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OPENSEQ.org
JMb
Genes: A B A+B
Length: 167 134 281
Sequences: 583 772 422
Seq/Len: 3.49 5.76 1.5
MirrorTree (Pazo et al. 2001) 0.79
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 0.02
2 0.00 0.00 0.09
5 0.00 0.00 1.09
10 0.00 0.00 1.37
20 0.00 0.03 1.40
100 0.01 0.05 1.44
∞ 0.09 0.13 1.51
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
55_P 36_H 2.36 1.00 0.98
74_F 38_P 1.57 0.89 0.79
94_E 35_R 1.51 0.87 0.75
55_P 76_W 1.46 0.84 0.70
130_W 47_P 1.41 0.81 0.66
64_K 125_L 1.41 0.81 0.66
131_R 17_D 1.38 0.79 0.63
57_V 35_R 1.37 0.79 0.62
57_V 9_F 1.37 0.78 0.62
122_Y 41_P 1.34 0.77 0.60
54_S 36_H 1.32 0.75 0.58
55_P 16_L 1.30 0.74 0.56
46_N 34_Y 1.23 0.68 0.48
33_T 109_Y 1.16 0.60 0.40
138_A 107_A 1.15 0.59 0.39
47_P 16_L 1.15 0.59 0.39
120_A 75_P 1.13 0.58 0.37
61_F 41_P 1.12 0.56 0.36
97_L 24_E 1.09 0.54 0.33
146_L 24_E 1.07 0.52 0.31
130_W 85_M 1.07 0.51 0.31
61_F 23_A 1.06 0.51 0.30
94_E 109_Y 1.05 0.49 0.29
21_A 78_L 1.05 0.49 0.28
37_L 70_E 1.03 0.48 0.27
37_L 62_M 1.03 0.47 0.27
73_D 103_G 1.03 0.47 0.27
63_L 131_P 1.03 0.47 0.27
21_A 132_V 1.02 0.46 0.26
116_V 123_A 1.01 0.45 0.25
75_F 17_D 1.00 0.44 0.24
123_R 17_D 1.00 0.44 0.24
116_V 73_T 0.99 0.44 0.24
110_E 20_V 0.99 0.43 0.24
51_G 34_Y 0.99 0.43 0.23
41_A 14_Y 0.99 0.43 0.23
97_L 51_D 0.99 0.43 0.23
51_G 61_K 0.98 0.42 0.23
109_V 22_R 0.98 0.42 0.23
18_A 11_L 0.98 0.42 0.22
35_L 109_Y 0.97 0.41 0.22
50_N 15_T 0.97 0.41 0.21
75_F 36_H 0.96 0.40 0.20
36_D 11_L 0.95 0.39 0.20
90_V 82_F 0.95 0.39 0.20
131_R 30_Q 0.95 0.39 0.20
78_Y 85_M 0.95 0.39 0.20
128_A 61_K 0.94 0.38 0.19
96_E 35_R 0.94 0.38 0.19
41_A 20_V 0.94 0.38 0.19
100_G 119_P 0.93 0.38 0.19
24_S 44_F 0.93 0.37 0.19
122_Y 134_L 0.93 0.37 0.18
110_E 25_F 0.92 0.36 0.18
104_E 32_M 0.92 0.36 0.17
72_A 6_Q 0.92 0.36 0.17
71_N 56_S 0.91 0.35 0.17
129_S 77_S 0.91 0.35 0.17
97_L 101_D 0.91 0.35 0.17
105_L 111_L 0.91 0.35 0.17
49_L 111_L 0.91 0.35 0.17
61_F 21_S 0.91 0.35 0.17
47_P 36_H 0.90 0.34 0.17
108_S 113_A 0.90 0.34 0.17
133_V 122_L 0.90 0.34 0.16
44_R 59_L 0.90 0.34 0.16
51_G 80_R 0.89 0.34 0.16
122_Y 98_L 0.89 0.33 0.16
135_P 5_P 0.89 0.33 0.16
130_W 78_L 0.89 0.33 0.16
84_T 127_S 0.88 0.33 0.15
121_A 37_G 0.88 0.33 0.15
