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OPENSEQ.org
3m4w_E_C
Genes: A B A+B
Length: 96 295 364
Sequences: 59 495 58
Seq/Len: 0.61 1.68 0.16
MirrorTree (Pazo et al. 2001) 0.94
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 0.15
2 0.00 0.00 0.15
5 0.00 0.00 0.15
10 0.00 0.00 0.15
20 0.00 0.00 0.15
100 0.00 0.00 0.15
∞ 0.00 0.00 0.15
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
53_I 231_Y 1.73 0.39 0.00
69_E 175_M 1.63 0.34 0.00
47_Q 187_L 1.63 0.34 0.00
16_F 53_M 1.56 0.31 0.00
25_A 5_G 1.48 0.27 0.00
54_N 118_C 1.35 0.21 0.00
69_E 12_N 1.33 0.21 0.00
50_R 274_V 1.32 0.20 0.00
53_I 19_N 1.30 0.19 0.00
67_H 186_L 1.27 0.18 0.00
46_V 123_V 1.26 0.18 0.00
48_E 29_K 1.25 0.18 0.00
55_A 22_L 1.24 0.17 0.00
16_F 115_D 1.23 0.17 0.00
57_L 50_L 1.21 0.16 0.00
34_S 284_R 1.21 0.16 0.00
26_S 241_N 1.21 0.16 0.00
47_Q 285_I 1.20 0.16 0.00
51_R 117_L 1.18 0.15 0.00
17_N 115_D 1.17 0.15 0.00
17_N 53_M 1.16 0.15 0.00
58_Q 150_L 1.16 0.15 0.00
59_D 56_P 1.14 0.14 0.00
59_D 76_P 1.14 0.14 0.00
45_Q 218_L 1.14 0.14 0.00
67_H 277_L 1.13 0.14 0.00
21_M 256_T 1.13 0.14 0.00
34_S 48_A 1.12 0.14 0.00
47_Q 188_S 1.11 0.14 0.00
32_V 34_S 1.09 0.13 0.00
26_S 115_D 1.09 0.13 0.00
69_E 43_D 1.08 0.13 0.00
67_H 147_V 1.08 0.13 0.00
12_E 94_T 1.07 0.13 0.00
51_R 72_P 1.07 0.13 0.00
2_N 91_L 1.07 0.13 0.00
57_L 203_W 1.07 0.13 0.00
26_S 276_E 1.06 0.12 0.00
63_Q 146_R 1.06 0.12 0.00
64_R 54_D 1.06 0.12 0.00
53_I 291_F 1.05 0.12 0.00
50_R 152_R 1.05 0.12 0.00
50_R 279_P 1.04 0.12 0.00
12_E 26_S 1.04 0.12 0.00
68_S 121_I 1.04 0.12 0.00
30_L 110_R 1.03 0.12 0.00
23_G 7_L 1.03 0.12 0.00
64_R 86_D 1.03 0.12 0.00
73_F 221_M 1.02 0.11 0.00
22_M 283_K 1.01 0.11 0.00
25_A 6_A 1.01 0.11 0.00
23_G 252_Q 1.01 0.11 0.00
69_E 94_T 1.01 0.11 0.00
53_I 116_R 1.01 0.11 0.00
58_Q 107_S 1.00 0.11 0.00
48_E 208_F 0.99 0.11 0.00
59_D 128_G 0.99 0.11 0.00
53_I 47_L 0.99 0.11 0.00
16_F 90_S 0.99 0.11 0.00
64_R 276_E 0.99 0.11 0.00
27_P 158_E 0.98 0.11 0.00
17_N 81_G 0.98 0.10 0.00
53_I 224_M 0.98 0.10 0.00
36_A 271_I 0.98 0.10 0.00
48_E 72_P 0.98 0.10 0.00
68_S 272_T 0.98 0.10 0.00
16_F 52_Q 0.98 0.10 0.00
6_E 268_N 0.97 0.10 0.00
2_N 89_P 0.97 0.10 0.00
64_R 241_N 0.97 0.10 0.00
58_Q 105_F 0.97 0.10 0.00
10_Q 97_K 0.97 0.10 0.00
56_M 73_G 0.97 0.10 0.00
57_L 178_L 0.96 0.10 0.00
24_K 60_V 0.96 0.10 0.00
47_Q 144_P 0.96 0.10 0.00
