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_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_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_40090.2	11	16S h34 ILa : Part of larger motif
19	IL_27618.2	11	23S H73 ILa : Part of larger Motif
20	IL_46648.1	11	23S H91 IL \| Single-Base Intercalation Site
21	IL_21304.1	11	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
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_47444.2	9	SRP Loop E-like motif
25	IL_58291.2	9	Recurrent Sub-motif found in junctions
26	IL_02809.1	8	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
27	IL_90459.2	8	cWW AG or UU
28	IL_92321.2	8	Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
29	IL_73000.2	7	cHS-cWS
30	IL_86357.2	7	LSU Helix 61 IL2
31	IL_83451.2	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
32	IL_13069.2	6	LSU 3WJ H32-H33-H35A
33	IL_89088.1	6	16S h19 IL and 23S H41 IL
34	IL_97057.2	6
35	IL_70237.3	6
36	IL_08926.1	6	23S H91 IL
37	IL_25230.2	6	Bacterial 5S rRNA Loop E
38	IL_44067.2	6	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
39	IL_24022.2	6
40	IL_53635.2	6	LSU Helix 32 (H32) IL
41	IL_10007.1	6	Single sheared with bulged bases
42	IL_72158.2	6	LSU Helix 62 (H62) IL
43	IL_77263.1	5	Kink-turn from U4
44	IL_78732.3	5	Double S-turn motif
45	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
46	IL_79083.2	5
47	IL_92484.1	5
48	IL_01239.1	5
49	IL_02359.2	5
50	IL_45262.2	5
51	IL_82188.1	5	LSU H68 IL from H.m.
52	IL_80179.2	5
53	IL_22732.1	4	tSH-inserted-tHS
54	IL_28572.1	4	16S h18 kink-turn like motif
55	IL_62661.2	4	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
56	IL_38807.2	4
57	IL_47758.1	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
58	IL_21333.1	4	tSH-tHW-bulge
59	IL_98591.2	4
60	IL_31066.2	4	SSU Helix 44 (h44) extension
61	IL_52173.1	3
62	IL_80494.2	3	LSU H58 IL2 H.m.
63	IL_23262.3	3
64	IL_43946.1	3
65	IL_71565.1	3
66	IL_75447.1	3
67	IL_16252.2	3	23S H91 IL
68	IL_34363.1	3	Kink-turn from 23S H42
69	IL_79955.2	3	SSU Helix (23) h23 IL1
70	IL_30840.1	3
71	IL_34628.2	3	Kink-turn
72	IL_58586.2	3
73	IL_37053.1	3	Kink-turn from 23S H58
74	IL_53774.1	3	Single sheared with bulged bases
75	IL_82563.1	3	Thi-box riboswitch T-loop
76	IL_95652.2	3	SSU Helix 27 (h27) IL Sarcin-Ricin motif
77	IL_21495.1	2
78	IL_37197.1	2
79	IL_46435.1	2
80	IL_99575.1	2
81	IL_12068.1	2
82	IL_25174.1	2
83	IL_31707.1	2	Vitamin B12 aptamer
84	IL_37406.1	2
85	IL_52940.1	2
86	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
87	IL_70280.1	2	Double sheared with wobble cWW.
88	IL_74876.1	2
89	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
90	IL_82831.2	2	Kink-turn from 16S H23
91	IL_90057.1	2
92	IL_00998.1	2
93	IL_12211.1	2
94	IL_14023.1	2
95	IL_40892.1	2
96	IL_97833.1	2
97	IL_01054.1	2
98	IL_23414.1	2
99	IL_28942.1	2
100	IL_55287.1	2
101	IL_81441.1	2
102	IL_87548.1	2
103	IL_12269.1	2
104	IL_25271.1	2	SSU Helix 8 (h8) IL E.c. and Yeast
105	IL_65137.1	2	Kink-turn like motif in Group I Intron
106	IL_98566.1	2
107	IL_09882.1	2
108	IL_16330.1	2
109	IL_41397.2	2	LSU Helix 96 (H96) IL2
110	IL_76095.3	2	Motif from Hairpin Ribozyme
111	IL_80093.1	2
112	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
113	IL_16415.1	2	SSU Helix 23 (h23) Kink-turn T. thermophilus
114	IL_45794.1	2
115	IL_50521.1	2
116	IL_11302.1	1
117	IL_17603.1	1
118	IL_26868.1	1
119	IL_31241.1	1
120	IL_41791.1	1
121	IL_46306.1	1
122	IL_53988.1	1
123	IL_60643.1	1
124	IL_67735.1	1
125	IL_82601.1	1	Tandem cWW water-inserted CU pairs
126	IL_85805.1	1
127	IL_98924.1	1
128	IL_02835.1	1
129	IL_11869.1	1
130	IL_13682.1	1
131	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
132	IL_22579.1	1
133	IL_25082.1	1
134	IL_26971.1	1
135	IL_37347.1	1
136	IL_40527.1	1	Kink-turn
137	IL_41849.1	1
138	IL_52509.1	1
139	IL_54450.1	1
140	IL_56513.1	1
141	IL_61723.1	1
142	IL_80505.1	1
143	IL_82650.1	1
144	IL_86059.1	1
145	IL_89794.1	1
146	IL_97073.1	1
147	IL_02957.1	1
148	IL_06468.1	1	16S h40 3WJ E.c.
149	IL_18755.1	1
150	IL_40845.1	1
151	IL_43316.1	1
152	IL_54576.1	1
153	IL_61730.1	1
154	IL_80652.1	1
155	IL_92280.1	1
156	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
157	IL_03110.1	1
158	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
159	IL_20775.1	1	tSH-inserted
160	IL_25181.1	1
161	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
162	IL_37715.1	1
163	IL_52958.1	1
164	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
165	IL_57977.1	1
166	IL_75415.1	1	Pseudo-knot forming internal loop
167	IL_78809.1	1
168	IL_81398.1	1
169	IL_83250.1	1	16S h40 3WJ T.th.
170	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
171	IL_03741.1	1
172	IL_12233.1	1
173	IL_15205.1	1
174	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
175	IL_37990.1	1
176	IL_41009.1	1
177	IL_47687.1	1
178	IL_53323.1	1
179	IL_63952.1	1
180	IL_90880.1	1
181	IL_97842.1	1
182	IL_05221.1	1
183	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
184	IL_23639.1	1	tWH-tHS-L-cWW
185	IL_29949.1	1
186	IL_41139.1	1
187	IL_53423.1	1
188	IL_55649.1	1
189	IL_58454.1	1
190	IL_71685.1	1	Sarcin-like with an intercalated basepair
191	IL_75688.1	1	Part of Helix 71 (H71) junction in 23S of D.r.
192	IL_82113.1	1
193	IL_83920.1	1
194	IL_91078.1	1
195	IL_05462.1	1
196	IL_12486.1	1
197	IL_25307.1	1
198	IL_55934.1	1	kink-turn-like
199	IL_65788.1	1
200	IL_71942.1	1
201	IL_85510.1	1
202	IL_88367.1	1
203	IL_91089.1	1
204	IL_02690.1	1
205	IL_06306.1	1
206	IL_12507.1	1
207	IL_21421.1	1
208	IL_26241.1	1
209	IL_39324.1	1
210	IL_59529.1	1
211	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
212	IL_76486.1	1	Sarcin-ricin motif with syn G
213	IL_88403.1	1
214	IL_91904.1	1
215	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast

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