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OPENSEQ.org
cI_A_J
Genes: A B A+B
Length: 184 325 496
Sequences: 2129 4760 1744
Seq/Len: 11.57 14.65 3.52
MirrorTree (Pazo et al. 2001) 0.77
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 0.25
2 0.00 0.00 2.71
5 0.00 0.00 3.10
10 0.01 0.01 3.22
20 0.01 0.01 3.30
100 0.02 0.02 3.38
∞ 0.03 0.05 3.43
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
53_A 114_I 2.99 1.00 1.00
27_H 79_D 1.79 0.99 0.97
52_G 297_V 1.19 0.86 0.74
70_V 294_Y 1.19 0.86 0.73
27_H 82_I 1.18 0.85 0.72
58_V 97_A 1.16 0.84 0.70
130_G 115_G 1.15 0.83 0.69
52_G 52_V 1.13 0.82 0.68
43_F 158_V 1.11 0.80 0.66
34_I 158_V 1.08 0.78 0.62
20_I 314_L 1.07 0.77 0.61
70_V 128_Y 1.07 0.76 0.61
153_V 110_A 1.05 0.74 0.59
74_L 294_Y 1.05 0.74 0.58
102_I 305_C 1.03 0.73 0.57
57_I 93_S 1.01 0.71 0.55
126_A 174_F 1.01 0.70 0.54
74_L 128_Y 1.00 0.70 0.53
67_F 159_F 1.00 0.69 0.53
141_V 39_L 1.00 0.69 0.53
3_F 11_I 0.99 0.69 0.52
67_F 294_Y 0.99 0.69 0.52
95_G 16_L 0.99 0.68 0.52
63_I 185_H 0.99 0.68 0.52
97_A 19_V 0.97 0.66 0.49
60_A 219_Q 0.96 0.65 0.48
65_V 161_G 0.94 0.62 0.46
25_P 294_Y 0.94 0.62 0.45
25_P 128_Y 0.93 0.61 0.44
4_A 234_F 0.92 0.60 0.44
143_L 225_Y 0.92 0.60 0.43
63_I 80_R 0.92 0.60 0.43
30_L 82_I 0.91 0.59 0.42
90_P 22_L 0.91 0.59 0.42
68_V 147_M 0.91 0.58 0.41
153_V 118_F 0.91 0.58 0.41
17_L 90_A 0.90 0.58 0.41
63_I 226_H 0.90 0.58 0.41
43_F 240_G 0.90 0.57 0.40
40_S 122_M 0.89 0.57 0.40
31_Y 196_F 0.88 0.55 0.38
150_A 265_L 0.88 0.54 0.38
160_R 194_F 0.87 0.54 0.37
20_I 245_I 0.87 0.53 0.37
13_I 240_G 0.87 0.53 0.36
23_T 129_A 0.86 0.52 0.36
64_M 161_G 0.84 0.50 0.33
92_V 240_G 0.84 0.50 0.33
46_L 162_L 0.83 0.49 0.32
146_M 196_F 0.83 0.48 0.32
74_L 161_G 0.82 0.48 0.32
18_R 130_V 0.82 0.47 0.31
58_V 18_A 0.81 0.47 0.30
29_L 151_A 0.81 0.46 0.30
134_F 128_Y 0.81 0.46 0.30
3_F 201_I 0.81 0.46 0.30
51_A 199_F 0.81 0.46 0.30
30_L 133_A 0.81 0.46 0.30
37_L 306_L 0.80 0.45 0.29
19_V 305_C 0.80 0.45 0.29
70_V 161_G 0.80 0.44 0.29
27_H 158_V 0.80 0.44 0.29
65_V 127_V 0.80 0.44 0.28
57_I 69_F 0.80 0.44 0.28
107_I 319_V 0.80 0.44 0.28
49_Y 112_L 0.79 0.43 0.28
70_V 298_M 0.79 0.43 0.28
