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OPENSEQ.org
2wiu_B_A
Genes: A B A+B
Length: 88 446 486
Sequences: 152 1606 123
Seq/Len: 1.73 3.6 0.25
MirrorTree (Pazo et al. 2001) 0.57
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 0.23
2 0.00 0.01 0.23
5 0.00 0.01 0.23
10 0.00 0.02 0.23
20 0.00 0.03 0.23
100 0.00 0.05 0.23
∞ 0.02 0.11 0.24
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
37_I 120_L 1.52 0.39 0.00
27_T 91_S 1.51 0.38 0.00
48_N 16_L 1.48 0.36 0.00
9_S 187_I 1.48 0.36 0.00
17_M 10_N 1.45 0.34 0.00
73_A 358_A 1.45 0.34 0.00
59_K 374_F 1.43 0.33 0.00
39_Q 176_T 1.36 0.29 0.00
7_I 87_F 1.30 0.26 0.00
68_M 110_V 1.29 0.26 0.00
13_L 328_T 1.28 0.25 0.00
60_I 145_N 1.26 0.24 0.00
17_M 218_P 1.25 0.24 0.00
17_M 41_L 1.23 0.23 0.00
45_F 218_P 1.23 0.23 0.00
14_A 364_T 1.22 0.22 0.00
42_I 340_L 1.22 0.22 0.00
23_Q 75_I 1.20 0.21 0.00
26_W 218_P 1.19 0.21 0.00
35_I 26_F 1.19 0.21 0.00
23_Q 327_L 1.19 0.21 0.00
61_L 262_P 1.18 0.21 0.00
18_K 180_I 1.18 0.20 0.00
29_S 36_R 1.18 0.20 0.00
41_T 101_V 1.17 0.20 0.00
58_F 126_E 1.15 0.20 0.00
58_F 279_M 1.15 0.19 0.00
69_T 86_P 1.15 0.19 0.00
40_A 126_E 1.14 0.19 0.00
27_T 301_F 1.14 0.19 0.00
77_S 122_E 1.13 0.19 0.00
18_K 53_T 1.12 0.18 0.00
54_L 269_S 1.11 0.18 0.00
39_Q 202_N 1.11 0.18 0.00
25_G 119_K 1.10 0.18 0.00
22_Q 229_R 1.10 0.17 0.00
32_A 410_L 1.10 0.17 0.00
50_D 428_R 1.09 0.17 0.00
11_T 93_I 1.08 0.17 0.00
77_S 305_I 1.07 0.16 0.00
32_A 58_F 1.07 0.16 0.00
30_E 295_F 1.06 0.16 0.00
58_F 292_R 1.05 0.16 0.00
56_T 151_V 1.05 0.16 0.00
30_E 38_A 1.05 0.16 0.00
26_W 71_V 1.05 0.15 0.00
57_F 233_V 1.04 0.15 0.00
57_F 305_I 1.04 0.15 0.00
64_L 300_V 1.04 0.15 0.00
53_T 26_F 1.03 0.15 0.00
45_F 382_R 1.03 0.15 0.00
67_S 216_N 1.03 0.15 0.00
36_G 123_A 1.03 0.15 0.00
9_S 269_S 1.02 0.15 0.00
35_I 317_V 1.02 0.15 0.00
27_T 169_I 1.02 0.15 0.00
18_K 395_F 1.02 0.15 0.00
53_T 25_T 1.01 0.14 0.00
49_P 103_L 1.00 0.14 0.00
57_F 10_N 0.99 0.14 0.00
8_Y 59_N 0.99 0.14 0.00
17_M 317_V 0.99 0.14 0.00
27_T 218_P 0.98 0.14 0.00
32_A 339_V 0.98 0.13 0.00
12_Q 200_V 0.98 0.13 0.00
26_W 104_I 0.98 0.13 0.00
55_T 325_Y 0.97 0.13 0.00
48_N 306_G 0.97 0.13 0.00
31_L 209_L 0.97 0.13 0.00
66_L 207_L 0.97 0.13 0.00
