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OPENSEQ.org
3-4
Genes: A B A+B
Length: 191 234 380
Sequences: 4749 1521 106
Seq/Len: 24.86 6.5 0.28
MirrorTree (Pazo et al. 2001) 0.68
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 0.04 0.07 0.08
2 0.04 0.07 0.12
5 0.05 0.07 0.20
10 0.05 0.07 0.23
20 0.05 0.07 0.25
100 0.08 0.08 0.28
∞ 0.15 0.09 0.75
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
96_S 188_M 1.36 0.31 0.00
62_P 202_V 1.21 0.24 0.00
22_F 225_S 1.17 0.22 0.00
155_R 103_D 1.16 0.21 0.00
155_R 130_H 1.16 0.21 0.00
155_R 158_K 1.16 0.21 0.00
155_R 222_G 1.16 0.21 0.00
142_P 105_E 1.15 0.21 0.00
82_L 175_F 1.15 0.21 0.00
60_T 146_F 1.14 0.20 0.00
26_M 26_I 1.09 0.18 0.00
159_F 136_L 1.09 0.18 0.00
151_V 155_D 1.08 0.18 0.00
36_R 28_R 1.07 0.18 0.00
61_I 221_P 1.06 0.17 0.00
64_I 200_S 1.06 0.17 0.00
47_V 95_L 1.06 0.17 0.00
124_V 212_H 1.04 0.17 0.00
74_F 103_D 1.04 0.17 0.00
74_F 130_H 1.04 0.17 0.00
74_F 158_K 1.04 0.17 0.00
74_F 222_G 1.04 0.17 0.00
154_R 67_V 1.04 0.16 0.00
35_G 98_G 1.04 0.16 0.00
97_C 233_L 1.03 0.16 0.00
25_G 201_R 1.03 0.16 0.00
30_G 201_R 1.03 0.16 0.00
82_L 161_G 1.03 0.16 0.00
78_E 103_D 1.03 0.16 0.00
78_E 130_H 1.03 0.16 0.00
78_E 158_K 1.03 0.16 0.00
78_E 222_G 1.03 0.16 0.00
98_G 103_D 1.03 0.16 0.00
98_G 130_H 1.03 0.16 0.00
98_G 158_K 1.03 0.16 0.00
98_G 222_G 1.03 0.16 0.00
99_G 103_D 1.03 0.16 0.00
99_G 130_H 1.03 0.16 0.00
99_G 158_K 1.03 0.16 0.00
99_G 222_G 1.03 0.16 0.00
75_R 211_S 1.03 0.16 0.00
41_L 200_S 1.02 0.16 0.00
35_G 22_A 1.02 0.16 0.00
71_W 14_L 1.02 0.16 0.00
141_R 155_D 1.02 0.16 0.00
155_R 37_E 1.00 0.15 0.00
155_R 39_R 1.00 0.15 0.00
155_R 41_D 1.00 0.15 0.00
123_L 200_S 1.00 0.15 0.00
33_T 189_I 0.99 0.15 0.00
171_H 26_I 0.99 0.15 0.00
76_Q 226_A 0.99 0.15 0.00
105_E 143_W 0.99 0.15 0.00
134_Y 14_L 0.98 0.14 0.00
26_M 58_L 0.98 0.14 0.00
29_A 65_P 0.98 0.14 0.00
159_F 132_P 0.97 0.14 0.00
86_I 47_E 0.97 0.14 0.00
112_I 152_Q 0.97 0.14 0.00
94_I 101_Y 0.97 0.14 0.00
37_W 126_I 0.97 0.14 0.00
39_S 183_H 0.97 0.14 0.00
104_T 156_V 0.96 0.14 0.00
159_F 211_S 0.96 0.14 0.00
70_G 103_D 0.96 0.14 0.00
70_G 130_H 0.96 0.14 0.00
70_G 158_K 0.96 0.14 0.00
70_G 222_G 0.96 0.14 0.00
94_I 183_H 0.96 0.14 0.00
75_R 135_K 0.96 0.14 0.00
27_R 160_V 0.95 0.14 0.00
48_D 91_Y 0.95 0.14 0.00
63_E 149_K 0.95 0.14 0.00
97_C 127_A 0.95 0.13 0.00
29_A 210_V 0.95 0.13 0.00
171_H 214_A 0.95 0.13 0.00
35_G 159_L 0.94 0.13 0.00
155_R 128_S 0.94 0.13 0.00
55_R 121_G 0.94 0.13 0.00
39_S 102_L 0.94 0.13 0.00
135_L 131_D 0.94 0.13 0.00
142_P 77_G 0.94 0.13 0.00
32_S 211_S 0.94 0.13 0.00
38_M 100_E 0.93 0.13 0.00
166_Q 150_A 0.93 0.13 0.00
29_A 194_G 0.93 0.13 0.00
110_L 146_F 0.93 0.13 0.00
32_S 212_H 0.93 0.13 0.00
55_R 93_T 0.92 0.13 0.00
60_T 200_S 0.92 0.13 0.00
