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OPENSEQ.org
IJ
Genes: A B A+B
Length: 121 198 311
Sequences: 694 618 532
Seq/Len: 5.74 3.12 1.71
MirrorTree (Pazo et al. 2001) 0.78
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 1.56
2 0.00 0.00 1.57
5 0.00 0.00 1.65
10 0.00 0.00 1.67
20 0.00 0.00 1.67
100 0.00 0.00 1.67
∞ 0.04 0.03 1.68
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
23_G 30_V 1.79 0.96 0.82
19_F 20_L 1.70 0.95 0.77
55_V 189_L 1.70 0.95 0.77
41_E 44_K 1.65 0.94 0.74
48_W 188_R 1.65 0.94 0.73
53_Q 173_G 1.58 0.92 0.69
26_V 34_V 1.55 0.91 0.66
48_W 55_F 1.53 0.90 0.65
19_F 23_L 1.52 0.90 0.64
19_F 30_V 1.52 0.89 0.64
14_V 94_S 1.47 0.87 0.59
90_D 143_M 1.34 0.80 0.48
76_A 106_P 1.29 0.76 0.43
48_W 59_A 1.28 0.76 0.42
10_I 11_V 1.25 0.73 0.39
18_V 11_V 1.24 0.72 0.37
59_L 160_W 1.20 0.69 0.34
80_W 61_D 1.19 0.67 0.33
103_R 37_A 1.15 0.64 0.29
59_L 173_G 1.14 0.63 0.29
101_V 113_V 1.14 0.63 0.29
99_V 93_F 1.14 0.62 0.29
102_R 176_V 1.14 0.62 0.28
43_K 27_A 1.13 0.61 0.27
30_T 37_A 1.12 0.61 0.27
16_L 16_A 1.09 0.57 0.24
12_V 17_L 1.08 0.57 0.24
92_P 93_F 1.08 0.57 0.24
20_A 188_R 1.08 0.56 0.23
30_T 34_V 1.07 0.56 0.23
99_V 39_T 1.07 0.55 0.23
18_V 170_L 1.06 0.55 0.22
18_V 69_R 1.05 0.53 0.21
19_F 26_A 1.04 0.52 0.21
44_T 45_G 1.04 0.52 0.21
56_Q 189_L 1.04 0.52 0.20
18_V 186_I 1.02 0.50 0.19
71_T 154_F 1.01 0.49 0.18
23_G 26_A 1.00 0.48 0.18
70_E 173_G 1.00 0.48 0.18
10_I 54_T 1.00 0.47 0.17
34_T 41_T 0.99 0.46 0.17
44_T 38_D 0.98 0.46 0.17
69_S 181_E 0.98 0.46 0.17
118_V 162_D 0.98 0.46 0.17
47_G 54_T 0.97 0.45 0.16
118_V 31_L 0.97 0.45 0.16
106_S 58_M 0.96 0.43 0.15
50_A 144_Q 0.96 0.43 0.15
13_M 186_I 0.95 0.43 0.15
44_T 54_T 0.95 0.43 0.15
26_V 28_V 0.95 0.43 0.15
111_V 35_M 0.95 0.43 0.15
94_L 18_A 0.95 0.42 0.15
54_L 108_S 0.95 0.42 0.14
31_L 19_I 0.95 0.42 0.14
80_W 147_V 0.94 0.42 0.14
7_M 94_S 0.94 0.41 0.14
51_D 33_N 0.94 0.41 0.14
85_Q 157_S 0.93 0.41 0.14
56_Q 116_R 0.93 0.40 0.14
52_N 61_D 0.93 0.40 0.13
9_L 122_L 0.93 0.40 0.13
59_L 124_R 0.93 0.40 0.13
13_M 58_M 0.92 0.39 0.13
88_E 15_L 0.92 0.39 0.13
97_L 189_L 0.92 0.39 0.13
47_G 127_Y 0.91 0.39 0.13
82_I 57_Q 0.91 0.39 0.13
45_L 37_A 0.91 0.38 0.12
75_A 29_T 0.91 0.38 0.12
118_V 23_L 0.90 0.38 0.12
2_K 3_Q 0.90 0.37 0.12
10_I 16_A 0.90 0.37 0.12
99_V 118_R 0.90 0.37 0.12
78_V 174_L 0.90 0.37 0.12
19_F 11_V 0.89 0.36 0.12
47_G 125_L 0.89 0.36 0.12
18_V 17_L 0.89 0.36 0.11
13_M 99_P 0.89 0.36 0.11
18_V 140_V 0.89 0.36 0.11
10_I 154_F 0.88 0.35 0.11
27_M 143_M 0.88 0.35 0.11
56_Q 145_R 0.88 0.35 0.11
