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OPENSEQ.org
HscBIscS
Genes: A B A+B
Length: 171 404 574
Sequences: 831 9826 316
Seq/Len: 4.86 24.32 0.55
MirrorTree (Pazo et al. 2001) 0.65
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.05 0.01
2 0.00 0.06 0.03
5 0.00 0.08 0.55
10 0.00 0.08 0.56
20 0.00 0.09 0.56
100 0.00 0.13 0.58
∞ 0.00 0.18 0.69
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
153_F 162_D 1.35 0.47 0.00
24_F 26_F 1.35 0.47 0.00
45_L 377_I 1.34 0.47 0.00
165_E 174_G 1.32 0.45 0.00
152_R 71_F 1.32 0.45 0.00
152_R 383_L 1.29 0.43 0.00
132_M 102_T 1.25 0.40 0.00
72_L 28_T 1.25 0.39 0.00
25_Q 360_F 1.24 0.39 0.00
69_E 58_I 1.19 0.35 0.00
69_E 71_F 1.18 0.34 0.00
157_L 28_T 1.16 0.33 0.00
72_L 20_A 1.13 0.31 0.00
48_V 366_I 1.10 0.29 0.00
153_F 247_H 1.08 0.28 0.00
135_Q 360_F 1.08 0.28 0.00
114_L 383_L 1.07 0.27 0.00
45_L 71_F 1.06 0.27 0.00
132_M 161_Q 1.05 0.26 0.00
132_M 133_D 1.03 0.25 0.00
51_S 399_I 1.03 0.25 0.00
156_K 7_L 1.03 0.24 0.00
44_Q 383_L 1.03 0.24 0.00
145_A 377_I 1.02 0.24 0.00
2_D 67_R 1.02 0.24 0.00
52_A 376_S 1.00 0.23 0.00
88_D 70_V 1.00 0.23 0.00
153_F 248_Q 0.99 0.22 0.00
22_L 79_D 0.98 0.22 0.00
108_A 292_D 0.97 0.21 0.00
26_D 226_I 0.95 0.20 0.00
78_D 230_M 0.95 0.20 0.00
51_S 274_R 0.95 0.20 0.00
25_Q 230_M 0.94 0.20 0.00
29_R 270_L 0.94 0.20 0.00
88_D 111_C 0.94 0.20 0.00
136_L 161_Q 0.94 0.20 0.00
146_D 98_I 0.93 0.19 0.00
28_Q 79_D 0.93 0.19 0.00
35_K 126_P 0.93 0.19 0.00
35_K 226_I 0.93 0.19 0.00
100_E 332_S 0.93 0.19 0.00
148_V 230_M 0.93 0.19 0.00
8_G 133_D 0.92 0.18 0.00
47_A 116_R 0.91 0.18 0.00
58_W 62_V 0.90 0.18 0.00
136_L 102_T 0.90 0.18 0.00
57_A 30_D 0.90 0.18 0.00
56_Q 71_F 0.90 0.18 0.00
60_T 24_M 0.90 0.18 0.00
56_Q 58_I 0.90 0.18 0.00
157_L 21_E 0.90 0.18 0.00
156_K 67_R 0.89 0.17 0.00
41_Q 226_I 0.89 0.17 0.00
74_L 394_V 0.89 0.17 0.00
160_S 70_V 0.89 0.17 0.00
13_Y 398_S 0.89 0.17 0.00
82_E 365_E 0.89 0.17 0.00
21_S 184_S 0.89 0.17 0.00
63_H 284_I 0.88 0.17 0.00
72_L 31_G 0.88 0.17 0.00
58_W 79_D 0.88 0.17 0.00
164_L 58_I 0.88 0.17 0.00
94_E 357_L 0.88 0.17 0.00
105_I 224_V 0.87 0.17 0.00
103_D 320_L 0.87 0.17 0.00
9_L 366_I 0.87 0.17 0.00
21_S 1_M 0.86 0.16 0.00
157_L 43_F 0.86 0.16 0.00
88_D 143_D 0.86 0.16 0.00
141_W 79_D 0.86 0.16 0.00
133_V 369_T 0.86 0.16 0.00
58_W 43_F 0.85 0.16 0.00
62_R 3_L 0.85 0.16 0.00
44_Q 353_I 0.85 0.15 0.00
153_F 10_S 0.85 0.15 0.00
44_Q 200_M 0.84 0.15 0.00
91_F 162_D 0.84 0.15 0.00
51_S 239_M 0.84 0.15 0.00
166_E 370_I 0.84 0.15 0.00
56_Q 52_D 0.83 0.15 0.00
157_L 179_V 0.83 0.15 0.00
