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OPENSEQ.org
L20-vs-S4
Genes: A B A+B
Length: 118 206 320
Sequences: 1984 1236 754
Seq/Len: 16.81 6 2.36
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 0.10 0.09 0.02
2 0.10 0.09 0.04
5 0.10 0.09 0.08
10 0.10 0.09 0.16
20 0.10 0.09 0.38
100 0.10 0.09 1.04
∞ 0.10 0.09 2.33
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
19_K 200_I 1.32 0.86 0.18
96_A 180_G 1.10 0.68 0.09
51_R 73_R 1.07 0.65 0.08
57_F 93_L 1.05 0.63 0.08
33_R 86_T 1.00 0.57 0.07
86_A 142_V 0.95 0.52 0.06
51_R 37_A 0.95 0.52 0.06
13_R 180_G 0.94 0.50 0.05
90_I 119_S 0.92 0.48 0.05
36_F 170_W 0.92 0.47 0.05
81_N 180_G 0.91 0.47 0.05
14_H 198_H 0.90 0.46 0.05
103_K 81_R 0.90 0.46 0.05
81_N 143_V 0.90 0.46 0.05
32_Y 198_H 0.90 0.45 0.04
80_I 132_I 0.89 0.45 0.04
14_H 3_R 0.89 0.44 0.04
79_F 128_R 0.88 0.43 0.04
31_V 121_K 0.86 0.41 0.04
13_R 105_M 0.86 0.41 0.04
39_V 140_N 0.85 0.40 0.04
27_A 62_R 0.84 0.39 0.04
41_K 193_A 0.83 0.38 0.04
91_D 50_D 0.83 0.38 0.04
56_Q 46_P 0.82 0.37 0.03
33_R 78_E 0.82 0.37 0.03
109_L 94_L 0.82 0.37 0.03
49_D 110_T 0.81 0.36 0.03
113_A 127_G 0.81 0.36 0.03
79_F 56_R 0.81 0.35 0.03
57_F 38_P 0.80 0.35 0.03
5_K 106_G 0.79 0.34 0.03
99_A 60_K 0.79 0.34 0.03
51_R 169_T 0.79 0.34 0.03
69_A 143_V 0.79 0.33 0.03
97_D 64_I 0.78 0.33 0.03
18_L 108_G 0.78 0.32 0.03
82_G 127_G 0.77 0.32 0.03
39_V 50_D 0.77 0.31 0.03
17_I 118_V 0.76 0.31 0.03
33_R 92_A 0.76 0.31 0.03
7_G 110_T 0.76 0.31 0.03
14_H 197_E 0.76 0.30 0.03
53_R 205_S 0.75 0.30 0.03
67_A 87_G 0.75 0.29 0.03
66_N 115_R 0.74 0.29 0.03
24_Y 157_A 0.74 0.29 0.03
43_G 47_R 0.74 0.29 0.02
84_K 175_A 0.74 0.28 0.02
38_A 119_S 0.74 0.28 0.02
27_A 49_S 0.74 0.28 0.02
21_A 119_S 0.74 0.28 0.02
14_H 40_Q 0.73 0.28 0.02
79_F 135_Y 0.73 0.28 0.02
6_R 5_L 0.73 0.27 0.02
98_I 5_L 0.73 0.27 0.02
39_V 118_V 0.72 0.27 0.02
105_A 201_V 0.72 0.26 0.02
86_A 181_T 0.71 0.26 0.02
94_I 81_R 0.71 0.26 0.02
79_F 57_E 0.70 0.25 0.02
86_A 158_A 0.70 0.25 0.02
108_A 76_Y 0.70 0.25 0.02
104_V 67_V 0.70 0.25 0.02
59_Q 174_D 0.70 0.25 0.02
48_R 152_Q 0.70 0.25 0.02
32_Y 151_K 0.70 0.25 0.02
22_K 77_K 0.70 0.25 0.02
9_I 200_I 0.69 0.24 0.02
71_Q 124_M 0.69 0.24 0.02
14_H 122_A 0.69 0.24 0.02
32_Y 175_A 0.69 0.24 0.02
74_I 185_K 0.69 0.24 0.02
10_A 8_K 0.69 0.24 0.02
10_A 5_L 0.69 0.24 0.02
43_G 182_F 0.69 0.24 0.02
43_G 15_E 0.68 0.23 0.02
90_I 178_M 0.68 0.23 0.02
53_R 156_K 0.68 0.23 0.02
4_V 159_L 0.68 0.23 0.02
49_D 131_N 0.68 0.23 0.02
21_A 118_V 0.67 0.23 0.02
6_R 19_L 0.67 0.23 0.02
111_E 142_V 0.67 0.23 0.02
25_Y 178_M 0.67 0.22 0.02
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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