47_Q 163_I 0.95 0.10 0.00
59_D 154_G 0.95 0.10 0.00
64_R 79_L 0.95 0.10 0.00
22_M 115_D 0.95 0.10 0.00
64_R 84_I 0.95 0.10 0.00
37_T 140_E 0.95 0.10 0.00
68_S 142_K 0.94 0.10 0.00
20_P 68_S 0.94 0.10 0.00
67_H 125_A 0.94 0.10 0.00
3_G 208_F 0.94 0.10 0.00
59_D 112_R 0.93 0.09 0.00
63_Q 203_W 0.93 0.09 0.00
33_P 34_S 0.92 0.09 0.00
34_S 80_N 0.92 0.09 0.00
22_M 263_T 0.92 0.09 0.00
13_T 250_T 0.92 0.09 0.00
31_G 90_S 0.92 0.09 0.00
56_M 193_E 0.92 0.09 0.00
59_D 258_R 0.92 0.09 0.00
53_I 106_I 0.92 0.09 0.00
67_H 79_L 0.92 0.09 0.00
43_Q 30_Q 0.91 0.09 0.00
53_I 166_N 0.91 0.09 0.00
64_R 277_L 0.91 0.09 0.00
27_P 273_I 0.91 0.09 0.00
32_V 126_R 0.91 0.09 0.00
55_A 43_D 0.91 0.09 0.00
59_D 132_S 0.91 0.09 0.00
51_R 13_L 0.90 0.09 0.00
63_Q 104_D 0.90 0.09 0.00
74_E 83_Y 0.90 0.09 0.00
75_Q 293_A 0.90 0.09 0.00
50_R 71_E 0.90 0.09 0.00
56_M 225_P 0.90 0.09 0.00
75_Q 100_S 0.90 0.09 0.00
66_L 136_W 0.90 0.09 0.00
63_Q 128_G 0.90 0.09 0.00
25_A 51_L 0.90 0.09 0.00
48_E 279_P 0.89 0.09 0.00
67_H 180_K 0.89 0.09 0.00
53_I 175_M 0.89 0.09 0.00
35_E 67_I 0.89 0.09 0.00
58_Q 19_N 0.89 0.09 0.00
64_R 115_D 0.89 0.09 0.00
26_S 54_D 0.89 0.09 0.00
16_F 241_N 0.88 0.09 0.00
17_N 276_E 0.88 0.09 0.00
66_L 153_D 0.88 0.09 0.00
16_F 216_R 0.88 0.09 0.00
24_K 212_S 0.88 0.09 0.00
39_N 198_S 0.88 0.09 0.00
24_K 145_M 0.88 0.08 0.00
23_G 255_R 0.87 0.08 0.00
31_G 34_S 0.87 0.08 0.00
38_A 224_M 0.87 0.08 0.00
68_S 82_D 0.87 0.08 0.00
33_P 271_I 0.87 0.08 0.00
17_N 52_Q 0.87 0.08 0.00
17_N 241_N 0.87 0.08 0.00
49_Q 60_V 0.87 0.08 0.00
55_A 39_H 0.87 0.08 0.00
48_E 190_P 0.87 0.08 0.00
32_V 229_R 0.86 0.08 0.00
63_Q 284_R 0.86 0.08 0.00
73_F 164_A 0.86 0.08 0.00
45_Q 121_I 0.86 0.08 0.00
21_M 168_N 0.86 0.08 0.00
43_Q 217_P 0.86 0.08 0.00
45_Q 62_Q 0.86 0.08 0.00
51_R 118_C 0.86 0.08 0.00
46_V 294_A 0.86 0.08 0.00
55_A 89_P 0.86 0.08 0.00
2_N 88_L 0.86 0.08 0.00
24_K 34_S 0.85 0.08 0.00
56_M 40_A 0.85 0.08 0.00
58_Q 230_L 0.85 0.08 0.00
73_F 267_D 0.85 0.08 0.00
55_A 286_A 0.85 0.08 0.00
17_N 49_Q 0.84 0.08 0.00
15_V 228_S 0.84 0.08 0.00
13_T 46_P 0.84 0.08 0.00
26_S 86_D 0.84 0.08 0.00
8_S 121_I 0.84 0.08 0.00
51_R 180_K 0.84 0.08 0.00
2_N 36_R 0.84 0.08 0.00
24_K 160_F 0.84 0.08 0.00
46_V 232_S 0.83 0.08 0.00
17_N 113_I 0.83 0.08 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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