110_D 93_K 0.83 0.15 0.00
88_D 31_G 0.83 0.15 0.00
13_Y 101_K 0.83 0.15 0.00
24_F 377_I 0.83 0.15 0.00
72_L 377_I 0.82 0.14 0.00
72_L 356_S 0.82 0.14 0.00
54_I 366_I 0.82 0.14 0.00
28_Q 361_T 0.82 0.14 0.00
49_Q 281_I 0.82 0.14 0.00
131_L 213_I 0.82 0.14 0.00
170_D 60_D 0.82 0.14 0.00
157_L 267_M 0.82 0.14 0.00
44_Q 175_I 0.82 0.14 0.00
47_A 306_N 0.81 0.14 0.00
58_W 320_L 0.81 0.14 0.00
149_R 229_Q 0.80 0.14 0.00
5_T 165_A 0.80 0.14 0.00
121_V 62_V 0.80 0.14 0.00
105_I 317_L 0.80 0.14 0.00
24_F 266_E 0.80 0.14 0.00
169_L 71_F 0.80 0.14 0.00
58_W 185_V 0.80 0.14 0.00
109_K 297_A 0.80 0.14 0.00
14_Q 379_R 0.80 0.14 0.00
69_E 52_D 0.79 0.13 0.00
123_K 175_I 0.79 0.13 0.00
148_V 285_E 0.79 0.13 0.00
50_Q 174_G 0.79 0.13 0.00
161_A 377_I 0.79 0.13 0.00
149_R 230_M 0.79 0.13 0.00
75_H 292_D 0.78 0.13 0.00
19_A 163_I 0.78 0.13 0.00
28_Q 387_W 0.78 0.13 0.00
36_F 116_R 0.78 0.13 0.00
136_L 132_I 0.78 0.13 0.00
151_L 71_F 0.78 0.13 0.00
157_L 147_L 0.78 0.13 0.00
44_Q 56_N 0.78 0.13 0.00
136_L 67_R 0.77 0.13 0.00
41_Q 191_D 0.77 0.13 0.00
78_D 316_A 0.77 0.13 0.00
46_A 97_I 0.77 0.13 0.00
71_L 402_A 0.77 0.13 0.00
43_E 286_E 0.77 0.13 0.00
2_D 133_D 0.77 0.12 0.00
64_P 17_P 0.77 0.12 0.00
62_R 197_V 0.77 0.12 0.00
15_L 98_I 0.77 0.12 0.00
83_Q 173_R 0.77 0.12 0.00
157_L 203_S 0.77 0.12 0.00
152_R 31_G 0.77 0.12 0.00
27_L 70_V 0.77 0.12 0.00
72_L 43_F 0.77 0.12 0.00
50_Q 52_D 0.77 0.12 0.00
73_S 379_R 0.76 0.12 0.00
98_L 97_I 0.76 0.12 0.00
74_L 70_V 0.76 0.12 0.00
48_V 190_I 0.76 0.12 0.00
117_F 169_M 0.76 0.12 0.00
95_Q 247_H 0.76 0.12 0.00
105_I 25_Q 0.75 0.12 0.00
7_F 285_E 0.75 0.12 0.00
132_M 159_V 0.75 0.12 0.00
121_V 22_K 0.75 0.12 0.00
129_H 298_P 0.75 0.12 0.00
106_E 394_V 0.75 0.12 0.00
63_H 307_Y 0.75 0.12 0.00
56_Q 46_Q 0.74 0.12 0.00
126_D 320_L 0.74 0.12 0.00
88_D 117_E 0.74 0.12 0.00
1_M 383_L 0.74 0.12 0.00
102_L 143_D 0.74 0.12 0.00
133_V 303_V 0.74 0.12 0.00
94_E 284_I 0.74 0.12 0.00
103_D 93_K 0.74 0.12 0.00
25_Q 320_L 0.74 0.12 0.00
50_Q 184_S 0.74 0.12 0.00
121_V 128_R 0.74 0.12 0.00
28_Q 239_M 0.74 0.12 0.00
160_S 345_N 0.74 0.12 0.00
95_Q 159_V 0.74 0.11 0.00
15_L 24_M 0.73 0.11 0.00
101_E 373_V 0.73 0.11 0.00
88_D 152_H 0.73 0.11 0.00
43_E 390_Y 0.73 0.11 0.00
157_L 31_G 0.73 0.11 0.00
3_Y 182_T 0.73 0.11 0.00
24_F 56_N 0.73 0.11 0.00
49_Q 125_A 0.73 0.11 0.00
47_A 21_E 0.73 0.11 0.00
95_Q 248_Q 0.73 0.11 0.00
97_E 391_K 0.73 0.11 0.00
44_Q 316_A 0.73 0.11 0.00
29_R 230_M 0.72 0.11 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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