068.1	2
81	IL_25174.1	2
82	IL_16330.1	2
83	IL_40892.1	2
84	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
85	IL_65137.1	2	Kink-turn like motif in Group I Intron
86	IL_12211.1	2
87	IL_41397.2	2	LSU Helix 96 (H96) IL2
88	IL_70280.1	2	Double sheared with wobble cWW.
89	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
90	IL_55287.1	2
91	IL_52940.1	2
92	IL_97833.1	2
93	IL_31707.1	2	Vitamin B12 aptamer
94	IL_76095.3	2	Motif from Hairpin Ribozyme
95	IL_82831.2	2	Kink-turn from 16S H23
96	IL_21495.1	2
97	IL_37406.1	2
98	IL_23414.1	2
99	IL_50521.1	2
100	IL_16415.1	2	SSU Helix 23 (h23) Kink-turn T. thermophilus
101	IL_87548.1	2
102	IL_25271.1	2	SSU Helix 8 (h8) IL E.c. and Yeast
103	IL_81441.1	2
104	IL_28942.1	2
105	IL_74876.1	2
106	IL_14023.1	2
107	IL_37197.1	2
108	IL_99575.1	2
109	IL_98566.1	2
110	IL_46435.1	2
111	IL_45794.1	2
112	IL_09882.1	2
113	IL_12269.1	2
114	IL_01054.1	2
115	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
116	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
117	IL_85805.1	1
118	IL_43316.1	1
119	IL_80505.1	1
120	IL_26868.1	1
121	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
122	IL_54450.1	1
123	IL_41849.1	1
124	IL_75328.1	1
125	IL_53423.1	1
126	IL_97842.1	1
127	IL_18755.1	1
128	IL_91089.1	1
129	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
130	IL_83250.1	1	16S h40 3WJ T.th.
131	IL_86059.1	1
132	IL_82650.1	1
133	IL_11302.1	1
134	IL_22579.1	1
135	IL_61730.1	1
136	IL_67735.1	1
137	IL_37347.1	1
138	IL_46306.1	1
139	IL_91904.1	1
140	IL_82601.1	1	Tandem cWW water-inserted CU pairs
141	IL_23448.1	1
142	IL_88865.1	1
143	IL_03110.1	1
144	IL_41791.1	1
145	IL_25307.1	1
146	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
147	IL_52958.1	1
148	IL_52509.1	1
149	IL_37715.1	1
150	IL_55934.1	1	kink-turn-like
151	IL_27243.1	1
152	IL_78809.1	1
153	IL_13682.1	1
154	IL_06306.1	1
155	IL_05221.1	1
156	IL_26971.1	1
157	IL_02957.1	1
158	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
159	IL_60643.1	1
160	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
161	IL_76263.1	1
162	IL_91379.1	1
163	IL_61723.1	1
164	IL_54576.1	1
165	IL_81398.1	1
166	IL_53323.1	1
167	IL_59529.1	1
168	IL_90880.1	1
169	IL_15205.1	1
170	IL_92280.1	1
171	IL_39324.1	1
172	IL_68827.1	1	Reverse Kink-Turn
173	IL_83920.1	1
174	IL_88403.1	1
175	IL_31006.1	1	tSH-tHW-L-bif-cWW
176	IL_55649.1	1
177	IL_20775.1	1	tSH-inserted
178	IL_65788.1	1
179	IL_75688.1	1	Part of Helix 71 (H71) junction in 23S of D.r.
180	IL_29949.1	1
181	IL_75415.1	1	Pseudo-knot forming internal loop
182	IL_82113.1	1
183	IL_98924.1	1
184	IL_25181.1	1
185	IL_17603.1	1
186	IL_85510.1	1
187	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
188	IL_06468.1	1	16S h40 3WJ E.c.
189	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
190	IL_11869.1	1
191	IL_41009.1	1
192	IL_25082.1	1
193	IL_71685.1	1	Sarcin-like with an intercalated basepair
194	IL_56513.1	1
195	IL_88367.1	1
196	IL_63952.1	1
197	IL_40845.1	1
198	IL_57977.1	1
199	IL_47687.1	1
200	IL_89794.1	1
201	IL_05462.1	1
202	IL_02690.1	1
203	IL_12233.1	1
204	IL_77014.1	1
205	IL_03741.1	1
206	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
207	IL_23639.1	1	tWH-tHS-L-cWW
208	IL_21421.1	1
209	IL_40527.1	1	Kink-turn
210	IL_02835.1	1
211	IL_12507.1	1
212	IL_53988.1	1
213	IL_80652.1	1
214	IL_97073.1	1
215	IL_12486.1	1
216	IL_31241.1	1
217	IL_26241.1	1
218	IL_71942.1	1
219	IL_91078.1	1
220	IL_76486.1	1	Sarcin-ricin motif with syn G
221	IL_37990.1	1
222	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
223	IL_58454.1	1
224	IL_41139.1	1

Updated motif groups

#	Motif id	Instances	Description
1	IL_97217.3	235
2	IL_47174.3	202	16S h34 ILa : Part of larger motif
3	IL_65553.3	23	Kink-turn
4	IL_94430.3	15	16S h32-h33-h34 3WJ
5	IL_39526.3	4
6	IL_40387.3	4
7	IL_98556.2	4
8	IL_89028.2	3	Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
9	IL_16166.2	3
10	IL_95150.3	3
11	IL_98421.2	3	SSU Helix 12 (h12) IL
12	IL_62499.3	3
13	IL_09348.3	3	cWW-L-cWW-cWW
14	IL_15840.2	2	Triple Sheared with unpaired, inserted A
15	IL_34156.3	2	cWW AG or UU

Removed motif groups

#	Motif id	Instances	Description
1	IL_07911.1	5
2	IL_64184.2	4
3	IL_45808.1	3
4	IL_43933.1	2
5	IL_74291.1	2
6	IL_78674.1	2	tHS tHH bulge with S-turn
7	IL_87173.1	2
8	IL_48285.1	2	Leadzyme Motif
9	IL_91026.1	2
10	IL_92459.1	2
11	IL_07675.1	1	tHS tHH bulge with S-turn
12	IL_13942.1	1
13	IL_47457.1	1
14	IL_22858.1	1
15	IL_24143.1	1	Yeast 18S
16	IL_52752.1	1
17	IL_25739.1	1	M-Box Riboswitch
18	IL_56779.1	1
19	IL_95939.1	1
20	IL_30390.1	1
21	IL_62352.1	1
22	IL_96260.1	1
23	IL_07375.1	1
24	IL_32080.1	1

Added motif groups

#	Motif id	Instances	Description
1	IL_54420.1	6
2	IL_90133.1	5
3	IL_93568.1	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
4	IL_86826.1	3	tHS tHH bulge with S-turn
5	IL_36254.1	3
6	IL_07300.1	2
7	IL_87336.1	2	LSU Eukaryal Helix 96 (H96) IL1
8	IL_11751.1	2
9	IL_91132.1	2
10	IL_73816.1	2	tHS tHH bulge with S-turn
11	IL_37737.1	2
12	IL_93782.1	2
13	IL_80755.1	2
14	IL_96446.1	2
15	IL_54965.1	2	Leadzyme Motif. SSU Decoding site motif, extended.
16	IL_06780.1	1
17	IL_57285.1	1
18	IL_61991.1	1
19	IL_62017.1	1	Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
20	IL_27668.1	1
21	IL_70550.1	1
22	IL_76256.1	1
23	IL_06471.1	1
24	IL_83856.1	1
25	IL_98688.1	1