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RLUD - Ribosomal large subunit pseudouridine synthase D
UniProt: P33643 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG12098
Length: 326 (306)
Sequences: 4028
Seq/Len: 13.16
RLUD
Paralog alert: 0.87 [within 20: 0.01] - ratio of genomes with paralogs
Cluster includes: RLUA RLUB RLUC RLUD RLUE RLUF RSUA TRUC
GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:
i j Scaled Score Prob
87_V 145_L 5.03 1.00
48_N 63_E 4.853 1.00
170_E 225_R 3.993 1.00
216_E 313_R 3.825 1.00
211_H 229_E 3.777 1.00
213_R 225_R 3.365 1.00
85_D 97_N 3.303 1.00
285_R 296_E 3.208 1.00
89_E 150_K 3.077 1.00
92_D 290_I 3.017 1.00
184_T 211_H 3.007 1.00
97_N 299_A 3.002 1.00
92_D 151_T 2.911 1.00
283_M 296_E 2.813 1.00
80_Q 112_D 2.688 1.00
183_G 212_Y 2.61 1.00
172_E 282_T 2.599 1.00
187_E 242_H 2.568 1.00
276_R 304_D 2.517 1.00
95_I 297_W 2.504 1.00
172_E 223_R 2.498 1.00
82_I 118_A 2.343 1.00
214_I 222_T 2.232 1.00
186_D 207_P 2.187 1.00
226_L 240_M 2.174 1.00
209_V 229_E 2.159 1.00
184_T 209_V 2.136 1.00
186_D 209_V 2.129 1.00
161_S 166_E 1.992 1.00
20_L 53_D 1.984 1.00
210_T 226_L 1.98 1.00
215_M 225_R 1.978 1.00
285_R 294_E 1.973 1.00
283_M 298_H 1.965 1.00
287_Y 294_E 1.964 1.00
168_T 227_R 1.953 1.00
90_D 288_H 1.951 1.00
173_A 226_L 1.92 1.00
143_T 280_H 1.915 1.00
151_T 154_A 1.905 1.00
115_V 146_M 1.884 1.00
12_S 15_Q 1.883 1.00
138_L 146_M 1.882 1.00
169_R 228_L 1.834 1.00
303_Q 307_E 1.827 1.00
278_A 305_M 1.822 1.00
81_D 121_H 1.814 1.00
80_Q 113_G 1.807 1.00
179_M 222_T 1.802 1.00
160_E 164_R 1.799 1.00
182_G 217_H 1.783 1.00
224_L 240_M 1.749 1.00
201_V 242_H 1.732 1.00
47_V 57_E 1.717 1.00
95_I 147_V 1.679 1.00
87_V 297_W 1.668 1.00
217_H 222_T 1.666 1.00
95_I 145_L 1.65 1.00
170_E 283_M 1.636 1.00
168_T 285_R 1.619 1.00
170_E 227_R 1.607 1.00
226_L 236_I 1.601 1.00
141_D 277_Q 1.586 1.00
185_V 243_I 1.563 1.00
175_A 224_L 1.56 1.00
157_R 161_S 1.552 1.00
210_T 228_L 1.533 1.00
53_D 57_E 1.525 1.00
104_V 146_M 1.507 1.00
46_L 66_A 1.486 1.00
189_I 238_V 1.483 1.00
90_D 93_I 1.458 1.00
288_H 295_M 1.442 1.00
135_V 149_A 1.429 1.00
274_F 278_A 1.429 1.00
93_I 286_L 1.427 1.00
172_E 225_R 1.42 1.00
119_L 148_V 1.416 1.00
23_A 27_M 1.395 0.99
278_A 308_L 1.364 0.99
153_P 290_I 1.363 0.99
177_G 222_T 1.36 0.99
212_Y 240_M 1.309 0.99
192_H 198_H 1.293 0.99
173_A 247_L 1.289 0.99
23_A 59_V 1.282 0.99
155_Q 159_V 1.279 0.99
100_R 143_T 1.268 0.99
184_T 229_E 1.26 0.99
59_V 65_V 1.259 0.99
102_L 118_A 1.256 0.99
301_I 305_M 1.255 0.99
282_T 298_H 1.247 0.99
99_P 102_L 1.247 0.99
189_I 199_M 1.237 0.98
107_G 110_N 1.234 0.98
103_V 110_N 1.228 0.98
307_E 311_V 1.218 0.98
174_V 308_L 1.204 0.98
172_E 215_M 1.2 0.98
127_A 130_P 1.196 0.98
172_E 301_I 1.192 0.98
228_L 236_I 1.19 0.98
20_L 40_I 1.188 0.98
211_H 227_R 1.187 0.98
93_I 154_A 1.186 0.98
306_V 310_E 1.182 0.98
288_H 291_S 1.175 0.98
126_I 129_V 1.172 0.98
135_V 158_L 1.17 0.97
280_H 299_A 1.164 0.97
185_V 240_M 1.163 0.97
157_R 160_E 1.156 0.97
100_R 276_R 1.153 0.97
276_R 280_H 1.151 0.97
175_A 240_M 1.15 0.97
173_A 224_L 1.141 0.97
177_G 245_H 1.134 0.97
221_H 248_V 1.133 0.97
169_R 229_E 1.128 0.97
37_K 41_L 1.128 0.97
274_F 305_M 1.123 0.97
94_I 119_L 1.117 0.96
145_L 297_W 1.113 0.96
197_T 252_V 1.113 0.96
240_M 247_L 1.111 0.96
47_V 65_V 1.107 0.96
174_V 221_H 1.107 0.96
10_T 64_Q 1.106 0.96
25_A 33_R 1.102 0.96
101_D 143_T 1.099 0.96
24_L 36_I 1.096 0.96
210_T 239_H 1.094 0.96
35_R 39_W 1.093 0.96
162_L 169_R 1.091 0.96
190_S 202_H 1.082 0.96
8_T 66_A 1.075 0.95
182_G 213_R 1.063 0.95
92_D 154_A 1.055 0.95
176_I 248_V 1.054 0.95
214_I 217_H 1.048 0.94
124_P 127_A 1.041 0.94
40_I 45_V 1.029 0.94
92_D 288_H 1.027 0.94
183_G 214_I 1.025 0.93
24_L 45_V 1.023 0.93
145_L 299_A 1.02 0.93
93_I 288_H 1.013 0.93
175_A 222_T 1.008 0.93
Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.
HHsearch Results: GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.
PDB Chains Cov P(%) HHΔ   Acc
1v9fA10.99391000.16Contact Map0.897
1v9kA20.69021000.355Contact Map0.837
2i82A40.65031000.383Contact Map0.896
4lgtA20.74851000.469Contact Map0.593
3dh3A40.76691000.474Contact Map0.518
1vioA20.73931000.477Contact Map0.67
1kskA10.70861000.483Contact Map0.63
2olwA20.64421000.536Contact Map0.618
2omlA10.52761000.543Contact Map0.64
2gmlA20.65951000.594Contact Map0.676
Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.
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