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OPENSEQ.org
AA_vs_AB
Genes: A B A+B
Length: 189 171 360
Sequences: 707 395 374
Seq/Len: 3.74 2.31 1.04
MirrorTree (Pazo et al. 2001) 0.64
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 0.01 0.00 1.03
2 0.01 0.00 1.04
5 0.01 0.00 1.04
10 0.01 0.00 1.04
20 0.01 0.00 1.04
100 0.01 0.00 1.04
∞ 0.01 0.00 1.04
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
12_M 8_V 1.95 0.95 0.72
75_E 51_T 1.58 0.83 0.44
9_P 1_M 1.38 0.69 0.27
112_F 51_T 1.38 0.69 0.27
93_A 169_L 1.27 0.59 0.19
33_R 122_D 1.24 0.57 0.18
74_E 42_L 1.24 0.57 0.17
32_I 111_L 1.22 0.55 0.16
82_V 162_A 1.18 0.51 0.14
16_L 4_L 1.18 0.51 0.14
95_R 122_D 1.18 0.51 0.14
61_I 7_A 1.14 0.47 0.12
97_I 4_L 1.12 0.45 0.12
16_L 103_L 1.11 0.45 0.11
63_S 114_F 1.10 0.44 0.11
12_M 110_V 1.10 0.43 0.11
146_Q 44_A 1.08 0.42 0.10
81_Y 38_A 1.08 0.42 0.10
18_E 55_T 1.07 0.41 0.10
136_W 75_F 1.07 0.41 0.10
136_W 41_S 1.07 0.41 0.10
68_Y 86_A 1.06 0.41 0.09
67_N 114_F 1.06 0.40 0.09
107_R 45_E 1.05 0.39 0.09
66_S 125_S 1.05 0.39 0.09
188_I 80_D 1.05 0.39 0.09
183_G 166_L 1.05 0.39 0.09
28_E 86_A 1.04 0.39 0.09
38_V 118_L 1.04 0.38 0.09
124_A 83_S 1.04 0.38 0.09
65_L 120_I 1.03 0.38 0.08
160_S 5_L 1.03 0.38 0.08
90_V 61_A 1.03 0.38 0.08
99_E 79_L 1.02 0.37 0.08
141_I 9_F 1.02 0.36 0.08
135_S 111_L 1.01 0.36 0.08
33_R 115_G 1.00 0.35 0.07
85_R 25_Y 0.99 0.34 0.07
182_A 165_L 0.98 0.33 0.07
117_A 152_E 0.98 0.33 0.07
116_I 71_L 0.97 0.33 0.07
131_L 22_A 0.96 0.32 0.06
63_S 151_N 0.96 0.32 0.06
174_I 11_V 0.96 0.31 0.06
90_V 58_Q 0.95 0.31 0.06
28_E 152_E 0.95 0.31 0.06
125_E 15_T 0.94 0.30 0.06
130_Y 110_V 0.94 0.30 0.06
66_S 53_L 0.94 0.30 0.06
49_L 1_M 0.94 0.30 0.06
125_E 142_A 0.94 0.30 0.06
107_R 51_T 0.94 0.30 0.06
40_L 140_S 0.94 0.30 0.06
143_G 57_S 0.93 0.29 0.06
140_L 94_L 0.93 0.29 0.06
9_P 50_H 0.93 0.29 0.05
10_E 110_V 0.93 0.29 0.05
182_A 156_K 0.93 0.29 0.05
37_P 103_L 0.92 0.28 0.05
64_R 114_F 0.92 0.28 0.05
67_N 51_T 0.91 0.28 0.05
64_R 44_A 0.91 0.28 0.05
182_A 95_K 0.91 0.28 0.05
184_C 36_R 0.90 0.27 0.05
127_L 162_A 0.90 0.27 0.05
66_S 150_K 0.90 0.27 0.05
61_I 107_E 0.90 0.27 0.05
77_L 44_A 0.90 0.27 0.05
78_K 30_R 0.90 0.27 0.05
84_I 13_A 0.90 0.27 0.05
93_A 123_R 0.89 0.26 0.05
8_L 138_E 0.89 0.26 0.05
126_P 160_F 0.89 0.26 0.04
114_I 160_F 0.89 0.26 0.04
101_G 22_A 0.89 0.26 0.04
9_P 38_A 0.89 0.26 0.04
157_A 115_G 0.89 0.26 0.04
100_N 17_T 0.88 0.26 0.04
135_S 5_L 0.88 0.26 0.04
77_L 22_A 0.88 0.26 0.04
77_L 106_S 0.88 0.25 0.04
