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OPENSEQ.org
1kqf_B_C
Genes: A B A+B
Length: 294 217 487
Sequences: 436 1689 284
Seq/Len: 1.48 7.78 0.58
MirrorTree (Pazo et al. 2001) 0.93
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 0.00 0.00 0.54
2 0.00 0.00 0.55
5 0.00 0.01 0.55
10 0.00 0.01 0.55
20 0.01 0.01 0.56
100 0.01 0.04 0.57
∞ 0.09 0.13 0.64
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
276_Y 177_K 1.50 0.61 0.00
259_P 25_F 1.48 0.59 0.00
286_D 3_K 1.42 0.55 0.00
104_E 122_S 1.36 0.49 0.00
190_K 66_V 1.28 0.43 0.00
287_D 20_T 1.27 0.43 0.00
47_V 170_M 1.27 0.43 0.00
38_T 185_E 1.26 0.42 0.00
72_L 61_G 1.24 0.40 0.00
96_R 117_F 1.24 0.40 0.00
258_K 88_W 1.22 0.39 0.00
188_T 184_I 1.22 0.38 0.00
213_V 7_I 1.21 0.38 0.00
262_A 40_L 1.21 0.38 0.00
152_K 69_M 1.19 0.36 0.00
114_S 41_Q 1.18 0.36 0.00
131_E 173_A 1.18 0.36 0.00
22_Q 157_A 1.17 0.35 0.00
243_D 130_T 1.17 0.35 0.00
188_T 53_G 1.16 0.34 0.00
243_D 154_I 1.16 0.34 0.00
120_Q 163_I 1.15 0.33 0.00
140_I 106_V 1.13 0.32 0.00
197_E 180_I 1.12 0.32 0.00
63_V 23_I 1.11 0.31 0.00
288_D 194_K 1.10 0.30 0.00
275_H 88_W 1.10 0.30 0.00
140_I 122_S 1.10 0.30 0.00
264_G 198_P 1.08 0.29 0.00
37_S 42_W 1.07 0.28 0.00
54_D 132_V 1.07 0.28 0.00
277_I 134_I 1.05 0.27 0.00
9_I 28_V 1.05 0.27 0.00
178_T 170_M 1.05 0.27 0.00
1_M 148_V 1.05 0.27 0.00
13_A 49_T 1.04 0.26 0.00
38_T 104_A 1.03 0.26 0.00
101_M 180_I 1.03 0.26 0.00
266_I 41_Q 1.03 0.26 0.00
287_D 130_T 1.03 0.25 0.00
279_I 195_K 1.02 0.25 0.00
201_A 125_F 1.02 0.25 0.00
208_Y 146_Q 1.02 0.25 0.00
130_S 166_I 1.02 0.25 0.00
27_K 129_V 1.02 0.25 0.00
213_V 45_Q 1.01 0.25 0.00
6_Q 187_K 1.01 0.24 0.00
252_L 143_F 1.01 0.24 0.00
116_G 61_G 1.00 0.24 0.00
201_A 93_V 1.00 0.23 0.00
178_T 136_R 0.99 0.23 0.00
13_A 52_M 0.99 0.23 0.00
2_A 14_D 0.99 0.23 0.00
106_P 159_G 0.99 0.23 0.00
251_S 125_F 0.98 0.23 0.00
37_S 108_K 0.98 0.23 0.00
78_T 149_R 0.98 0.23 0.00
1_M 201_Y 0.98 0.23 0.00
152_K 203_E 0.98 0.22 0.00
76_S 130_T 0.98 0.22 0.00
1_M 14_D 0.97 0.22 0.00
130_S 164_H 0.97 0.22 0.00
130_S 24_C 0.97 0.22 0.00
152_K 141_Q 0.96 0.22 0.00
245_K 90_L 0.96 0.22 0.00
