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OPENSEQ.org
11134
Genes: A B A+B
Length: 298 236 512
Sequences: 1211 7334 71
Seq/Len: 4.06 31.08 0.14
MirrorTree (Pazo et al. 2001) 0.46
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 0.04 0.01 0.05
2 0.05 0.01 0.08
5 0.06 0.01 0.09
10 0.07 0.01 0.11
20 0.07 0.02 0.13
100 0.09 0.05 0.23
∞ 0.17 0.19 0.51
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
160_E 68_T 1.62 0.30 0.00
247_A 175_F 1.30 0.18 0.00
231_S 77_S 1.24 0.16 0.00
156_Q 104_V 1.21 0.15 0.00
87_A 35_L 1.17 0.14 0.00
282_R 193_L 1.16 0.14 0.00
210_D 118_D 1.16 0.14 0.00
210_D 141_T 1.15 0.14 0.00
280_L 221_L 1.15 0.14 0.00
141_D 49_S 1.15 0.13 0.00
12_D 75_S 1.13 0.13 0.00
243_S 137_I 1.13 0.13 0.00
211_Y 120_Y 1.13 0.13 0.00
236_F 158_V 1.12 0.13 0.00
108_S 91_E 1.11 0.13 0.00
280_L 119_L 1.11 0.13 0.00
71_L 88_A 1.11 0.13 0.00
245_D 88_A 1.11 0.12 0.00
297_W 203_S 1.10 0.12 0.00
165_R 115_Q 1.10 0.12 0.00
210_D 115_Q 1.10 0.12 0.00
295_H 183_N 1.10 0.12 0.00
217_E 115_Q 1.09 0.12 0.00
186_I 40_S 1.09 0.12 0.00
6_R 142_G 1.09 0.12 0.00
185_S 182_M 1.08 0.12 0.00
134_K 182_M 1.08 0.12 0.00
3_L 145_F 1.07 0.12 0.00
122_L 56_E 1.07 0.12 0.00
210_D 63_R 1.07 0.12 0.00
65_Y 56_E 1.06 0.12 0.00
168_N 177_I 1.06 0.11 0.00
210_D 179_D 1.05 0.11 0.00
53_P 50_L 1.05 0.11 0.00
53_P 53_D 1.05 0.11 0.00
53_P 54_D 1.05 0.11 0.00
53_P 57_D 1.05 0.11 0.00
53_P 62_R 1.05 0.11 0.00
53_P 114_G 1.05 0.11 0.00
53_P 180_D 1.05 0.11 0.00
297_W 88_A 1.05 0.11 0.00
71_L 72_F 1.05 0.11 0.00
192_A 21_I 1.05 0.11 0.00
78_E 105_L 1.04 0.11 0.00
265_R 106_E 1.04 0.11 0.00
277_S 194_C 1.03 0.11 0.00
81_S 167_L 1.03 0.11 0.00
72_I 142_G 1.03 0.11 0.00
215_E 68_T 1.03 0.11 0.00
94_A 72_F 1.03 0.11 0.00
51_I 137_I 1.03 0.11 0.00
245_D 181_Y 1.03 0.11 0.00
55_A 44_T 1.02 0.11 0.00
164_Y 21_I 1.02 0.11 0.00
236_F 142_G 1.02 0.10 0.00
48_S 66_P 1.01 0.10 0.00
157_T 88_A 1.01 0.10 0.00
155_A 93_A 1.00 0.10 0.00
45_G 150_R 1.00 0.10 0.00
165_R 196_D 1.00 0.10 0.00
294_N 119_L 1.00 0.10 0.00
185_S 198_D 0.99 0.10 0.00
165_R 191_K 0.99 0.10 0.00
214_W 64_G 0.99 0.10 0.00
32_G 101_L 0.99 0.10 0.00
217_E 50_L 0.99 0.10 0.00
217_E 53_D 0.99 0.10 0.00
217_E 54_D 0.99 0.10 0.00
217_E 57_D 0.99 0.10 0.00
217_E 62_R 0.99 0.10 0.00
217_E 114_G 0.99 0.10 0.00
217_E 180_D 0.99 0.10 0.00
209_N 63_R 0.99 0.10 0.00
128_D 152_M 0.98 0.10 0.00
293_G 43_N 0.98 0.10 0.00
280_L 186_D 0.98 0.10 0.00
216_R 59_S 0.97 0.10 0.00
298_C 137_I 0.97 0.10 0.00
247_A 196_D 0.96 0.10 0.00
90_G 61_L 0.96 0.09 0.00
197_I 55_L 0.96 0.09 0.00
74_D 50_L 0.96 0.09 0.00
74_D 53_D 0.96 0.09 0.00
74_D 54_D 0.96 0.09 0.00
74_D 57_D 0.96 0.09 0.00
74_D 62_R 0.96 0.09 0.00
74_D 114_G 0.96 0.09 0.00
74_D 180_D 0.96 0.09 0.00
209_N 66_P 0.95 0.09 0.00
247_A 50_L 0.95 0.09 0.00
