0.8 | 0.9

Changes in PDB files used for clustering

Release 0.8 has 191 PDB files, release 0.9 has 195 PDB files, 191 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_85647.2	16	Sarcin-ricin parent motif with 15 Nts
14	IL_06429.1	16	16S h19 IL and 23S H41 IL \| 1 or 2 bulged bases
15	IL_24982.3	15	SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
16	IL_31555.2	15	16S decoding site
17	IL_49493.2	14	Sarcin-ricin Parent Motif - bacterial LSU H95 IL
18	IL_21304.1	11	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
19	IL_40090.2	11	16S h34 ILa : Part of larger motif
20	IL_27618.2	11	23S H73 ILa : Part of larger Motif
21	IL_46648.1	11	23S H91 IL \| Single-Base Intercalation Site
22	IL_24546.2	10	23S H41 IL and 16S h18 IL : Has large bulge on one side
23	IL_47444.2	9	SRP Loop E-like motif
24	IL_58291.2	9	Recurrent Sub-motif found in junctions
25	IL_92114.2	9	GAAA loop receptor "platform" motif
26	IL_90459.2	8	cWW AG or UU
27	IL_92321.2	8	Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
28	IL_02809.1	8	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
29	IL_83451.2	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
30	IL_73000.2	7	cHS-cWS
31	IL_86357.2	7	LSU Helix 61 IL2
32	IL_08926.1	6	23S H91 IL
33	IL_25230.2	6	Bacterial 5S rRNA Loop E
34	IL_44067.2	6	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
35	IL_24022.2	6
36	IL_53635.2	6	LSU Helix 32 (H32) IL
37	IL_10007.1	6	Single sheared with bulged bases
38	IL_72158.2	6	LSU Helix 62 (H62) IL
39	IL_13069.2	6	LSU 3WJ H32-H33-H35A
40	IL_89088.1	6	16S h19 IL and 23S H41 IL
41	IL_97057.2	6
42	IL_70237.3	6
43	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
44	IL_79083.2	5
45	IL_92484.1	5
46	IL_01239.1	5
47	IL_02359.2	5
48	IL_45262.2	5
49	IL_82188.1	5	LSU H68 IL from H.m.
50	IL_80179.2	5
51	IL_77263.1	5	Kink-turn from U4
52	IL_78732.3	5	Double S-turn motif
53	IL_28572.1	4	16S h18 kink-turn like motif
54	IL_62661.2	4	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
55	IL_38807.2	4
56	IL_47758.1	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
57	IL_21333.1	4	tSH-tHW-bulge
58	IL_98591.2	4
59	IL_31066.2	4	SSU Helix 44 (h44) extension
60	IL_22732.1	4	tSH-inserted-tHS
61	IL_23262.3	3
62	IL_43946.1	3
63	IL_71565.1	3
64	IL_75447.1	3
65	IL_16252.2	3	23S H91 IL
66	IL_34363.1	3	Kink-turn from 23S H42
67	IL_79955.2	3	SSU Helix (23) h23 IL1
68	IL_30840.1	3
69	IL_34628.2	3	Kink-turn
70	IL_58586.2	3
71	IL_37053.1	3	Kink-turn from 23S H58
72	IL_53774.1	3	Single sheared with bulged bases
73	IL_82563.1	3	Thi-box riboswitch T-loop
74	IL_95652.2	3	SSU Helix 27 (h27) IL Sarcin-Ricin motif
75	IL_52173.1	3
76	IL_80494.2	3	LSU H58 IL2 H.m.
77	IL_00998.1	2
78	IL_12211.1	2
79	IL_14023.1	2
80	IL_40892.1	2
81	IL_97833.1	2
82	IL_01054.1	2
83	IL_23414.1	2
84	IL_28942.1	2
85	IL_55287.1	2
86	IL_81441.1	2
87	IL_87548.1	2
88	IL_12269.1	2
89	IL_25271.1	2	SSU Helix 8 (h8) IL E.c. and Yeast
90	IL_65137.1	2	Kink-turn like motif in Group I Intron
91	IL_98566.1	2
92	IL_09882.1	2
93	IL_16330.1	2
94	IL_41397.2	2	LSU Helix 96 (H96) IL2
95	IL_76095.3	2	Motif from Hairpin Ribozyme
96	IL_80093.1	2
97	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
98	IL_16415.1	2	SSU Helix 23 (h23) Kink-turn T. thermophilus
99	IL_45794.1	2
100	IL_50521.1	2
101	IL_21495.1	2
102	IL_37197.1	2
103	IL_46435.1	2
104	IL_99575.1	2
105	IL_12068.1	2
106	IL_25174.1	2
107	IL_31707.1	2	Vitamin B12 aptamer
108	IL_37406.1	2
109	IL_52940.1	2
110	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
