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OPENSEQ.org
2avu_B_E
Genes: A B A+B
Length: 116 192 279
Sequences: 170 169 147
Seq/Len: 1.47 0.88 0.53
MirrorTree (Pazo et al. 2001) 0.74
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 0.06 0.02 0.47
2 0.06 0.02 0.47
5 0.06 0.02 0.48
10 0.06 0.02 0.48
20 0.06 0.02 0.48
100 0.07 0.03 0.48
∞ 0.08 0.04 0.48
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
46_L 41_I 1.78 0.77 0.02
32_A 45_K 1.48 0.57 0.01
66_H 92_V 1.38 0.48 0.01
3_T 1_M 1.37 0.48 0.01
50_T 136_S 1.29 0.42 0.01
79_T 105_Q 1.29 0.42 0.01
7_L 104_E 1.29 0.42 0.01
51_L 69_Q 1.28 0.41 0.01
39_N 131_L 1.25 0.39 0.01
34_F 100_R 1.25 0.38 0.01
29_K 156_A 1.23 0.37 0.01
62_Q 116_A 1.21 0.36 0.01
11_Y 75_M 1.21 0.36 0.01
50_T 56_M 1.20 0.35 0.01
45_T 105_Q 1.20 0.35 0.01
94_I 6_I 1.19 0.35 0.01
70_D 45_K 1.19 0.34 0.01
78_L 78_N 1.16 0.32 0.00
18_L 40_L 1.16 0.32 0.00
58_A 48_R 1.15 0.32 0.00
94_I 13_I 1.14 0.31 0.00
69_F 64_F 1.14 0.31 0.00
50_T 113_P 1.14 0.31 0.00
11_Y 28_M 1.14 0.31 0.00
62_Q 117_L 1.14 0.31 0.00
104_V 103_L 1.14 0.31 0.00
25_I 159_L 1.13 0.30 0.00
89_Q 129_S 1.13 0.30 0.00
23_R 146_T 1.13 0.30 0.00
19_L 164_S 1.12 0.30 0.00
49_L 33_T 1.12 0.29 0.00
28_D 97_K 1.12 0.29 0.00
25_I 98_A 1.11 0.29 0.00
75_I 6_I 1.11 0.29 0.00
31_S 1_M 1.11 0.29 0.00
54_M 129_S 1.11 0.29 0.00
58_A 42_K 1.11 0.29 0.00
70_D 141_G 1.10 0.28 0.00
46_L 71_V 1.10 0.28 0.00
43_A 66_T 1.09 0.28 0.00
53_Q 43_L 1.09 0.28 0.00
58_A 75_M 1.09 0.28 0.00
16_S 78_N 1.09 0.28 0.00
89_Q 155_F 1.08 0.27 0.00
75_I 125_R 1.08 0.27 0.00
66_H 79_A 1.06 0.26 0.00
24_L 77_C 1.06 0.26 0.00
23_R 100_R 1.06 0.26 0.00
69_F 42_K 1.06 0.26 0.00
89_Q 26_L 1.05 0.25 0.00
71_S 155_F 1.05 0.25 0.00
67_F 6_I 1.04 0.25 0.00
57_L 77_C 1.04 0.25 0.00
65_C 39_R 1.03 0.24 0.00
63_L 28_M 1.03 0.24 0.00
74_T 82_F 1.03 0.24 0.00
11_Y 116_A 1.02 0.24 0.00
52_P 116_A 1.02 0.24 0.00
74_T 92_V 1.02 0.23 0.00
73_Q 82_F 1.02 0.23 0.00
92_T 169_R 1.01 0.23 0.00
58_A 73_A 1.01 0.23 0.00
21_A 128_E 1.01 0.23 0.00
97_S 30_E 1.01 0.23 0.00
93_G 125_R 1.00 0.23 0.00
16_S 112_G 1.00 0.22 0.00
98_T 92_V 0.99 0.22 0.00
92_T 123_L 0.99 0.22 0.00
46_L 139_C 0.99 0.22 0.00
60_T 98_A 0.99 0.22 0.00
88_Q 117_L 0.97 0.21 0.00
89_Q 64_F 0.96 0.21 0.00
57_L 59_F 0.96 0.20 0.00
75_I 122_T 0.95 0.20 0.00
48_A 138_N 0.95 0.20 0.00
98_T 97_K 0.95 0.20 0.00
28_D 78_N 0.94 0.19 0.00
13_I 170_R 0.94 0.19 0.00
38_I 7_V 0.94 0.19 0.00
