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2OZA_BA

Genes: A B A+B
Length: 366 356 637
Sequences: 5719 2849 72
Seq/Len: 15.63 8 0.11
MirrorTree (Pazo et al. 2001) 0.22
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.

Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.05 0.02 0.01
2 0.05 0.02 0.01
5 0.06 0.03 0.03
10 0.07 0.03 0.05
20 0.08 0.04 0.10
100 0.18 0.06 0.35
0.26 0.14 0.70
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!

GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution.
Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
269_A 138_I 1.34 0.17 0.00
144_L 196_Y 1.33 0.16 0.00
290_L 71_P 1.26 0.14 0.00
289_D 256_M 1.23 0.14 0.00
214_S 181_Y 1.21 0.13 0.00
85_K 161_L 1.20 0.13 0.00
304_T 93_V 1.18 0.12 0.00
314_F 73_I 1.18 0.12 0.00
178_A 210_Y 1.17 0.12 0.00
222_L 143_V 1.17 0.12 0.00
304_T 26_L 1.14 0.12 0.00
311_H 102_L 1.13 0.12 0.00
56_V 116_E 1.13 0.12 0.00
199_I 126_I 1.13 0.11 0.00
244_L 15_I 1.13 0.11 0.00
128_L 106_I 1.13 0.11 0.00
26_V 260_N 1.12 0.11 0.00
31_Q 196_Y 1.12 0.11 0.00
123_V 254_V 1.11 0.11 0.00
219_M 40_K 1.11 0.11 0.00
285_P 270_M 1.11 0.11 0.00
170_L 255_K 1.10 0.11 0.00
56_V 251_S 1.08 0.10 0.00
152_I 98_D 1.08 0.10 0.00
178_A 70_C 1.07 0.10 0.00
297_L 176_L 1.07 0.10 0.00
309_L 185_Y 1.07 0.10 0.00
191_T 130_I 1.06 0.10 0.00
42_G 133_L 1.05 0.10 0.00
276_F 138_I 1.05 0.10 0.00
304_T 138_I 1.05 0.10 0.00
81_L 235_I 1.05 0.10 0.00
206_Y 215_G 1.04 0.10 0.00
199_I 25_V 1.04 0.10 0.00
108_V 208_I 1.03 0.10 0.00
265_I 61_V 1.03 0.10 0.00
209_T 94_M 1.03 0.10 0.00
314_F 185_Y 1.02 0.09 0.00
162_L 196_Y 1.02 0.09 0.00
291_L 115_T 1.01 0.09 0.00
58_V 47_A 1.00 0.09 0.00
220_A 114_F 1.00 0.09 0.00
90_I 73_I 1.00 0.09 0.00
63_R 159_L 1.00 0.09 0.00
81_L 138_I 0.99 0.09 0.00
207_N 223_H 0.99 0.09 0.00
305_A 118_E 0.99 0.09 0.00
240_L 186_V 0.99 0.09 0.00
295_L 32_G 0.99 0.09 0.00
78_L 106_I 0.99 0.09 0.00
275_N 122_I 0.99 0.09 0.00
197_P 29_G 0.99 0.09 0.00
304_T 22_T 0.98 0.09 0.00
247_T 260_N 0.98 0.09 0.00
42_G 90_L 0.96 0.08 0.00
82_K 64_H 0.96 0.08 0.00
209_T 129_A 0.96 0.08 0.00
298_D 26_L 0.95 0.08 0.00
143_G 271_T 0.95 0.08 0.00
198_E 163_D 0.95 0.08 0.00
89_V 260_N 0.94 0.08 0.00
144_L 32_G 0.94 0.08 0.00
93_L 42_T 0.94 0.08 0.00
175_F 160_K 0.94 0.08 0.00
90_I 101_E 0.94 0.08 0.00
294_M 129_A 0.93 0.08 0.00
134_Q 190_V 0.93 0.08 0.00
31_Q 39_N 0.93 0.08 0.00
137_I 161_L 0.92 0.08 0.00
113_H 47_A 0.92 0.08 0.00
305_A 197_D 0.92 0.08 0.00
128_L 162_T 0.91 0.08 0.00
58_V 48_L 0.91 0.08 0.00
246_G 269_R 0.91 0.08 0.00
294_M 71_P 0.91 0.07 0.00
47_A 251_S 0.91 0.07 0.00
191_T 281_I 0.90 0.07 0.00