111	IL_70280.1	2	Double sheared with wobble cWW.
112	IL_74876.1	2
113	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
114	IL_82831.2	2	Kink-turn from 16S H23
115	IL_90057.1	2
116	IL_03110.1	1
117	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
118	IL_20775.1	1	tSH-inserted
119	IL_25181.1	1
120	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
121	IL_37715.1	1
122	IL_52958.1	1
123	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
124	IL_57977.1	1
125	IL_75415.1	1	Pseudo-knot forming internal loop
126	IL_78809.1	1
127	IL_81398.1	1
128	IL_83250.1	1	16S h40 3WJ T.th.
129	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
130	IL_03741.1	1
131	IL_12233.1	1
132	IL_15205.1	1
133	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
134	IL_37990.1	1
135	IL_41009.1	1
136	IL_47687.1	1
137	IL_53323.1	1
138	IL_63952.1	1
139	IL_90880.1	1
140	IL_97842.1	1
141	IL_05221.1	1
142	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
143	IL_23639.1	1	tWH-tHS-L-cWW
144	IL_29949.1	1
145	IL_41139.1	1
146	IL_53423.1	1
147	IL_55649.1	1
148	IL_58454.1	1
149	IL_71685.1	1	Sarcin-like with an intercalated basepair
150	IL_75688.1	1	Part of Helix 71 (H71) junction in 23S of D.r.
151	IL_82113.1	1
152	IL_83920.1	1
153	IL_91078.1	1
154	IL_05462.1	1
155	IL_12486.1	1
156	IL_25307.1	1
157	IL_55934.1	1	kink-turn-like
158	IL_65788.1	1
159	IL_71942.1	1
160	IL_85510.1	1
161	IL_88367.1	1
162	IL_91089.1	1
163	IL_02690.1	1
164	IL_06306.1	1
165	IL_12507.1	1
166	IL_21421.1	1
167	IL_26241.1	1
168	IL_39324.1	1
169	IL_59529.1	1
170	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
171	IL_76486.1	1	Sarcin-ricin motif with syn G
172	IL_88403.1	1
173	IL_91904.1	1
174	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
175	IL_11302.1	1
176	IL_17603.1	1
177	IL_26868.1	1
178	IL_31241.1	1
179	IL_41791.1	1
180	IL_46306.1	1
181	IL_53988.1	1
182	IL_60643.1	1
183	IL_67735.1	1
184	IL_82601.1	1	Tandem cWW water-inserted CU pairs
185	IL_85805.1	1
186	IL_98924.1	1
187	IL_02835.1	1
188	IL_11869.1	1
189	IL_13682.1	1
190	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
191	IL_22579.1	1
192	IL_25082.1	1
193	IL_26971.1	1
194	IL_37347.1	1
195	IL_40527.1	1	Kink-turn
196	IL_41849.1	1
197	IL_52509.1	1
198	IL_54450.1	1
199	IL_56513.1	1
200	IL_61723.1	1
201	IL_80505.1	1
202	IL_82650.1	1
203	IL_86059.1	1
204	IL_89794.1	1
205	IL_97073.1	1
206	IL_02957.1	1
207	IL_06468.1	1	16S h40 3WJ E.c.
208	IL_18755.1	1
209	IL_40845.1	1
210	IL_43316.1	1
211	IL_54576.1	1
212	IL_61730.1	1
213	IL_80652.1	1
214	IL_92280.1	1
215	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.

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_16166.2	3
9	IL_95150.3	3
10	IL_98421.2	3	SSU Helix 12 (h12) IL
11	IL_62499.3	3
12	IL_09348.3	3	cWW-L-cWW-cWW
13	IL_89028.2	3	Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
14	IL_34156.3	2	cWW AG or UU
15	IL_15840.2	2	Triple Sheared with unpaired, inserted A

Removed motif groups

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

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_36254.1	3
5	IL_86826.1	3	tHS tHH bulge with S-turn
6	IL_07300.1	2
7	IL_91132.1	2
8	IL_11751.1	2
9	IL_73816.1	2	tHS tHH bulge with S-turn
10	IL_93782.1	2
11	IL_37737.1	2
12	IL_80755.1	2
13	IL_54965.1	2	Leadzyme Motif. SSU Decoding site motif, extended.
14	IL_87336.1	2	LSU Eukaryal Helix 96 (H96) IL1
15	IL_70550.1	1
16	IL_76256.1	1
17	IL_98688.1	1
18	IL_83856.1	1
19	IL_06471.1	1
20	IL_61991.1	1
21	IL_06780.1	1
22	IL_62017.1	1	Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena