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OPENSEQ.org
dltc-dltd_bs
Genes: A B A+B
Length: 78 392 432
Sequences: 190 295 229
Seq/Len: 2.44 0.75 0.53
MirrorTree (Pazo et al. 2001) 0.79
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 0.08 0.00 0.45
2 0.08 0.00 0.46
5 0.08 0.01 0.49
10 0.08 0.01 0.49
20 0.08 0.01 0.49
100 0.08 0.02 0.49
∞ 0.09 0.05 0.50
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
50_F 334_Y 1.51 0.59 0.00
14_V 245_K 1.34 0.46 0.00
30_E 338_V 1.34 0.46 0.00
52_I 251_G 1.29 0.42 0.00
58_E 383_F 1.28 0.41 0.00
70_I 338_V 1.27 0.40 0.00
30_E 259_D 1.26 0.40 0.00
3_F 307_A 1.25 0.38 0.00
34_L 346_G 1.21 0.36 0.00
71_V 257_S 1.21 0.36 0.00
52_I 239_S 1.17 0.33 0.00
56_I 84_F 1.16 0.32 0.00
50_F 300_D 1.16 0.32 0.00
64_W 100_G 1.15 0.32 0.00
50_F 48_F 1.15 0.31 0.00
44_L 352_F 1.14 0.31 0.00
78_K 118_K 1.12 0.30 0.00
38_G 384_Y 1.12 0.29 0.00
37_F 108_L 1.12 0.29 0.00
64_W 65_P 1.11 0.29 0.00
51_D 275_P 1.10 0.28 0.00
44_L 208_Y 1.10 0.28 0.00
50_F 331_R 1.08 0.27 0.00
70_I 128_P 1.08 0.27 0.00
43_L 376_V 1.08 0.27 0.00
57_T 363_K 1.07 0.26 0.00
64_W 311_F 1.07 0.26 0.00
17_D 331_R 1.06 0.26 0.00
74_L 64_L 1.06 0.26 0.00
29_F 129_Q 1.06 0.26 0.00
74_L 166_K 1.05 0.25 0.00
50_F 335_Y 1.05 0.25 0.00
28_I 267_Y 1.05 0.25 0.00
62_D 271_K 1.05 0.25 0.00
11_L 50_G 1.05 0.25 0.00
41_E 331_R 1.04 0.25 0.00
51_D 137_D 1.04 0.25 0.00
25_D 352_F 1.04 0.25 0.00
40_V 40_A 1.02 0.24 0.00
10_V 211_M 1.02 0.24 0.00
43_L 238_K 1.01 0.23 0.00
32_G 370_W 1.00 0.23 0.00
13_E 292_Y 1.00 0.23 0.00
57_T 309_P 1.00 0.22 0.00
5_Q 53_L 1.00 0.22 0.00
9_D 355_H 0.99 0.22 0.00
51_D 213_E 0.99 0.22 0.00
31_E 138_E 0.99 0.22 0.00
15_C 91_F 0.99 0.22 0.00
64_W 95_L 0.98 0.21 0.00
58_E 103_S 0.97 0.21 0.00
56_I 166_K 0.97 0.21 0.00
42_L 359_P 0.97 0.21 0.00
7_V 322_D 0.97 0.21 0.00
62_D 256_G 0.97 0.21 0.00
47_E 175_K 0.96 0.20 0.00
27_E 296_E 0.96 0.20 0.00
30_E 211_M 0.95 0.20 0.00
57_T 123_V 0.95 0.20 0.00
62_D 295_F 0.94 0.20 0.00
9_D 283_G 0.94 0.20 0.00
54_V 106_H 0.94 0.19 0.00
63_V 374_V 0.94 0.19 0.00
68_N 292_Y 0.94 0.19 0.00
62_D 386_T 0.94 0.19 0.00
74_L 54_Q 0.94 0.19 0.00
30_E 385_K 0.94 0.19 0.00
38_G 211_M 0.94 0.19 0.00
70_I 295_F 0.94 0.19 0.00
11_L 212_L 0.93 0.19 0.00
46_I 54_Q 0.93 0.19 0.00
31_E 353_S 0.93 0.19 0.00
78_K 261_H 0.93 0.19 0.00
27_E 32_T 0.93 0.19 0.00
20_V 308_E 0.93 0.19 0.00
71_V 190_M 0.92 0.18 0.00
57_T 383_F 0.92 0.18 0.00
42_L 128_P 0.92 0.18 0.00
25_D 304_D 0.92 0.18 0.00
43_L 63_Y 0.92 0.18 0.00
10_V 279_G 0.92 0.18 0.00
65_N 339_N 0.91 0.18 0.00
20_V 115_D 0.91 0.18 0.00
68_N 332_T 0.91 0.18 0.00
56_I 74_R 0.90 0.18 0.00
63_V 203_P 0.90 0.18 0.00
67_P 124_F 0.90 0.17 0.00
45_A 312_V 0.90 0.17 0.00
64_W 302_L 0.90 0.17 0.00
50_F 143_P 0.90 0.17 0.00
7_V 283_G 0.89 0.17 0.00
64_W 171_M 0.89 0.17 0.00
37_F 111_A 0.89 0.17 0.00
32_G 369_G 0.89 0.17 0.00
14_V 167_M 0.89 0.17 0.00
28_I 346_G 0.89 0.17 0.00
67_P 146_S 0.89 0.17 0.00
49_R 306_G 0.88 0.17 0.00
72_N 42_A 0.88 0.17 0.00
62_D 236_K 0.88 0.16 0.00
44_L 350_A 0.88 0.16 0.00
14_V 165_K 0.88 0.16 0.00
14_V 193_G 0.87 0.16 0.00
34_L 273_K 0.87 0.16 0.00
59_F 74_R 0.87 0.16 0.00
50_F 98_K 0.87 0.16 0.00
53_L 352_F 0.87 0.16 0.00
47_E 143_P 0.86 0.16 0.00
9_D 343_R 0.86 0.16 0.00
7_V 201_L 0.85 0.15 0.00
9_D 194_Q 0.85 0.15 0.00
16_Q 326_F 0.85 0.15 0.00
58_E 140_H 0.85 0.15 0.00
47_E 214_K 0.85 0.15 0.00
33_L 267_Y 0.85 0.15 0.00
20_V 125_I 0.85 0.15 0.00
44_L 147_A 0.84 0.15 0.00
42_L 271_K 0.84 0.15 0.00
71_V 145_Y 0.84 0.15 0.00
55_P 74_R 0.84 0.15 0.00
19_I 368_I 0.84 0.15 0.00
45_A 246_L 0.84 0.15 0.00
68_N 59_K 0.84 0.15 0.00
16_Q 66_I 0.84 0.15 0.00
18_D 351_D 0.84 0.15 0.00
3_F 318_G 0.84 0.15 0.00
65_N 264_N 0.84 0.15 0.00
39_T 74_R 0.83 0.15 0.00
20_V 322_D 0.83 0.15 0.00
31_E 43_L 0.83 0.15 0.00
71_V 83_Y 0.83 0.15 0.00
8_L 371_K 0.83 0.15 0.00
54_V 353_S 0.83 0.15 0.00
26_I 242_E 0.83 0.15 0.00
75_S 192_N 0.83 0.14 0.00
32_G 74_R 0.82 0.14 0.00
57_T 99_G 0.82 0.14 0.00
57_T 377_D 0.82 0.14 0.00
38_G 283_G 0.82 0.14 0.00
42_L 380_I 0.82 0.14 0.00
37_F 302_L 0.82 0.14 0.00
14_V 113_H 0.82 0.14 0.00
65_N 90_G 0.82 0.14 0.00
45_A 213_E 0.82 0.14 0.00
46_I 381_D 0.82 0.14 0.00
6_E 254_H 0.82 0.14 0.00
65_N 278_K 0.82 0.14 0.00
64_W 94_Y 0.81 0.14 0.00
28_I 259_D 0.81 0.14 0.00
7_V 114_M 0.81 0.14 0.00
4_K 275_P 0.81 0.14 0.00
31_E 196_W 0.81 0.14 0.00
71_V 254_H 0.81 0.14 0.00
27_E 376_V 0.81 0.14 0.00
24_P 307_A 0.81 0.14 0.00
30_E 38_E 0.81 0.14 0.00
14_V 287_A 0.81 0.14 0.00
22_E 329_K 0.81 0.14 0.00
40_V 341_Q 0.81 0.14 0.00
45_A 208_Y 0.81 0.14 0.00
15_C 63_Y 0.81 0.14 0.00
69_N 312_V 0.81 0.14 0.00
10_V 44_N 0.81 0.14 0.00
40_V 370_W 0.81 0.14 0.00
38_G 45_P 0.81 0.14 0.00
61_R 168_M 0.81 0.14 0.00
53_L 260_F 0.81 0.14 0.00
51_D 52_Y 0.80 0.14 0.00
34_L 106_H 0.80 0.13 0.00
35_D 70_S 0.80 0.13 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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