5_T 148_V 0.96 0.22 0.00
279_I 198_P 0.96 0.22 0.00
13_A 37_F 0.96 0.22 0.00
208_Y 194_K 0.95 0.21 0.00
134_I 112_G 0.95 0.21 0.00
195_L 53_G 0.95 0.21 0.00
129_Q 26_F 0.95 0.21 0.00
261_A 7_I 0.94 0.21 0.00
105_D 80_I 0.94 0.21 0.00
47_V 148_V 0.94 0.20 0.00
217_E 80_I 0.93 0.20 0.00
267_A 55_I 0.93 0.20 0.00
200_V 124_I 0.93 0.20 0.00
16_S 154_I 0.93 0.20 0.00
208_Y 147_V 0.92 0.20 0.00
146_N 80_I 0.92 0.20 0.00
260_L 129_V 0.92 0.19 0.00
270_A 106_V 0.91 0.19 0.00
257_L 97_K 0.91 0.19 0.00
122_A 203_E 0.91 0.19 0.00
32_K 192_W 0.91 0.19 0.00
37_S 123_M 0.91 0.19 0.00
46_Q 36_F 0.91 0.19 0.00
67_D 121_M 0.91 0.19 0.00
245_K 125_F 0.90 0.18 0.00
164_V 41_Q 0.90 0.18 0.00
115_A 41_Q 0.90 0.18 0.00
22_Q 130_T 0.90 0.18 0.00
1_M 136_R 0.90 0.18 0.00
65_V 208_E 0.90 0.18 0.00
70_A 79_N 0.90 0.18 0.00
176_V 129_V 0.90 0.18 0.00
268_T 22_V 0.89 0.18 0.00
23_V 69_M 0.89 0.18 0.00
79_V 40_L 0.89 0.18 0.00
201_A 129_V 0.89 0.18 0.00
122_A 66_V 0.89 0.18 0.00
128_F 38_P 0.89 0.18 0.00
172_E 179_S 0.89 0.18 0.00
156_R 12_F 0.88 0.17 0.00
165_D 54_R 0.88 0.17 0.00
184_I 124_I 0.88 0.17 0.00
10_K 29_A 0.88 0.17 0.00
13_A 53_G 0.88 0.17 0.00
194_E 133_I 0.87 0.17 0.00
12_S 168_I 0.87 0.17 0.00
265_F 120_I 0.87 0.17 0.00
40_I 61_G 0.87 0.17 0.00
277_I 194_K 0.87 0.17 0.00
149_R 113_Q 0.87 0.17 0.00
74_A 21_V 0.87 0.17 0.00
10_K 28_V 0.87 0.17 0.00
261_A 75_F 0.87 0.17 0.00
14_T 136_R 0.87 0.17 0.00
23_V 125_F 0.87 0.17 0.00
181_T 197_H 0.86 0.17 0.00
232_D 15_R 0.86 0.17 0.00
69_P 143_F 0.86 0.17 0.00
12_S 52_M 0.86 0.17 0.00
190_K 147_V 0.86 0.17 0.00
185_H 35_F 0.86 0.17 0.00
69_P 162_L 0.86 0.17 0.00
76_S 106_V 0.86 0.16 0.00
131_E 6_M 0.86 0.16 0.00
73_S 5_K 0.86 0.16 0.00
153_E 176_V 0.86 0.16 0.00
258_K 113_Q 0.85 0.16 0.00
63_V 204_I 0.85 0.16 0.00
257_L 37_F 0.85 0.16 0.00
2_A 28_V 0.85 0.16 0.00
125_I 118_W 0.85 0.16 0.00
89_G 45_Q 0.85 0.16 0.00
41_G 151_S 0.85 0.16 0.00
178_T 193_A 0.85 0.16 0.00
64_G 72_F 0.85 0.16 0.00
186_F 196_H 0.85 0.16 0.00
155_N 198_P 0.85 0.16 0.00
41_G 54_R 0.85 0.16 0.00
202_K 89_L 0.84 0.16 0.00
178_T 189_S 0.84 0.16 0.00
131_E 126_V 0.84 0.16 0.00