159_F 105_E 0.92 0.13 0.00
21_I 206_F 0.92 0.12 0.00
49_L 68_Y 0.92 0.12 0.00
170_P 173_T 0.91 0.12 0.00
53_L 171_A 0.91 0.12 0.00
79_L 150_A 0.91 0.12 0.00
111_L 16_V 0.91 0.12 0.00
50_D 201_R 0.91 0.12 0.00
130_Q 125_I 0.91 0.12 0.00
33_T 232_A 0.90 0.12 0.00
33_T 217_S 0.90 0.12 0.00
155_R 69_T 0.90 0.12 0.00
159_F 168_D 0.90 0.12 0.00
148_I 99_V 0.90 0.12 0.00
25_G 197_G 0.90 0.12 0.00
30_G 197_G 0.90 0.12 0.00
152_Y 62_A 0.90 0.12 0.00
141_R 221_P 0.90 0.12 0.00
63_E 35_A 0.90 0.12 0.00
36_R 167_A 0.90 0.12 0.00
95_F 196_A 0.90 0.12 0.00
142_P 211_S 0.90 0.12 0.00
31_K 201_R 0.89 0.12 0.00
72_E 143_W 0.89 0.12 0.00
72_E 230_R 0.89 0.12 0.00
68_E 27_P 0.89 0.12 0.00
53_L 143_W 0.89 0.12 0.00
150_E 185_N 0.89 0.12 0.00
155_R 223_Q 0.88 0.12 0.00
124_V 128_S 0.88 0.12 0.00
129_D 82_E 0.88 0.12 0.00
20_S 188_M 0.88 0.11 0.00
155_R 71_R 0.88 0.11 0.00
74_F 37_E 0.88 0.11 0.00
74_F 39_R 0.88 0.11 0.00
74_F 41_D 0.88 0.11 0.00
125_H 165_E 0.88 0.11 0.00
148_I 200_S 0.87 0.11 0.00
59_M 68_Y 0.87 0.11 0.00
122_L 129_H 0.87 0.11 0.00
34_A 102_L 0.87 0.11 0.00
42_L 231_Q 0.87 0.11 0.00
159_F 135_K 0.87 0.11 0.00
78_E 37_E 0.87 0.11 0.00
78_E 39_R 0.87 0.11 0.00
78_E 41_D 0.87 0.11 0.00
98_G 37_E 0.87 0.11 0.00
98_G 39_R 0.87 0.11 0.00
98_G 41_D 0.87 0.11 0.00
99_G 37_E 0.87 0.11 0.00
99_G 39_R 0.87 0.11 0.00
99_G 41_D 0.87 0.11 0.00
132_V 94_G 0.87 0.11 0.00
108_R 229_I 0.86 0.11 0.00
162_C 156_V 0.86 0.11 0.00
94_I 167_A 0.86 0.11 0.00
112_I 67_V 0.86 0.11 0.00
29_A 108_M 0.86 0.11 0.00
71_W 160_V 0.86 0.11 0.00
123_L 65_P 0.86 0.11 0.00
107_A 135_K 0.86 0.11 0.00
53_L 169_N 0.86 0.11 0.00
155_R 220_A 0.86 0.11 0.00
155_R 201_R 0.85 0.11 0.00
109_K 122_F 0.85 0.11 0.00
22_F 16_V 0.85 0.11 0.00
25_G 103_D 0.85 0.11 0.00
25_G 130_H 0.85 0.11 0.00
25_G 158_K 0.85 0.11 0.00
25_G 222_G 0.85 0.11 0.00
30_G 103_D 0.85 0.11 0.00
30_G 130_H 0.85 0.11 0.00
30_G 158_K 0.85 0.11 0.00
30_G 222_G 0.85 0.11 0.00
22_F 96_R 0.85 0.10 0.00
52_E 189_I 0.85 0.10 0.00
48_D 69_T 0.85 0.10 0.00
95_F 159_L 0.84 0.10 0.00
28_G 155_D 0.84 0.10 0.00
39_S 211_S 0.84 0.10 0.00
133_E 228_E 0.84 0.10 0.00
32_S 93_T 0.83 0.10 0.00
65_I 219_A 0.83 0.10 0.00
95_F 145_P 0.83 0.10 0.00
153_E 104_L 0.83 0.10 0.00
95_F 210_V 0.83 0.10 0.00
155_R 105_E 0.83 0.10 0.00
101_I 186_K 0.83 0.10 0.00
83_Q 225_S 0.83 0.10 0.00
74_F 128_S 0.83 0.10 0.00
127_D 60_A 0.83 0.10 0.00
25_G 37_E 0.83 0.10 0.00
25_G 39_R 0.83 0.10 0.00
25_G 41_D 0.83 0.10 0.00
30_G 37_E 0.83 0.10 0.00
30_G 39_R 0.83 0.10 0.00
30_G 41_D 0.83 0.10 0.00
130_Q 172_L 0.83 0.10 0.00
24_V 60_A 0.83 0.10 0.00
124_V 213_P 0.83 0.10 0.00
151_V 176_K 0.83 0.10 0.00
94_I 67_V 0.83 0.10 0.00
123_L 22_A 0.82 0.10 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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