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OPENSEQ.org
RND - Ribonuclease D
UniProt: P09155 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG10858
Length: 375 (371)
Sequences: 815
Seq/Len: 2.20
RND
Paralog alert: 0.01 [within 20: 0.00] - ratio of genomes with paralogs
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
20_R 72_D 3.5 1.00
219_L 281_K 3.402 1.00
212_R 290_L 3.136 1.00
8_T 11_A 3.09 1.00
216_C 279_V 3.019 1.00
220_L 244_L 2.723 1.00
123_E 129_T 2.708 1.00
15_L 53_A 2.332 1.00
175_W 178_A 2.292 1.00
107_A 121_M 2.217 1.00
247_V 279_V 2.199 1.00
43_L 57_P 2.183 1.00
285_L 289_A 2.046 0.99
286_P 289_A 2.035 0.99
77_K 99_P 2.034 0.99
254_S 257_E 1.999 0.99
18_A 51_H 1.899 0.99
46_L 55_I 1.879 0.99
184_R 187_Q 1.839 0.98
181_D 356_G 1.816 0.98
110_C 173_S 1.812 0.98
206_A 217_L 1.807 0.98
15_L 19_V 1.779 0.98
216_C 251_M 1.77 0.98
177_P 181_D 1.767 0.98
239_V 244_L 1.738 0.97
169_E 172_A 1.734 0.97
184_R 188_M 1.731 0.97
128_V 158_Y 1.725 0.97
282_A 285_L 1.721 0.97
6_I 12_L 1.696 0.97
78_F 160_L 1.673 0.96
44_I 57_P 1.635 0.96
126_S 162_I 1.634 0.96
209_L 213_Q 1.63 0.96
179_A 183_C 1.607 0.95
42_G 140_L 1.573 0.94
16_C 65_P 1.563 0.94
255_L 273_K 1.545 0.94
310_I 334_I 1.536 0.93
69_I 75_I 1.52 0.93
154_A 157_W 1.511 0.93
25_I 46_L 1.505 0.93
236_N 241_E 1.502 0.92
146_E 150_E 1.501 0.92
203_I 217_L 1.498 0.92
33_R 87_E 1.493 0.92
124_E 169_E 1.477 0.92
72_D 77_K 1.463 0.91
27_L 79_L 1.462 0.91
167_M 176_L 1.435 0.90
274_T 278_L 1.434 0.90
318_S 328_L 1.407 0.89
65_P 68_A 1.407 0.89
282_A 286_P 1.406 0.89
12_L 55_I 1.402 0.89
202_D 241_E 1.381 0.88
72_D 99_P 1.377 0.87
219_L 222_D 1.364 0.87
285_L 290_L 1.357 0.86
54_L 149_C 1.353 0.86
73_P 98_Q 1.345 0.86
122_V 130_L 1.343 0.86
329_A 362_M 1.338 0.85
52_L 157_W 1.336 0.85
239_V 275_L 1.334 0.85
217_L 244_L 1.329 0.85
47_F 157_W 1.322 0.84
101_I 106_L 1.318 0.84
31_F 358_R 1.31 0.84
106_L 166_L 1.309 0.84
226_R 230_E 1.308 0.83
211_T 287_E 1.302 0.83
363_A 367_H 1.298 0.83
137_T 148_Q 1.279 0.82
278_L 282_A 1.276 0.81
7_T 11_A 1.274 0.81
9_D 61_T 1.27 0.81
176_L 180_L 1.263 0.80
31_F 148_Q 1.263 0.80
225_L 235_V 1.262 0.80
317_V 320_T 1.259 0.80
11_A 14_S 1.231 0.78
247_V 258_L 1.226 0.78
125_Y 169_E 1.225 0.78
215_A 291_P 1.224 0.77
171_E 176_L 1.224 0.77
25_I 69_I 1.215 0.77
47_F 52_L 1.212 0.76
31_F 104_Q 1.211 0.76
320_T 365_A 1.204 0.76
19_V 53_A 1.199 0.75
317_V 365_A 1.199 0.75
56_D 142_R 1.197 0.75
14_S 226_R 1.188 0.74
236_N 318_S 1.18 0.74
13_A 17_E 1.179 0.74
78_F 113_P 1.178 0.74
32_V 140_L 1.175 0.73
78_F 164_A 1.172 0.73
244_L 248_A 1.171 0.73
337_L 353_L 1.171 0.73
6_I 15_L 1.171 0.73
10_D 14_S 1.167 0.73
214_L 291_P 1.166 0.72
314_I 362_M 1.166 0.72
251_M 279_V 1.162 0.72
199_A 221_A 1.157 0.72
40_Q 232_D 1.156 0.72
134_E 153_A 1.151 0.71
84_E 136_R 1.151 0.71
145_T 148_Q 1.149 0.71
321_H 361_L 1.145 0.71
169_E 334_I 1.139 0.70
81_A 88_V 1.137 0.70
273_K 277_A 1.135 0.70
223_W 227_K 1.132 0.69
134_E 148_Q 1.126 0.69
72_D 98_Q 1.122 0.68
81_A 116_W 1.115 0.68
364_E 368_N 1.114 0.67
86_L 96_L 1.107 0.67
83_S 135_S 1.105 0.67
280_E 284_T 1.103 0.66
89_F 117_G 1.092 0.65
216_C 283_Q 1.087 0.65
18_A 44_I 1.086 0.65
227_K 230_E 1.076 0.64
23_P 74_S 1.071 0.63
54_L 134_E 1.069 0.63
119_A 131_D 1.066 0.62
182_E 290_L 1.062 0.62
29_T 117_G 1.062 0.62
125_Y 162_I 1.061 0.62
20_R 68_A 1.06 0.62
34_T 42_G 1.057 0.61
220_L 275_L 1.056 0.61
49_G 153_A 1.055 0.61
13_A 65_P 1.053 0.61
25_I 73_P 1.046 0.60
219_L 282_A 1.046 0.60
33_R 36_T 1.045 0.60
118_F 122_V 1.043 0.60
186_M 189_R 1.041 0.60
31_F 39_P 1.04 0.60
317_V 321_H 1.039 0.60
118_F 241_E 1.037 0.59
148_Q 358_R 1.035 0.59
107_A 166_L 1.034 0.59
8_T 257_E 1.034 0.59
213_Q 238_V 1.033 0.59
272_G 276_L 1.032 0.59
42_G 58_L 1.029 0.58
66_L 89_F 1.025 0.58
238_V 262_G 1.025 0.58
287_E 292_Q 1.02 0.57
314_I 318_S 1.01 0.56
33_R 38_Y 1.009 0.56
24_A 164_A 1.009 0.56
67_K 93_F 1.008 0.56
161_P 164_A 1.008 0.56
359_G 364_E 1.007 0.56
41_L 88_V 1.005 0.56
110_C 166_L 1.005 0.56
12_L 38_Y 1.005 0.56
123_E 127_G 1.001 0.55
12_L 60_I 1 0.55
188_M 257_E 1 0.55
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
1yt3A111000.347Contact Map0.618
3cymA10.9841000.414Contact Map0.614
2hbjA10.8241000.497Contact Map0.58
3safA20.81871000.523Contact Map0.643
1vk0A60.44271000.705Contact Map0.396
2e6mA10.4881000.712Contact Map0.506
3pv8A20.882799.90.779Contact Map0.47
2kfnA10.8499.90.785Contact Map0.56
1x9mA10.89699.60.851Contact Map0.275
1wudA30.234799.60.859Contact Map0.608
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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