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OPENSEQ.org
ExR
Genes: A B A+B
Length: 98 255 342
Sequences: 888 1848 684
Seq/Len: 9.06 7.25 2
MirrorTree (Pazo et al. 2001) 0.74
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 0.00
2 0.00 0.00 0.00
5 0.00 0.01 0.01
10 0.00 0.01 0.10
20 0.00 0.02 1.78
100 0.01 0.03 1.94
∞ 0.01 0.07 2.19
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
85_K 113_D 1.61 0.94 0.68
62_L 232_L 1.45 0.89 0.54
96_T 209_F 1.32 0.82 0.42
86_A 73_I 1.31 0.81 0.41
61_D 211_L 1.29 0.80 0.39
40_L 210_N 1.28 0.79 0.38
58_Q 126_I 1.27 0.79 0.37
37_I 42_K 1.26 0.78 0.36
97_Q 199_F 1.21 0.74 0.32
54_I 206_M 1.21 0.74 0.32
95_R 108_M 1.19 0.72 0.31
71_K 214_I 1.18 0.71 0.30
76_M 196_D 1.18 0.71 0.29
81_E 209_F 1.18 0.71 0.29
92_E 211_L 1.15 0.69 0.27
31_K 162_P 1.15 0.69 0.27
69_I 101_A 1.15 0.68 0.27
63_H 185_S 1.15 0.68 0.27
54_I 119_S 1.11 0.64 0.24
76_M 213_V 1.09 0.62 0.23
74_S 33_S 1.07 0.60 0.21
72_A 35_N 1.06 0.59 0.21
93_I 16_M 1.06 0.59 0.20
55_A 199_F 1.05 0.57 0.20
95_R 220_I 1.03 0.56 0.18
75_S 49_L 1.03 0.55 0.18
93_I 38_P 1.03 0.55 0.18
37_I 51_M 1.02 0.55 0.18
85_K 49_L 1.01 0.54 0.17
81_E 135_F 1.01 0.54 0.17
50_A 210_N 1.01 0.54 0.17
67_I 70_L 1.01 0.54 0.17
95_R 196_D 1.00 0.52 0.16
81_E 75_E 0.99 0.51 0.16
98_I 112_L 0.99 0.51 0.16
85_K 115_S 0.98 0.50 0.15
42_K 47_L 0.97 0.49 0.15
91_K 139_D 0.97 0.49 0.15
22_S 49_L 0.97 0.49 0.15
85_K 87_Q 0.96 0.48 0.14
94_T 212_L 0.96 0.48 0.14
97_Q 128_N 0.95 0.47 0.14
49_A 123_T 0.95 0.47 0.14
60_K 211_L 0.94 0.46 0.13
97_Q 220_I 0.94 0.46 0.13
86_A 58_R 0.94 0.45 0.13
72_A 80_M 0.93 0.45 0.13
27_D 42_K 0.93 0.45 0.13
98_I 226_V 0.93 0.45 0.13
24_G 124_S 0.93 0.45 0.13
61_D 186_F 0.93 0.44 0.13
93_I 133_M 0.93 0.44 0.12
60_K 45_I 0.92 0.44 0.12
77_K 162_P 0.92 0.44 0.12
35_N 132_L 0.92 0.43 0.12
74_S 20_A 0.92 0.43 0.12
95_R 219_K 0.91 0.43 0.12
51_M 115_S 0.91 0.43 0.12
30_A 185_S 0.91 0.43 0.12
87_I 239_K 0.91 0.42 0.12
92_E 155_I 0.91 0.42 0.12
49_A 181_G 0.91 0.42 0.12
52_T 12_V 0.91 0.42 0.12
72_A 228_I 0.91 0.42 0.12
86_A 54_Y 0.91 0.42 0.12
69_I 192_S 0.90 0.42 0.12
70_T 209_F 0.90 0.41 0.11
