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OPENSEQ.org
aO bP
Genes: A B A+B
Length: 215 181 373
Sequences: 1002 695 633
Seq/Len: 4.66 3.84 1.7
MirrorTree (Pazo et al. 2001) 0.87
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 1.60
2 0.00 0.00 1.60
5 0.00 0.00 1.60
10 0.00 0.00 1.60
20 0.00 0.00 1.60
100 0.00 0.00 1.60
∞ 0.00 0.00 1.60
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
147_E 52_Y 2.61 1.00 0.99
65_K 33_E 1.85 0.97 0.94
61_K 26_W 1.79 0.96 0.92
16_H 156_S 1.49 0.88 0.78
124_P 153_N 1.48 0.88 0.78
59_E 90_F 1.48 0.87 0.77
69_I 36_A 1.45 0.86 0.76
147_E 54_P 1.33 0.79 0.66
33_A 7_L 1.32 0.78 0.65
194_T 50_P 1.32 0.78 0.64
124_P 98_V 1.31 0.77 0.63
52_E 46_L 1.30 0.77 0.63
124_P 75_E 1.29 0.76 0.61
7_K 27_M 1.28 0.75 0.61
30_A 147_I 1.25 0.73 0.57
65_K 30_T 1.25 0.72 0.57
139_S 100_I 1.25 0.72 0.57
124_P 128_Q 1.21 0.69 0.53
127_P 42_Q 1.17 0.65 0.49
68_S 31_R 1.17 0.65 0.49
149_I 163_L 1.15 0.64 0.47
37_L 122_V 1.15 0.63 0.46
102_P 153_N 1.14 0.62 0.45
39_Y 86_T 1.14 0.62 0.45
122_V 64_D 1.13 0.62 0.44
52_E 114_E 1.13 0.62 0.44
140_I 124_N 1.11 0.60 0.42
154_R 50_P 1.11 0.59 0.42
119_L 117_V 1.10 0.59 0.41
93_K 152_G 1.10 0.58 0.41
164_T 98_V 1.10 0.58 0.41
153_T 136_I 1.10 0.58 0.40
88_F 38_I 1.09 0.57 0.40
107_E 97_Y 1.09 0.57 0.40
150_S 149_D 1.09 0.57 0.40
119_L 35_K 1.08 0.56 0.39
153_T 39_I 1.08 0.56 0.39
122_V 59_G 1.08 0.56 0.38
61_K 30_T 1.07 0.55 0.38
33_A 14_S 1.05 0.53 0.35
148_Q 65_F 1.04 0.52 0.34
37_L 27_M 1.04 0.52 0.34
85_R 32_R 1.02 0.50 0.32
160_S 77_A 1.02 0.49 0.32
50_L 149_D 1.01 0.49 0.31
154_R 42_Q 1.01 0.48 0.30
167_S 125_Y 1.00 0.48 0.30
82_A 14_S 1.00 0.47 0.30
20_L 15_A 1.00 0.47 0.30
58_T 104_G 0.99 0.47 0.29
81_L 47_P 0.99 0.47 0.29
160_S 90_F 0.98 0.46 0.28
77_L 26_W 0.98 0.46 0.28
64_Y 18_Q 0.98 0.45 0.28
183_K 11_L 0.98 0.45 0.28
112_G 27_M 0.97 0.45 0.27
170_I 141_I 0.97 0.45 0.27
174_P 111_I 0.97 0.44 0.27
56_K 84_K 0.97 0.44 0.27
157_G 97_Y 0.97 0.44 0.27
200_S 59_G 0.96 0.44 0.26
93_K 84_K 0.96 0.43 0.26
130_D 17_S 0.96 0.43 0.26
39_Y 119_T 0.95 0.43 0.25
157_G 107_V 0.95 0.43 0.25
35_L 90_F 0.95 0.42 0.25
153_T 54_P 0.95 0.42 0.25
112_G 117_V 0.95 0.42 0.25
196_Y 58_T 0.94 0.41 0.24
160_S 148_E 0.94 0.41 0.24
112_G 79_D 0.93 0.40 0.23
174_P 85_E 0.93 0.40 0.23
168_L 59_G 0.93 0.40 0.23
91_M 155_V 0.93 0.40 0.23
29_L 96_R 0.93 0.40 0.23
133_I 41_F 0.92 0.40 0.23
24_L 51_V 0.92 0.40 0.23
23_R 94_N 0.92 0.39 0.22
101_I 47_P 0.92 0.39 0.22
102_P 140_S 0.92 0.39 0.22
165_L 38_I 0.91 0.38 0.21
89_D 36_A 0.91 0.38 0.21
32_A 28_A 0.91 0.38 0.21
208_A 137_T 0.91 0.38 0.21
162_I 88_E 0.91 0.38 0.21
39_Y 52_Y 0.90 0.37 0.21
186_I 5_A 0.89 0.36 0.20
161_R 88_E 0.89 0.36 0.20
28_L 71_D 0.89 0.36 0.20
148_Q 49_A 0.89 0.36 0.19
20_L 10_F 0.88 0.35 0.19
67_K 63_F 0.88 0.35 0.19
39_Y 143_L 0.88 0.35 0.19
34_V 104_G 0.87 0.35 0.18
163_I 42_Q 0.87 0.34 0.18
109_H 91_S 0.87 0.34 0.18
94_Q 129_N 0.87 0.34 0.18
36_G 73_K 0.87 0.34 0.18
30_A 137_T 0.86 0.33 0.17
48_E 135_S 0.86 0.33 0.17