99_V 187_R 0.88 0.35 0.11
10_I 39_T 0.88 0.35 0.11
81_H 176_V 0.87 0.34 0.10
105_K 119_G 0.87 0.34 0.10
72_T 43_D 0.87 0.34 0.10
65_A 186_I 0.86 0.34 0.10
21_L 147_V 0.86 0.33 0.10
1_M 84_L 0.86 0.33 0.10
3_K 6_R 0.86 0.33 0.10
78_V 54_T 0.86 0.33 0.10
45_L 183_S 0.86 0.33 0.10
107_D 15_L 0.86 0.33 0.10
2_K 6_R 0.85 0.33 0.10
10_I 49_Q 0.85 0.33 0.10
10_I 110_I 0.85 0.33 0.10
86_G 24_S 0.85 0.33 0.10
18_V 104_I 0.85 0.32 0.10
41_E 186_I 0.85 0.32 0.10
54_L 174_L 0.85 0.32 0.10
7_M 156_A 0.84 0.32 0.10
111_V 52_Q 0.84 0.32 0.09
20_A 30_V 0.84 0.31 0.09
92_P 146_N 0.84 0.31 0.09
116_T 182_Q 0.84 0.31 0.09
27_M 42_R 0.84 0.31 0.09
32_Q 35_M 0.84 0.31 0.09
42_E 100_N 0.84 0.31 0.09
13_M 60_A 0.83 0.31 0.09
41_E 40_L 0.83 0.31 0.09
115_R 19_I 0.82 0.30 0.09
117_Y 155_Y 0.82 0.30 0.08
20_A 28_V 0.82 0.29 0.08
82_I 173_G 0.82 0.29 0.08
34_T 48_M 0.82 0.29 0.08
17_A 23_L 0.81 0.29 0.08
38_G 121_R 0.81 0.29 0.08
13_M 125_L 0.81 0.29 0.08
21_L 5_A 0.81 0.29 0.08
56_Q 187_R 0.81 0.28 0.08
41_E 30_V 0.81 0.28 0.08
116_T 165_Q 0.80 0.28 0.08
26_V 29_T 0.80 0.28 0.08
42_E 123_E 0.80 0.28 0.08
85_Q 15_L 0.80 0.28 0.08
39_R 94_S 0.80 0.28 0.07
52_N 51_L 0.80 0.28 0.07
5_A 192_L 0.79 0.27 0.07
19_F 98_W 0.79 0.27 0.07
12_V 28_V 0.79 0.27 0.07
48_W 190_F 0.79 0.27 0.07
101_V 53_L 0.79 0.27 0.07
90_D 37_A 0.79 0.27 0.07
41_E 122_L 0.79 0.27 0.07
79_S 152_L 0.78 0.27 0.07
10_I 157_S 0.78 0.26 0.07
13_M 102_L 0.78 0.26 0.07
8_T 23_L 0.78 0.26 0.07
83_R 143_M 0.78 0.26 0.07
41_E 184_G 0.78 0.26 0.07
40_M 29_T 0.77 0.26 0.07
7_M 143_M 0.77 0.26 0.07
96_A 51_L 0.77 0.26 0.07
111_V 178_L 0.77 0.25 0.07
40_M 27_A 0.77 0.25 0.07
59_L 191_L 0.77 0.25 0.07
98_D 23_L 0.76 0.25 0.07
30_T 70_S 0.76 0.25 0.06
79_S 46_G 0.76 0.25 0.06
86_G 55_F 0.76 0.25 0.06
49_L 147_V 0.76 0.24 0.06
34_T 42_R 0.76 0.24 0.06
80_W 97_G 0.76 0.24 0.06
7_M 95_R 0.76 0.24 0.06
62_R 158_G 0.76 0.24 0.06
102_R 59_A 0.76 0.24 0.06
52_N 188_R 0.75 0.24 0.06
10_I 69_R 0.75 0.24 0.06
107_D 91_I 0.75 0.24 0.06
60_E 178_L 0.75 0.24 0.06
90_D 119_G 0.75 0.24 0.06
73_V 13_M 0.75 0.24 0.06
29_A 193_T 0.75 0.23 0.06
18_V 135_G 0.75 0.23 0.06
95_R 39_T 0.74 0.23 0.06
80_W 52_Q 0.74 0.23 0.06
28_Q 141_T 0.74 0.23 0.06
57_L 153_R 0.74 0.23 0.06
91_L 20_L 0.74 0.23 0.06
99_V 128_D 0.74 0.23 0.06
21_L 166_Q 0.74 0.23 0.06
73_V 127_Y 0.74 0.23 0.06
19_F 183_S 0.74 0.23 0.06
93_Q 145_R 0.74 0.23 0.06
14_V 49_Q 0.74 0.23 0.06
94_L 169_T 0.74 0.23 0.06
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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