Changes in PDB files used for clustering

Release 0.7 has 191 PDB files, release 0.8 has 191 PDB files, 191 of them are identical.

No equivalence class representatives have been replaced.

No new PDB files have been added.

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

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Changes in motif groups

Release 0.7 has 263 motif groups, release 0.8 has 263 motif groups, 263 of them are identical.

0 motif groups were updated, 0 groups are present only in release 0.7, 0 groups are only in release 0.8.

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 idInstancesDescription
1IL_97217.2234
2IL_47174.220016S h34 ILa : Part of larger motif
3IL_39199.255Hoogsteen-edge Platform, Single bulged base
4IL_41766.249Tandem cWW pairs (Not AU or GC)
5IL_56465.245Single, unpaired intercalated base, consensus A
6IL_44540.243Sugar-edge, 1-base platform, consensus tHS
7IL_87904.231Triple sheared
8IL_06390.125cWH basepair with syn base
9IL_13959.224Double Sheared (tSH-tHS)
10IL_93424.222tSH-inserted-tHW
11IL_65553.221Kink-turn
12IL_32390.22116S h19 IL and 23S H41 IL
13IL_73276.120C-loop
14IL_55938.219LSU Helix 89 (H89) IL2. cSH Platform.
15IL_92027.21716S h21 S8 binding site
16IL_06429.11616S h19 IL and 23S H41 IL | 1 or 2 bulged bases
17IL_85647.216Sarcin-ricin parent motif with 15 Nts
18IL_24982.315SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
19IL_31555.21516S decoding site
20IL_94430.21416S h32-h33-h34 3WJ
21IL_49493.214Sarcin-ricin Parent Motif - bacterial LSU H95 IL
22IL_40090.21116S h34 ILa : Part of larger motif
23IL_46648.11123S H91 IL | Single-Base Intercalation Site
24IL_21304.111Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
25IL_27618.21123S H73 ILa : Part of larger Motif
26IL_24546.21023S H41 IL and 16S h18 IL : Has large bulge on one side
27IL_92114.29GAAA loop receptor "platform" motif
28IL_58291.29Recurrent Sub-motif found in junctions
29IL_47444.29SRP Loop E-like motif
30IL_02809.18REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
31IL_90459.28cWW AG or UU
32IL_92321.28Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
33IL_86357.27LSU Helix 61 IL2
34IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
35IL_73000.27cHS-cWS
36IL_24022.26
37IL_89088.1616S h19 IL and 23S H41 IL
38IL_08926.1623S H91 IL
39IL_72158.26LSU Helix 62 (H62) IL
40IL_10007.16Single sheared with bulged bases
41IL_53635.26LSU Helix 32 (H32) IL
42IL_70237.36
43IL_13069.26LSU 3WJ H32-H33-H35A
44IL_44067.26Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
45IL_97057.26
46IL_25230.26Bacterial 5S rRNA Loop E
47IL_02359.25
48IL_07911.15
49IL_45262.25
50IL_40387.25
51IL_79083.25
52IL_82188.15LSU H68 IL from H.m.
53IL_77263.15Kink-turn from U4
54IL_80179.25
55IL_92484.15
56IL_01239.15
57IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
58IL_78732.35Double S-turn motif
59IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
60IL_22732.14tSH-inserted-tHS
61IL_31066.24SSU Helix 44 (h44) extension
62IL_38807.24
63IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
64IL_98556.14
65IL_21333.14tSH-tHW-bulge
66IL_28572.1416S h18 kink-turn like motif
67IL_39526.24
68IL_64184.24
69IL_98591.24
70IL_71565.13
71IL_75447.13
72IL_45808.13
73IL_95150.23
74IL_09348.23
75IL_30840.13
76IL_34156.23cWW AG or UU
77IL_79955.23SSU Helix (23) h23 IL1
78IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
79IL_15840.13
80IL_34363.13Kink-turn from 23S H42
81IL_62499.23
82IL_98421.13
83IL_23262.33
84IL_34628.23Kink-turn
85IL_43946.13
86IL_82563.13Thi-box riboswitch T-loop
87IL_16252.2323S H91 IL
88IL_37053.13Kink-turn from 23S H58
89IL_52173.13
90IL_53774.13Single sheared with bulged bases
91IL_58586.23