191_A 153_N 0.86 0.33 0.17
124_P 159_A 0.86 0.33 0.17
37_L 39_I 0.86 0.33 0.17
61_K 130_Y 0.86 0.33 0.17
102_P 132_R 0.86 0.33 0.17
198_A 157_R 0.86 0.33 0.17
38_G 54_P 0.86 0.33 0.17
24_L 124_N 0.86 0.33 0.17
63_T 117_V 0.86 0.33 0.17
23_R 97_Y 0.85 0.33 0.17
195_T 157_R 0.85 0.33 0.17
154_R 38_I 0.85 0.33 0.17
34_V 161_L 0.85 0.33 0.17
19_N 60_P 0.85 0.33 0.17
210_Q 141_I 0.85 0.32 0.17
157_G 49_A 0.85 0.32 0.17
24_L 71_D 0.85 0.32 0.17
88_F 44_P 0.85 0.32 0.16
134_K 59_G 0.85 0.32 0.16
93_K 24_N 0.84 0.32 0.16
175_E 5_A 0.84 0.32 0.16
75_N 9_S 0.84 0.32 0.16
83_S 36_A 0.84 0.32 0.16
111_A 33_E 0.84 0.32 0.16
174_P 45_T 0.84 0.31 0.16
51_E 90_F 0.83 0.31 0.16
199_K 128_Q 0.83 0.31 0.16
154_R 15_A 0.83 0.31 0.15
139_S 109_G 0.83 0.31 0.15
93_K 154_W 0.83 0.31 0.15
115_N 148_E 0.83 0.30 0.15
46_Q 105_Q 0.83 0.30 0.15
118_R 146_L 0.83 0.30 0.15
158_S 90_F 0.82 0.30 0.15
69_I 92_L 0.82 0.30 0.15
191_A 159_A 0.82 0.30 0.15
113_S 35_K 0.82 0.30 0.15
59_E 163_L 0.82 0.30 0.15
30_A 166_S 0.82 0.30 0.14
40_A 111_I 0.82 0.29 0.14
202_E 115_G 0.82 0.29 0.14
21_P 109_G 0.82 0.29 0.14
55_A 105_Q 0.82 0.29 0.14
94_Q 45_T 0.82 0.29 0.14
138_Y 110_F 0.82 0.29 0.14
38_G 63_F 0.81 0.29 0.14
77_L 38_I 0.81 0.29 0.14
49_S 137_T 0.81 0.29 0.14
195_T 149_D 0.81 0.29 0.14
86_S 84_K 0.81 0.29 0.14
101_I 153_N 0.81 0.29 0.14
56_K 90_F 0.81 0.29 0.14
86_S 136_I 0.81 0.29 0.14
190_S 31_R 0.81 0.29 0.14
167_S 113_A 0.81 0.29 0.14
57_E 22_D 0.81 0.28 0.14
63_T 19_G 0.81 0.28 0.14
142_I 94_N 0.80 0.28 0.13
111_A 129_N 0.80 0.28 0.13
110_Q 85_E 0.80 0.28 0.13
15_L 10_F 0.80 0.28 0.13
187_L 123_G 0.80 0.28 0.13
206_A 12_A 0.80 0.28 0.13
107_E 148_E 0.80 0.28 0.13
65_K 10_F 0.80 0.28 0.13
25_F 7_L 0.80 0.28 0.13
55_A 73_K 0.80 0.28 0.13
164_T 133_I 0.79 0.27 0.13
110_Q 152_G 0.79 0.27 0.13
36_G 96_R 0.79 0.27 0.13
51_E 141_I 0.79 0.27 0.13
82_A 121_G 0.79 0.27 0.13
30_A 163_L 0.79 0.27 0.13
204_L 136_I 0.79 0.27 0.12
55_A 14_S 0.79 0.27 0.12
86_S 125_Y 0.79 0.27 0.12
193_A 59_G 0.79 0.27 0.12
77_L 42_Q 0.79 0.27 0.12
66_Q 92_L 0.79 0.27 0.12
202_E 32_R 0.79 0.27 0.12
70_D 83_I 0.79 0.27 0.12
67_K 112_E 0.79 0.27 0.12
22_A 122_V 0.78 0.27 0.12
122_V 153_N 0.78 0.27 0.12
41_G 90_F 0.78 0.27 0.12
193_A 38_I 0.78 0.26 0.12
189_L 47_P 0.78 0.26 0.12
65_K 34_A 0.78 0.26 0.12
157_G 74_G 0.78 0.26 0.12
62_N 10_F 0.78 0.26 0.12
99_A 77_A 0.78 0.26 0.12
159_L 150_S 0.78 0.26 0.12
6_S 165_S 0.78 0.26 0.12
23_R 81_K 0.78 0.26 0.12
153_T 137_T 0.78 0.26 0.12
78_R 147_I 0.78 0.26 0.12
13_N 48_V 0.77 0.26 0.12
209_A 9_S 0.77 0.26 0.12
188_N 161_L 0.77 0.26 0.12
43_F 64_D 0.77 0.26 0.12
40_A 95_M 0.77 0.26 0.12
170_I 9_S 0.77 0.25 0.12
64_Y 27_M 0.77 0.25 0.12
21_P 101_L 0.77 0.25 0.12
131_G 42_Q 0.77 0.25 0.12
7_K 86_T 0.77 0.25 0.12
175_E 137_T 0.77 0.25 0.12
30_A 70_T 0.77 0.25 0.12
95_L 88_E 0.77 0.25 0.12
115_N 24_N 0.77 0.25 0.11
113_S 129_N 0.77 0.25 0.11
170_I 7_L 0.77 0.25 0.11
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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