79_M 149_S 0.90 0.41 0.11
97_Q 218_I 0.90 0.41 0.11
68_A 210_N 0.90 0.41 0.11
62_L 75_E 0.90 0.41 0.11
87_I 148_L 0.90 0.41 0.11
25_I 37_I 0.90 0.41 0.11
63_H 203_M 0.90 0.41 0.11
28_E 72_L 0.89 0.41 0.11
71_K 177_I 0.89 0.40 0.11
67_I 47_L 0.89 0.40 0.11
64_Q 19_L 0.89 0.40 0.11
37_I 92_I 0.89 0.40 0.11
63_H 138_F 0.89 0.40 0.11
54_I 25_L 0.89 0.40 0.11
34_K 12_V 0.88 0.39 0.10
50_A 43_S 0.88 0.39 0.10
40_L 122_I 0.88 0.39 0.10
63_H 224_F 0.87 0.38 0.10
85_K 168_H 0.87 0.38 0.10
34_K 220_I 0.87 0.38 0.10
79_M 210_N 0.87 0.38 0.10
78_F 195_A 0.86 0.38 0.10
16_T 204_K 0.86 0.38 0.10
65_A 209_F 0.86 0.37 0.10
62_L 84_L 0.86 0.37 0.10
91_K 224_F 0.86 0.37 0.10
80_L 86_L 0.86 0.37 0.10
86_A 110_S 0.85 0.36 0.09
69_I 182_F 0.85 0.36 0.09
18_K 82_A 0.85 0.35 0.09
50_A 29_F 0.85 0.35 0.09
31_K 43_S 0.84 0.35 0.09
70_T 246_F 0.84 0.35 0.09
80_L 26_I 0.84 0.35 0.09
49_A 85_M 0.84 0.35 0.09
93_I 212_L 0.84 0.35 0.09
48_E 19_L 0.84 0.34 0.09
87_I 211_L 0.84 0.34 0.09
86_A 18_L 0.83 0.34 0.09
67_I 201_L 0.83 0.34 0.09
24_G 112_L 0.83 0.34 0.08
20_Q 54_Y 0.83 0.34 0.08
37_I 244_E 0.82 0.33 0.08
42_K 225_V 0.82 0.33 0.08
86_A 157_L 0.82 0.33 0.08
72_A 129_L 0.82 0.33 0.08
70_T 183_T 0.82 0.33 0.08
35_N 199_F 0.82 0.33 0.08
67_I 15_F 0.82 0.33 0.08
79_M 116_S 0.82 0.33 0.08
51_M 222_L 0.81 0.32 0.08
94_T 121_P 0.81 0.32 0.08
93_I 46_V 0.81 0.32 0.08
55_A 139_D 0.81 0.32 0.08
22_S 73_I 0.81 0.32 0.08
88_S 136_L 0.81 0.32 0.08
70_T 86_L 0.81 0.32 0.08
51_M 73_I 0.81 0.32 0.07
46_S 17_L 0.81 0.32 0.07
77_K 214_I 0.81 0.31 0.07
39_D 177_I 0.80 0.31 0.07
39_D 145_L 0.80 0.31 0.07
73_E 136_L 0.80 0.31 0.07
76_M 106_F 0.80 0.31 0.07
55_A 72_L 0.80 0.31 0.07
95_R 6_Y 0.80 0.31 0.07
87_I 199_F 0.79 0.30 0.07
50_A 63_H 0.79 0.30 0.07
40_L 84_L 0.79 0.30 0.07
46_S 222_L 0.79 0.30 0.07
45_E 123_T 0.79 0.30 0.07
75_S 20_A 0.79 0.30 0.07
64_Q 204_K 0.79 0.30 0.07
82_V 29_F 0.79 0.30 0.07
95_R 194_L 0.79 0.30 0.07
97_Q 208_Q 0.79 0.30 0.07
45_E 26_I 0.79 0.30 0.07
28_E 81_I 0.79 0.30 0.07
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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