37_S 37_F 0.84 0.16 0.00
131_E 148_V 0.84 0.16 0.00
134_I 32_G 0.84 0.16 0.00
276_Y 205_E 0.84 0.16 0.00
259_P 64_I 0.84 0.16 0.00
242_K 208_E 0.84 0.15 0.00
242_K 23_I 0.83 0.15 0.00
252_L 40_L 0.83 0.15 0.00
93_W 135_W 0.83 0.15 0.00
73_S 94_E 0.83 0.15 0.00
227_V 103_V 0.83 0.15 0.00
289_E 132_V 0.82 0.15 0.00
267_A 87_P 0.82 0.15 0.00
278_G 59_F 0.82 0.15 0.00
152_K 144_P 0.82 0.15 0.00
97_K 149_R 0.82 0.15 0.00
270_A 151_S 0.82 0.15 0.00
150_L 130_T 0.82 0.15 0.00
23_V 77_H 0.82 0.15 0.00
130_S 87_P 0.82 0.15 0.00
254_K 25_F 0.82 0.15 0.00
239_G 93_V 0.82 0.15 0.00
208_Y 158_A 0.82 0.15 0.00
259_P 7_I 0.82 0.15 0.00
81_R 28_V 0.81 0.15 0.00
7_D 122_S 0.81 0.15 0.00
90_K 141_Q 0.81 0.15 0.00
54_D 56_L 0.81 0.15 0.00
197_E 99_N 0.81 0.15 0.00
89_G 122_S 0.81 0.15 0.00
239_G 102_K 0.81 0.15 0.00
57_D 134_I 0.81 0.14 0.00
196_A 63_A 0.81 0.14 0.00
146_N 122_S 0.81 0.14 0.00
99_G 117_F 0.81 0.14 0.00
200_V 84_K 0.81 0.14 0.00
235_E 23_I 0.81 0.14 0.00
2_A 126_V 0.81 0.14 0.00
49_C 57_H 0.81 0.14 0.00
49_C 131_G 0.81 0.14 0.00
49_C 155_H 0.81 0.14 0.00
49_C 169_H 0.81 0.14 0.00
49_C 186_G 0.81 0.14 0.00
108_C 57_H 0.81 0.14 0.00
108_C 131_G 0.81 0.14 0.00
108_C 155_H 0.81 0.14 0.00
108_C 169_H 0.81 0.14 0.00
108_C 186_G 0.81 0.14 0.00
112_C 57_H 0.81 0.14 0.00
112_C 131_G 0.81 0.14 0.00
112_C 155_H 0.81 0.14 0.00
112_C 169_H 0.81 0.14 0.00
112_C 186_G 0.81 0.14 0.00
133_C 57_H 0.81 0.14 0.00
133_C 131_G 0.81 0.14 0.00
133_C 155_H 0.81 0.14 0.00
133_C 169_H 0.81 0.14 0.00
133_C 186_G 0.81 0.14 0.00
139_C 57_H 0.81 0.14 0.00
139_C 131_G 0.81 0.14 0.00
139_C 155_H 0.81 0.14 0.00
139_C 169_H 0.81 0.14 0.00
139_C 186_G 0.81 0.14 0.00
143_C 57_H 0.81 0.14 0.00
143_C 131_G 0.81 0.14 0.00
143_C 155_H 0.81 0.14 0.00
143_C 169_H 0.81 0.14 0.00
143_C 186_G 0.81 0.14 0.00
179_C 57_H 0.81 0.14 0.00
179_C 131_G 0.81 0.14 0.00
179_C 155_H 0.81 0.14 0.00
179_C 169_H 0.81 0.14 0.00
179_C 186_G 0.81 0.14 0.00
203_L 36_F 0.81 0.14 0.00
267_A 93_V 0.81 0.14 0.00
105_D 29_A 0.81 0.14 0.00
63_V 111_A 0.81 0.14 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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