29_L 133_A 0.79 0.43 0.27
14_L 19_V 0.79 0.43 0.27
41_G 232_M 0.79 0.43 0.27
15_A 300_F 0.78 0.42 0.27
89_K 223_D 0.78 0.42 0.27
133_L 308_L 0.78 0.42 0.26
36_L 98_F 0.78 0.41 0.26
131_I 197_I 0.77 0.41 0.26
145_S 201_I 0.77 0.41 0.25
140_A 288_S 0.77 0.40 0.25
92_V 118_F 0.77 0.40 0.25
67_F 127_V 0.76 0.40 0.25
158_V 17_K 0.76 0.40 0.24
69_F 144_L 0.76 0.39 0.24
97_A 190_I 0.76 0.39 0.24
4_A 51_R 0.76 0.39 0.24
13_I 84_T 0.75 0.39 0.24
45_S 78_S 0.75 0.39 0.24
130_G 100_I 0.75 0.38 0.23
11_I 201_I 0.75 0.38 0.23
123_P 251_L 0.75 0.38 0.23
74_L 159_F 0.75 0.38 0.23
30_L 180_V 0.75 0.38 0.23
152_L 159_F 0.75 0.38 0.23
43_F 233_K 0.75 0.38 0.23
119_I 15_V 0.74 0.37 0.23
61_G 87_P 0.74 0.37 0.23
147_L 50_N 0.74 0.37 0.22
72_M 83_F 0.74 0.37 0.22
73_M 300_F 0.73 0.36 0.22
70_V 147_M 0.73 0.36 0.22
33_I 26_V 0.73 0.36 0.22
158_V 256_F 0.73 0.36 0.22
129_V 21_I 0.73 0.36 0.21
36_L 29_G 0.73 0.36 0.21
95_G 89_I 0.73 0.36 0.21
30_L 132_F 0.73 0.35 0.21
106_V 64_M 0.73 0.35 0.21
103_M 244_G 0.72 0.35 0.21
129_V 223_D 0.72 0.35 0.21
142_E 93_S 0.72 0.35 0.21
75_N 282_F 0.72 0.35 0.21
76_L 128_Y 0.72 0.34 0.20
33_I 294_Y 0.71 0.34 0.20
9_G 269_I 0.71 0.34 0.20
145_S 221_L 0.71 0.34 0.20
6_Y 97_A 0.71 0.34 0.20
20_I 31_F 0.71 0.33 0.20
39_I 174_F 0.71 0.33 0.20
155_A 285_I 0.71 0.33 0.19
106_V 16_L 0.71 0.33 0.19
26_V 247_T 0.71 0.33 0.19
68_V 128_Y 0.71 0.33 0.19
100_S 314_L 0.70 0.33 0.19
25_P 219_Q 0.70 0.33 0.19
103_M 257_F 0.70 0.33 0.19
44_F 114_I 0.70 0.33 0.19
76_L 294_Y 0.70 0.33 0.19
110_A 253_V 0.70 0.32 0.18
24_N 125_L 0.70 0.32 0.18
109_Y 85_L 0.69 0.32 0.18
18_R 120_L 0.69 0.31 0.18
6_Y 317_A 0.69 0.31 0.18
115_N 61_V 0.69 0.31 0.18
30_L 40_L 0.68 0.30 0.17
146_M 34_F 0.68 0.30 0.17
138_V 153_T 0.68 0.30 0.17
56_I 68_F 0.68 0.30 0.17
134_F 287_A 0.68 0.30 0.17
144_A 169_A 0.68 0.30 0.17
26_V 167_V 0.68 0.30 0.17
71_V 108_V 0.68 0.30 0.17
154_V 124_G 0.68 0.30 0.17
13_I 126_A 0.68 0.30 0.17
35_S 136_S 0.68 0.30 0.17
8_C 111_D 0.68 0.30 0.17
138_V 44_Q 0.68 0.30 0.17
73_M 292_P 0.68 0.30 0.17
43_F 254_T 0.67 0.29 0.16
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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