313_Y 45_K 0.90 0.07 0.00
30_Y 129_A 0.90 0.07 0.00
207_N 260_N 0.90 0.07 0.00
58_V 193_P 0.90 0.07 0.00
42_G 149_L 0.90 0.07 0.00
140_I 71_P 0.90 0.07 0.00
244_L 105_R 0.89 0.07 0.00
44_V 262_L 0.89 0.07 0.00
144_L 219_F 0.89 0.07 0.00
191_T 106_I 0.89 0.07 0.00
59_K 218_P 0.89 0.07 0.00
174_D 218_P 0.89 0.07 0.00
57_A 134_H 0.88 0.07 0.00
58_V 96_C 0.88 0.07 0.00
77_E 188_P 0.88 0.07 0.00
77_E 189_E 0.88 0.07 0.00
77_E 201_D 0.88 0.07 0.00
77_E 206_G 0.88 0.07 0.00
158_K 188_P 0.88 0.07 0.00
158_K 189_E 0.88 0.07 0.00
158_K 201_D 0.88 0.07 0.00
158_K 206_G 0.88 0.07 0.00
161_N 188_P 0.88 0.07 0.00
161_N 189_E 0.88 0.07 0.00
161_N 201_D 0.88 0.07 0.00
161_N 206_G 0.88 0.07 0.00
176_G 188_P 0.88 0.07 0.00
176_G 189_E 0.88 0.07 0.00
176_G 201_D 0.88 0.07 0.00
176_G 206_G 0.88 0.07 0.00
211_D 188_P 0.88 0.07 0.00
211_D 189_E 0.88 0.07 0.00
211_D 201_D 0.88 0.07 0.00
211_D 206_G 0.88 0.07 0.00
213_W 188_P 0.88 0.07 0.00
213_W 189_E 0.88 0.07 0.00
213_W 201_D 0.88 0.07 0.00
213_W 206_G 0.88 0.07 0.00
245_V 280_W 0.88 0.07 0.00
197_P 142_D 0.88 0.07 0.00
78_L 57_A 0.88 0.07 0.00
44_V 219_F 0.88 0.07 0.00
314_F 244_N 0.88 0.07 0.00
164_V 79_V 0.88 0.07 0.00
276_F 143_V 0.87 0.07 0.00
157_L 239_Q 0.87 0.07 0.00
113_H 234_R 0.87 0.07 0.00
42_G 162_T 0.87 0.07 0.00
170_L 261_L 0.87 0.07 0.00
224_T 240_Y 0.87 0.07 0.00
219_M 268_Q 0.86 0.07 0.00
285_P 243_P 0.86 0.07 0.00
155_R 70_C 0.86 0.07 0.00
314_F 129_A 0.86 0.07 0.00
216_G 29_G 0.86 0.07 0.00
299_S 147_N 0.86 0.07 0.00
196_A 76_I 0.85 0.07 0.00
304_T 185_Y 0.85 0.07 0.00
61_L 91_L 0.85 0.07 0.00
49_D 251_S 0.85 0.07 0.00
108_V 176_L 0.85 0.07 0.00
313_Y 167_A 0.85 0.07 0.00
36_V 132_Y 0.85 0.07 0.00
303_I 32_G 0.84 0.07 0.00
196_A 252_E 0.84 0.07 0.00
280_F 130_I 0.84 0.07 0.00
266_Q 213_L 0.84 0.07 0.00
175_F 134_H 0.84 0.07 0.00
200_M 126_I 0.84 0.07 0.00
43_S 119_A 0.84 0.07 0.00
190_A 197_D 0.84 0.07 0.00
198_E 147_N 0.84 0.07 0.00
140_I 278_H 0.84 0.07 0.00
295_L 161_L 0.83 0.07 0.00
210_V 38_F 0.83 0.07 0.00
234_H 130_I 0.83 0.07 0.00
297_L 167_A 0.83 0.07 0.00
94_D 196_Y 0.83 0.07 0.00
307_Q 55_P 0.83 0.07 0.00
294_M 92_I 0.83 0.07 0.00
138_Y 137_N 0.83 0.07 0.00
219_M 251_S 0.82 0.06 0.00
85_K 137_N 0.82 0.06 0.00
244_L 252_E 0.82 0.06 0.00
245_V 149_L 0.82 0.06 0.00
201_L 60_E 0.82 0.06 0.00
40_A 255_K 0.82 0.06 0.00
245_V 92_I 0.82 0.06 0.00
164_V 256_M 0.82 0.06 0.00
191_T 62_E 0.82 0.06 0.00
238_L 72_H 0.82 0.06 0.00
222_L 88_K 0.81 0.06 0.00
32_N 210_Y 0.81 0.06 0.00
115_M 283_Q 0.81 0.06 0.00
36_V 209_M 0.81 0.06 0.00
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)

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