92IL_80494.23LSU H58 IL2 H.m.
93IL_89028.13Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
94IL_12068.12
95IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
96IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
97IL_28942.12
98IL_65137.12Kink-turn like motif in Group I Intron
99IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
100IL_82831.22Kink-turn from 16S H23
101IL_12211.12
102IL_21495.12
103IL_37406.12
104IL_45794.12
105IL_52940.12
106IL_94744.12Sarcin-ricin motif with extra cWW GA pair
107IL_14023.12
108IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
109IL_81441.12
110IL_87173.12
111IL_90057.12
112IL_97833.12
113IL_99575.12
114IL_12269.12
115IL_48285.12Leadzyme Motif
116IL_55287.12
117IL_76095.32Motif from Hairpin Ribozyme
118IL_87548.12
119IL_09882.12
120IL_40892.12
121IL_43933.12
122IL_46435.12
123IL_80093.12
124IL_00998.12
125IL_16166.12
126IL_25174.12
127IL_50521.12
128IL_91026.12
129IL_92459.12
130IL_01054.12
131IL_23414.12
132IL_70280.12Double sheared with wobble cWW.
133IL_74291.12
134IL_78674.12tHS tHH bulge with S-turn
135IL_98566.12
136IL_16330.12
137IL_31707.12Vitamin B12 aptamer
138IL_37197.12
139IL_41397.22LSU Helix 96 (H96) IL2
140IL_74876.12
141IL_05462.11
142IL_13942.11
143IL_21421.11
144IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
145IL_37347.11
146IL_47457.11
147IL_52752.11
148IL_54450.11
149IL_56513.11
150IL_60643.11
151IL_75415.11Pseudo-knot forming internal loop
152IL_80652.11
153IL_91904.11
154IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
155IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
156IL_02690.11
157IL_06306.11
158IL_17603.11
159IL_24143.11Yeast 18S
160IL_25307.11
161IL_29949.11
162IL_32080.11
163IL_41791.11
164IL_47687.11
165IL_54576.11
166IL_56779.11
167IL_61723.11
168IL_71685.11Sarcin-like with an intercalated basepair
169IL_78809.11
170IL_81398.11
171IL_83250.1116S h40 3WJ T.th.
172IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
173IL_89794.11
174IL_98924.11
175IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
176IL_12233.11
177IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
178IL_22579.11
179IL_25739.11M-Box Riboswitch
180IL_30390.11
181IL_37715.11
182IL_40527.11Kink-turn
183IL_41849.11
184IL_52958.11
185IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
186IL_61730.11
187IL_65788.11
188IL_71942.11
189IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
190IL_02835.11
191IL_15205.11
192IL_18755.11
193IL_26241.11
194IL_37990.11
195IL_40845.11
196IL_43316.11
197IL_46306.11
198IL_53323.11
199IL_57977.11
200IL_62352.11
201IL_66744.11SSU Helix 21 (h21) IL2 E.coli
202IL_82113.11
203IL_83920.11
204IL_92280.11
205IL_97842.11
206IL_02957.11
207IL_06468.1116S h40 3WJ E.c.
208IL_12486.11
209IL_20775.11tSH-inserted
210IL_22858.11
211IL_25082.11
212IL_26868.11
213IL_53423.11
214IL_55649.11
215IL_67735.11
216IL_76486.11Sarcin-ricin motif with syn G
217IL_85510.11
218IL_90880.11
219IL_95939.11
220IL_03110.11
221IL_06808.11Double sheared (tSH-tSH) one bulged base.
222IL_12507.11
223IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
224IL_26971.11
225IL_31241.11
226IL_41009.11
227IL_55934.11kink-turn-like
228IL_58454.11
229IL_88367.11
230IL_96260.11
231IL_03741.11
232IL_07375.11
233IL_11302.11
234IL_25181.11
235IL_39324.11
236IL_41139.11
237IL_63952.11
238IL_82601.11Tandem cWW water-inserted CU pairs
239IL_85805.11
240IL_88403.11
241IL_91078.11
242IL_05221.11
243IL_07675.11tHS tHH bulge with S-turn
244IL_11869.11
245IL_13682.11
246IL_23639.11tWH-tHS-L-cWW
247IL_52509.11
248IL_53988.11
249IL_59529.11
250IL_80505.11
251IL_82650.11
252IL_86059.11
253IL_91089.11
254IL_97073.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription