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OPENSEQ.org
S3_S10
Genes: A B A+B
Length: 221 118 275
Sequences: 1267 718 613
Seq/Len: 5.73 6.08 2.23
MirrorTree (Pazo et al. 2001) 0.80
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 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.03
10 0.00 0.00 1.81
20 0.00 0.00 1.81
100 0.00 0.00 1.97
∞ 0.00 0.00 2.30
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_R 26_K 1.83 0.98 0.92
98_C 17_R 1.45 0.91 0.74
62_K 37_D 1.42 0.89 0.72
48_V 39_M 1.39 0.88 0.70
139_V 40_K 1.39 0.88 0.69
115_A 31_I 1.23 0.78 0.54
189_I 26_K 1.19 0.75 0.50
157_Y 67_S 1.15 0.71 0.46
25_L 31_I 1.11 0.68 0.42
185_I 18_R 1.11 0.67 0.42
135_C 69_C 1.10 0.67 0.41
180_Q 69_C 1.09 0.66 0.40
157_Y 111_V 1.08 0.65 0.39
163_E 70_G 1.08 0.64 0.38
115_A 77_D 1.07 0.63 0.37
45_R 95_E 1.06 0.62 0.37
117_R 83_I 1.06 0.62 0.36
153_F 69_C 1.05 0.61 0.35
158_L 46_N 1.02 0.58 0.33
192_P 27_N 0.99 0.54 0.29
62_K 111_V 0.99 0.54 0.29
137_V 64_T 0.97 0.53 0.28
130_S 88_I 0.97 0.52 0.28
154_R 74_N 0.97 0.52 0.27
51_R 26_K 0.96 0.51 0.27
44_I 40_K 0.96 0.51 0.26
126_H 97_V 0.95 0.50 0.26
29_L 112_E 0.95 0.50 0.26
169_V 23_L 0.94 0.49 0.25
93_E 61_R 0.94 0.49 0.25
112_K 42_A 0.93 0.48 0.24
106_L 28_L 0.93 0.48 0.24
190_M 88_I 0.93 0.47 0.24
94_H 44_E 0.93 0.47 0.24
143_L 78_R 0.93 0.47 0.23
172_A 107_P 0.92 0.47 0.23
112_K 31_I 0.92 0.47 0.23
27_R 49_V 0.91 0.45 0.22
119_A 62_I 0.91 0.45 0.22
157_Y 71_E 0.91 0.45 0.22
42_T 50_S 0.90 0.45 0.22
45_R 31_I 0.89 0.43 0.21
54_R 111_V 0.89 0.43 0.20
137_V 70_G 0.89 0.43 0.20
90_E 77_D 0.89 0.42 0.20
94_H 37_D 0.88 0.42 0.20
108_Y 111_V 0.87 0.41 0.19
137_V 68_P 0.87 0.41 0.19
103_A 80_E 0.87 0.41 0.19
189_I 25_S 0.87 0.41 0.19
54_R 90_L 0.87 0.41 0.19
48_V 18_R 0.87 0.41 0.19
185_I 87_L 0.86 0.40 0.18
40_R 96_V 0.86 0.40 0.18
153_F 24_T 0.86 0.40 0.18
25_L 97_V 0.85 0.39 0.18
42_T 26_K 0.85 0.38 0.17
183_L 45_K 0.84 0.38 0.17
160_S 14_Y 0.84 0.38 0.17
58_V 36_S 0.84 0.37 0.16
27_R 28_L 0.84 0.37 0.16
192_P 64_T 0.83 0.37 0.16
115_A 79_F 0.83 0.37 0.16
89_A 76_W 0.83 0.37 0.16
32_D 80_E 0.83 0.37 0.16
132_A 53_V 0.83 0.37 0.16
168_F 46_N 0.83 0.36 0.16
189_I 30_A 0.83 0.36 0.16
34_Y 99_Q 0.83 0.36 0.16
157_Y 70_G 0.83 0.36 0.16
28_I 98_T 0.82 0.36 0.16
34_Y 15_R 0.82 0.36 0.15
24_F 65_R 0.82 0.35 0.15
53_T 66_K 0.81 0.35 0.15
106_L 107_P 0.81 0.35 0.15
59_L 99_Q 0.81 0.35 0.15
144_R 58_K 0.81 0.35 0.15
35_S 23_L 0.81 0.34 0.15
157_Y 64_T 0.80 0.34 0.14
49_I 81_L 0.80 0.34 0.14
125_R 104_N 0.80 0.34 0.14
126_H 111_V 0.80 0.34 0.14
157_Y 42_A 0.80 0.33 0.14
150_S 99_Q 0.80 0.33 0.14
57_E 36_S 0.80 0.33 0.14
58_V 92_S 0.80 0.33 0.14
104_E 60_L 0.80 0.33 0.14
58_V 106_D 0.79 0.32 0.14
21_L 88_I 0.79 0.32 0.13
117_R 82_R 0.79 0.32 0.13
120_C 107_P 0.78 0.32 0.13
64_R 75_T 0.78 0.31 0.13
146_Q 72_G 0.78 0.31 0.13
91_R 38_I 0.78 0.31 0.13
78_F 31_I 0.77 0.30 0.12
180_Q 65_R 0.77 0.30 0.12
72_L 98_T 0.77 0.30 0.12
106_L 108_V 0.77 0.30 0.12
90_E 102_S 0.76 0.30 0.12
135_C 27_N 0.76 0.29 0.12
105_S 112_E 0.76 0.29 0.12
138_I 95_E 0.76 0.29 0.12
133_K 70_G 0.76 0.29 0.12
33_G 20_R 0.76 0.29 0.12
84_S 53_V 0.76 0.29 0.11
126_H 74_N 0.76 0.29 0.11
147_R 72_G 0.75 0.29 0.11
65_R 69_C 0.75 0.29 0.11
76_R 25_S 0.75 0.28 0.11
174_R 26_K 0.75 0.28 0.11
128_M 103_I 0.75 0.28 0.11
177_Q 71_E 0.75 0.28 0.11
177_Q 67_S 0.74 0.28 0.11
121_Y 63_T 0.74 0.28 0.11
165_S 75_T 0.74 0.28 0.11
43_P 21_I 0.74 0.28 0.11
44_I 65_R 0.74 0.27 0.11
90_E 42_A 0.74 0.27 0.10
94_H 102_S 0.74 0.27 0.10
157_Y 68_P 0.73 0.27 0.10
129_E 34_V 0.73 0.27 0.10
67_R 61_R 0.73 0.27 0.10
133_K 16_L 0.73 0.27 0.10
109_K 41_G 0.73 0.27 0.10
100_M 90_L 0.73 0.27 0.10
116_V 98_T 0.73 0.27 0.10
112_K 58_K 0.73 0.27 0.10
38_E 106_D 0.73 0.26 0.10
95_R 101_T 0.72 0.26 0.10
133_K 102_S 0.72 0.26 0.10
94_H 106_D 0.72 0.26 0.10
74_Q 33_K 0.72 0.26 0.10
161_T 14_Y 0.72 0.26 0.10
47_E 104_N 0.72 0.26 0.10
34_Y 34_V 0.72 0.26 0.10
115_A 49_V 0.72 0.25 0.10
105_S 101_T 0.71 0.25 0.09
121_Y 78_R 0.71 0.25 0.09
78_F 21_I 0.71 0.25 0.09
158_L 80_E 0.71 0.25 0.09
137_V 107_P 0.71 0.24 0.09
115_A 60_L 0.71 0.24 0.09
192_P 67_S 0.71 0.24 0.09
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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