82_K 73_T 0.88 0.32 0.15
37_L 45_K 0.88 0.32 0.15
35_L 125_L 0.87 0.32 0.14
142_T 9_F 0.87 0.32 0.14
15_A 73_T 0.87 0.32 0.14
123_R 105_L 0.87 0.31 0.14
49_L 133_Q 0.87 0.31 0.14
116_V 89_Y 0.87 0.31 0.14
39_L 19_G 0.87 0.31 0.14
94_E 17_D 0.87 0.31 0.14
122_Y 109_Y 0.86 0.31 0.14
133_V 116_T 0.86 0.31 0.14
78_Y 28_D 0.86 0.31 0.14
99_P 74_G 0.86 0.31 0.14
19_L 55_T 0.86 0.30 0.14
40_S 86_Q 0.86 0.30 0.14
155_N 25_F 0.85 0.30 0.13
23_C 74_G 0.85 0.30 0.13
89_L 45_K 0.85 0.30 0.13
125_L 38_P 0.85 0.30 0.13
153_I 51_D 0.85 0.30 0.13
20_L 28_D 0.85 0.30 0.13
22_G 132_V 0.85 0.29 0.13
153_I 13_P 0.85 0.29 0.13
125_L 17_D 0.84 0.29 0.12
138_A 7_V 0.84 0.29 0.12
136_V 88_E 0.84 0.29 0.12
54_S 16_L 0.83 0.28 0.12
117_G 16_L 0.83 0.28 0.12
116_V 98_L 0.83 0.28 0.12
78_Y 12_E 0.83 0.28 0.12
81_P 27_F 0.82 0.28 0.12
113_S 12_E 0.82 0.28 0.12
126_G 106_R 0.82 0.28 0.12
39_L 125_L 0.82 0.28 0.12
112_G 88_E 0.82 0.27 0.12
114_R 59_L 0.82 0.27 0.12
57_V 98_L 0.82 0.27 0.11
78_Y 58_V 0.82 0.27 0.11
21_A 8_R 0.82 0.27 0.11
58_V 102_L 0.81 0.27 0.11
82_K 25_F 0.81 0.27 0.11
44_R 83_D 0.81 0.27 0.11
16_V 11_L 0.81 0.27 0.11
159_L 133_Q 0.81 0.27 0.11
16_V 86_Q 0.81 0.26 0.11
117_G 104_G 0.81 0.26 0.11
142_T 107_A 0.81 0.26 0.11
105_L 49_D 0.81 0.26 0.11
121_A 36_H 0.80 0.26 0.10
61_F 34_Y 0.80 0.26 0.10
22_G 68_G 0.80 0.26 0.10
88_D 120_F 0.80 0.26 0.10
69_F 38_P 0.80 0.26 0.10
100_G 83_D 0.80 0.26 0.10
92_S 51_D 0.80 0.26 0.10
73_D 83_D 0.80 0.26 0.10
79_E 40_V 0.80 0.25 0.10
48_D 126_R 0.80 0.25 0.10
127_E 104_G 0.80 0.25 0.10
45_V 5_P 0.79 0.25 0.10
53_P 72_N 0.79 0.25 0.10
118_V 15_T 0.79 0.25 0.10
73_D 38_P 0.79 0.25 0.10
128_A 36_H 0.79 0.25 0.10
111_E 52_G 0.79 0.24 0.10
95_L 104_G 0.78 0.24 0.10
109_V 71_R 0.78 0.24 0.10
87_P 66_P 0.78 0.24 0.10
43_E 78_L 0.78 0.24 0.09
122_Y 62_M 0.78 0.24 0.09
115_Y 129_R 0.78 0.24 0.09
59_R 3_A 0.78 0.24 0.09
43_E 58_V 0.78 0.24 0.09
105_L 85_M 0.78 0.24 0.09
119_L 85_M 0.78 0.24 0.09
53_P 47_P 0.78 0.24 0.09
60_L 127_S 0.77 0.24 0.09
23_C 46_W 0.77 0.24 0.09
72_A 95_V 0.77 0.23 0.09
65_H 96_M 0.77 0.23 0.09
128_A 23_A 0.77 0.23 0.09
78_Y 134_L 0.77 0.23 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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