30_A 1_M 0.94 0.19 0.00
12_D 125_R 0.93 0.19 0.00
89_Q 170_R 0.93 0.19 0.00
83_R 45_K 0.93 0.19 0.00
83_R 151_P 0.93 0.19 0.00
83_R 117_L 0.93 0.19 0.00
37_G 95_V 0.93 0.19 0.00
19_L 15_L 0.93 0.19 0.00
67_F 116_A 0.93 0.19 0.00
47_A 136_S 0.93 0.19 0.00
65_C 43_L 0.93 0.19 0.00
91_H 123_L 0.93 0.19 0.00
59_E 95_V 0.92 0.18 0.00
23_R 161_Q 0.92 0.18 0.00
75_I 68_E 0.92 0.18 0.00
23_R 162_P 0.92 0.18 0.00
100_L 105_Q 0.92 0.18 0.00
92_T 145_I 0.91 0.18 0.00
45_T 28_M 0.91 0.18 0.00
1_M 50_S 0.90 0.18 0.00
27_Q 114_L 0.90 0.17 0.00
53_Q 104_E 0.90 0.17 0.00
87_L 129_S 0.90 0.17 0.00
4_S 133_Q 0.90 0.17 0.00
51_L 164_S 0.89 0.17 0.00
37_G 159_L 0.89 0.17 0.00
12_D 133_Q 0.89 0.17 0.00
97_S 85_K 0.89 0.17 0.00
57_L 3_E 0.89 0.17 0.00
13_I 117_L 0.89 0.17 0.00
12_D 50_S 0.88 0.17 0.00
85_D 146_T 0.88 0.17 0.00
25_I 78_N 0.88 0.17 0.00
96_L 105_Q 0.88 0.17 0.00
87_L 149_H 0.88 0.16 0.00
87_L 15_L 0.88 0.16 0.00
72_H 19_L 0.87 0.16 0.00
43_A 167_V 0.87 0.16 0.00
100_L 12_D 0.87 0.16 0.00
46_L 47_L 0.87 0.16 0.00
97_S 128_E 0.87 0.16 0.00
101_L 42_K 0.86 0.16 0.00
13_I 31_S 0.86 0.16 0.00
79_T 68_E 0.86 0.16 0.00
16_S 155_F 0.86 0.16 0.00
68_R 82_F 0.86 0.16 0.00
39_N 12_D 0.86 0.16 0.00
24_L 1_M 0.86 0.16 0.00
76_T 71_V 0.86 0.16 0.00
11_Y 51_P 0.86 0.16 0.00
84_V 61_T 0.86 0.16 0.00
56_K 142_G 0.86 0.15 0.00
46_L 110_E 0.85 0.15 0.00
16_S 130_G 0.85 0.15 0.00
28_D 79_A 0.85 0.15 0.00
87_L 18_E 0.85 0.15 0.00
82_S 130_G 0.85 0.15 0.00
45_T 145_I 0.85 0.15 0.00
30_A 141_G 0.84 0.15 0.00
88_Q 50_S 0.84 0.15 0.00
37_G 92_V 0.84 0.15 0.00
42_M 164_S 0.84 0.15 0.00
23_R 89_C 0.84 0.15 0.00
28_D 117_L 0.84 0.15 0.00
94_I 159_L 0.83 0.15 0.00
37_G 82_F 0.83 0.15 0.00
40_E 47_L 0.83 0.14 0.00
71_S 136_S 0.83 0.14 0.00
77_Q 64_F 0.83 0.14 0.00
17_Y 62_D 0.83 0.14 0.00
12_D 122_T 0.82 0.14 0.00
16_S 111_E 0.82 0.14 0.00
54_M 28_M 0.82 0.14 0.00
83_R 48_R 0.82 0.14 0.00
39_N 22_L 0.82 0.14 0.00
92_T 124_V 0.82 0.14 0.00
9_H 167_V 0.81 0.14 0.00
8_K 31_S 0.81 0.14 0.00
21_A 35_L 0.81 0.14 0.00
40_E 45_K 0.81 0.14 0.00
27_Q 100_R 0.81 0.14 0.00
33_M 148_A 0.81 0.14 0.00
46_L 161_Q 0.81 0.14 0.00
13_I 81_Q 0.81 0.14 0.00
75_I 51_P 0.81 0.14 0.00
97_S 81_Q 0.80 0.13 0.00
1_M 132_L 0.80 0.13 0.00
61_N 26_L 0.80 0.13 0.00
94_I 36_S 0.80 0.13 0.00
16_S 138_N 0.80 0.13 0.00
96_L 8_Q 0.79 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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