247_A 53_D 0.95 0.09 0.00
247_A 54_D 0.95 0.09 0.00
247_A 57_D 0.95 0.09 0.00
247_A 62_R 0.95 0.09 0.00
247_A 114_G 0.95 0.09 0.00
247_A 180_D 0.95 0.09 0.00
211_Y 142_G 0.95 0.09 0.00
247_A 179_D 0.95 0.09 0.00
186_I 175_F 0.95 0.09 0.00
287_A 22_E 0.95 0.09 0.00
216_R 55_L 0.95 0.09 0.00
183_G 175_F 0.95 0.09 0.00
185_S 40_S 0.95 0.09 0.00
9_P 56_E 0.95 0.09 0.00
247_A 66_P 0.95 0.09 0.00
279_K 194_C 0.94 0.09 0.00
188_E 78_I 0.94 0.09 0.00
140_R 130_E 0.94 0.09 0.00
190_E 213_H 0.94 0.09 0.00
200_A 130_E 0.93 0.09 0.00
188_E 86_V 0.93 0.09 0.00
269_L 212_N 0.93 0.09 0.00
72_I 20_L 0.93 0.09 0.00
243_S 171_F 0.92 0.09 0.00
213_S 50_L 0.92 0.09 0.00
213_S 53_D 0.92 0.09 0.00
213_S 54_D 0.92 0.09 0.00
213_S 57_D 0.92 0.09 0.00
213_S 62_R 0.92 0.09 0.00
213_S 114_G 0.92 0.09 0.00
213_S 180_D 0.92 0.09 0.00
268_D 183_N 0.92 0.09 0.00
53_P 64_G 0.90 0.08 0.00
144_L 119_L 0.90 0.08 0.00
211_Y 170_L 0.90 0.08 0.00
131_L 152_M 0.90 0.08 0.00
251_V 203_S 0.90 0.08 0.00
184_M 188_T 0.89 0.08 0.00
12_D 157_E 0.89 0.08 0.00
210_D 50_L 0.89 0.08 0.00
210_D 53_D 0.89 0.08 0.00
210_D 54_D 0.89 0.08 0.00
210_D 57_D 0.89 0.08 0.00
210_D 62_R 0.89 0.08 0.00
210_D 114_G 0.89 0.08 0.00
210_D 180_D 0.89 0.08 0.00
4_P 92_V 0.88 0.08 0.00
91_E 145_F 0.88 0.08 0.00
6_R 88_A 0.88 0.08 0.00
60_L 148_L 0.88 0.08 0.00
238_R 75_S 0.88 0.08 0.00
209_N 50_L 0.88 0.08 0.00
209_N 53_D 0.88 0.08 0.00
209_N 54_D 0.88 0.08 0.00
209_N 57_D 0.88 0.08 0.00
209_N 62_R 0.88 0.08 0.00
209_N 114_G 0.88 0.08 0.00
209_N 180_D 0.88 0.08 0.00
23_Q 181_Y 0.87 0.08 0.00
160_E 80_A 0.87 0.08 0.00
170_G 217_R 0.87 0.08 0.00
261_D 78_I 0.87 0.08 0.00
53_P 172_G 0.87 0.08 0.00
105_A 154_A 0.87 0.08 0.00
179_Q 168_T 0.87 0.08 0.00
261_D 203_S 0.87 0.08 0.00
108_S 35_L 0.87 0.08 0.00
265_R 86_V 0.86 0.08 0.00
47_W 108_L 0.86 0.08 0.00
92_L 173_R 0.86 0.08 0.00
178_L 105_L 0.86 0.08 0.00
116_L 224_F 0.86 0.08 0.00
136_L 36_D 0.85 0.08 0.00
247_A 59_S 0.85 0.08 0.00
291_V 131_A 0.85 0.08 0.00
192_A 224_F 0.85 0.08 0.00
210_D 191_K 0.85 0.07 0.00
135_M 63_R 0.85 0.07 0.00
188_E 137_I 0.85 0.07 0.00
6_R 132_E 0.85 0.07 0.00
49_S 55_L 0.85 0.07 0.00
57_P 67_S 0.84 0.07 0.00
4_P 93_A 0.84 0.07 0.00
188_E 68_T 0.84 0.07 0.00
16_A 70_I 0.84 0.07 0.00
262_F 202_F 0.84 0.07 0.00
270_Y 103_A 0.84 0.07 0.00
50_L 68_T 0.84 0.07 0.00
287_A 85_F 0.84 0.07 0.00
242_L 36_D 0.84 0.07 0.00
251_V 28_L 0.83 0.07 0.00
30_R 151_I 0.83 0.07 0.00
255_I 64_G 0.83 0.07 0.00
8_H 213_H 0.83 0.07 0.00
53_P 140_K 0.83 0.07 0.00
53_P 176_Q 0.83 0.07 0.00
3_L 151_I 0.83 0.07 0.00
184_M 193_L 0.83 0.07 0.00
291_V 108_L 0.83 0.07 0.00
153_K 190_Q 0.83 0.07 0.00
210_D 201_K 0.83 0.07 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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