87_E 247_L 0.96 0.13 0.00
7_I 279_M 0.96 0.13 0.00
60_I 376_A 0.96 0.13 0.00
19_L 26_F 0.96 0.13 0.00
39_Q 159_A 0.95 0.13 0.00
77_S 414_F 0.94 0.12 0.00
13_L 13_V 0.94 0.12 0.00
36_G 305_I 0.94 0.12 0.00
62_Q 325_Y 0.94 0.12 0.00
42_I 126_E 0.94 0.12 0.00
69_T 269_S 0.94 0.12 0.00
37_I 142_R 0.94 0.12 0.00
45_F 355_G 0.94 0.12 0.00
25_G 270_D 0.93 0.12 0.00
27_T 308_T 0.92 0.12 0.00
63_S 364_T 0.92 0.12 0.00
76_A 327_L 0.92 0.12 0.00
56_T 16_L 0.92 0.12 0.00
27_T 334_I 0.92 0.12 0.00
57_F 336_A 0.91 0.12 0.00
8_Y 101_V 0.91 0.11 0.00
76_A 36_R 0.91 0.11 0.00
58_F 129_L 0.91 0.11 0.00
19_L 49_R 0.90 0.11 0.00
41_T 255_M 0.90 0.11 0.00
14_A 259_F 0.90 0.11 0.00
6_K 175_P 0.89 0.11 0.00
27_T 46_P 0.89 0.11 0.00
31_L 171_K 0.89 0.11 0.00
72_D 414_F 0.89 0.11 0.00
12_Q 411_P 0.89 0.11 0.00
6_K 293_Y 0.88 0.11 0.00
18_K 36_R 0.88 0.11 0.00
8_Y 356_L 0.88 0.11 0.00
32_A 406_V 0.88 0.11 0.00
27_T 362_K 0.88 0.11 0.00
36_G 317_V 0.88 0.11 0.00
64_L 251_P 0.88 0.11 0.00
58_F 145_N 0.87 0.11 0.00
63_S 132_Y 0.87 0.10 0.00
75_N 392_L 0.87 0.10 0.00
73_A 263_S 0.87 0.10 0.00
14_A 358_A 0.87 0.10 0.00
29_S 417_N 0.86 0.10 0.00
57_F 179_I 0.86 0.10 0.00
19_L 287_E 0.86 0.10 0.00
31_L 414_F 0.86 0.10 0.00
48_N 6_T 0.86 0.10 0.00
55_T 175_P 0.86 0.10 0.00
36_G 175_P 0.86 0.10 0.00
55_T 169_I 0.85 0.10 0.00
32_A 276_A 0.85 0.10 0.00
51_N 334_I 0.85 0.10 0.00
29_S 369_I 0.85 0.10 0.00
35_I 299_Q 0.85 0.10 0.00
66_L 358_A 0.84 0.10 0.00
42_I 269_S 0.84 0.10 0.00
28_Q 65_L 0.84 0.10 0.00
14_A 263_S 0.84 0.10 0.00
30_E 162_R 0.84 0.10 0.00
69_T 209_L 0.84 0.10 0.00
25_G 37_Y 0.84 0.10 0.00
68_M 398_M 0.84 0.10 0.00
59_K 395_F 0.84 0.10 0.00
25_G 74_R 0.83 0.10 0.00
65_E 52_I 0.83 0.10 0.00
40_A 10_N 0.83 0.10 0.00
64_L 240_W 0.83 0.10 0.00
12_Q 199_S 0.83 0.10 0.00
76_A 392_L 0.82 0.09 0.00
44_N 71_V 0.82 0.09 0.00
18_K 224_K 0.82 0.09 0.00
60_I 292_R 0.82 0.09 0.00
45_F 327_L 0.82 0.09 0.00
48_N 132_Y 0.81 0.09 0.00
36_G 17_T 0.81 0.09 0.00
79_E 245_T 0.81 0.09 0.00
45_F 371_P 0.81 0.09 0.00
9_S 388_M 0.81 0.09 0.00
25_G 107_D 0.81 0.09 0.00
36_G 107_D 0.81 0.09 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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