109_I 131_K 0.88 0.25 0.04
53_G 32_I 0.88 0.25 0.04
57_D 33_R 0.88 0.25 0.04
167_M 107_E 0.88 0.25 0.04
44_G 134_L 0.88 0.25 0.04
74_E 48_Y 0.88 0.25 0.04
53_G 35_L 0.88 0.25 0.04
140_L 89_A 0.87 0.25 0.04
28_E 90_W 0.87 0.25 0.04
157_A 146_Q 0.87 0.25 0.04
66_S 45_E 0.87 0.25 0.04
68_Y 151_N 0.87 0.25 0.04
92_L 63_Q 0.87 0.25 0.04
67_N 167_I 0.87 0.25 0.04
95_R 161_L 0.87 0.24 0.04
12_M 97_V 0.87 0.24 0.04
106_L 25_Y 0.86 0.24 0.04
143_G 54_H 0.86 0.24 0.04
118_R 133_A 0.86 0.24 0.04
44_G 157_S 0.86 0.24 0.04
141_I 53_L 0.86 0.24 0.04
48_Y 152_E 0.86 0.24 0.04
85_R 155_I 0.86 0.24 0.04
108_D 114_F 0.86 0.24 0.04
13_K 8_V 0.85 0.24 0.04
39_E 107_E 0.85 0.24 0.04
111_S 125_S 0.85 0.24 0.04
25_L 96_K 0.85 0.24 0.04
35_N 82_G 0.85 0.23 0.04
66_S 155_I 0.85 0.23 0.04
45_Q 105_K 0.85 0.23 0.04
157_A 7_A 0.85 0.23 0.04
48_Y 83_S 0.85 0.23 0.04
175_V 97_V 0.85 0.23 0.04
28_E 125_S 0.85 0.23 0.04
81_Y 26_T 0.85 0.23 0.04
132_Y 164_L 0.85 0.23 0.04
64_R 2_L 0.85 0.23 0.04
81_Y 80_D 0.85 0.23 0.04
70_M 169_L 0.85 0.23 0.04
62_L 44_A 0.84 0.23 0.04
188_I 100_T 0.84 0.23 0.04
90_V 52_P 0.84 0.23 0.04
71_Y 75_F 0.84 0.23 0.04
120_K 156_K 0.84 0.23 0.04
84_I 165_L 0.84 0.23 0.04
183_G 90_W 0.84 0.23 0.04
57_D 158_L 0.83 0.22 0.04
146_Q 161_L 0.83 0.22 0.04
64_R 68_V 0.83 0.22 0.04
46_P 168_L 0.83 0.22 0.04
82_V 114_F 0.83 0.22 0.04
5_A 71_L 0.83 0.22 0.03
42_R 32_I 0.82 0.22 0.03
125_E 5_L 0.82 0.22 0.03
22_Q 153_K 0.82 0.21 0.03
163_G 158_L 0.82 0.21 0.03
26_E 9_F 0.82 0.21 0.03
27_I 171_M 0.82 0.21 0.03
116_I 94_L 0.81 0.21 0.03
78_K 45_E 0.81 0.21 0.03
182_A 15_T 0.81 0.21 0.03
174_I 165_L 0.81 0.21 0.03
186_R 157_S 0.81 0.21 0.03
182_A 157_S 0.81 0.20 0.03
11_S 160_F 0.81 0.20 0.03
90_V 59_Q 0.80 0.20 0.03
10_E 19_F 0.80 0.20 0.03
1_M 10_I 0.80 0.20 0.03
117_A 46_I 0.79 0.20 0.03
188_I 140_S 0.79 0.20 0.03
26_E 52_P 0.79 0.20 0.03
118_R 38_A 0.79 0.20 0.03
71_Y 46_I 0.79 0.19 0.03
142_I 160_F 0.79 0.19 0.03
109_I 149_A 0.79 0.19 0.03
55_A 48_Y 0.79 0.19 0.03
102_G 97_V 0.79 0.19 0.03
12_M 65_A 0.78 0.19 0.03
72_T 103_L 0.78 0.19 0.03
70_M 131_K 0.78 0.19 0.03
118_R 144_A 0.78 0.19 0.03
144_P 85_S 0.78 0.19 0.03
40_L 147_A 0.78 0.19 0.03
53_G 41_S 0.78 0.19 0.03
11_S 17_T 0.78 0.19 0.03
134_N 11_V 0.78 0.19 0.03
185_L 154_M 0.77 0.19 0.03
12_M 21_M 0.77 0.19 0.03
141_I 64_L 0.77 0.19 0.03
106_L 36_R 0.77 0.19 0.03
53_G 69_S 0.77 0.19 0.03
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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