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OPENSEQ.org
1ze3_D_C
Genes: A B A+B
Length: 125 205 328
Sequences: 294 2071 239
Seq/Len: 2.35 10.1 0.73
MirrorTree (Pazo et al. 2001) 0.74
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 0.01 0.01 0.65
2 0.01 0.03 0.70
5 0.01 0.14 0.72
10 0.01 0.15 0.72
20 0.01 0.16 0.72
100 0.01 0.20 0.73
∞ 0.05 0.26 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
8_F 106_A 2.07 0.94 0.64
5_N 104_Q 2.02 0.93 0.61
90_C 106_A 1.71 0.81 0.36
63_C 106_A 1.50 0.68 0.22
113_L 114_Y 1.43 0.62 0.18
109_Q 104_Q 1.38 0.58 0.15
8_F 87_V 1.31 0.52 0.12
9_L 185_I 1.30 0.51 0.12
26_Q 59_G 1.28 0.50 0.11
110_R 10_I 1.24 0.47 0.10
90_C 82_L 1.22 0.45 0.09
114_T 101_N 1.21 0.44 0.09
4_F 32_L 1.18 0.41 0.08
51_F 187_Y 1.18 0.41 0.08
11_D 63_N 1.16 0.40 0.07
39_L 15_Q 1.15 0.39 0.07
60_I 88_K 1.14 0.38 0.07
63_C 82_L 1.14 0.38 0.07
51_F 33_I 1.13 0.37 0.06
18_D 32_L 1.12 0.37 0.06
76_T 67_I 1.12 0.37 0.06
110_R 197_T 1.12 0.36 0.06
35_V 185_I 1.11 0.36 0.06
63_C 92_S 1.11 0.36 0.06
49_V 10_I 1.10 0.35 0.06
2_L 30_T 1.10 0.35 0.06
60_I 37_V 1.09 0.34 0.06
72_M 61_K 1.08 0.34 0.05
1_D 103_L 1.07 0.33 0.05
65_T 105_L 1.07 0.33 0.05
19_L 145_P 1.07 0.33 0.05
14_Q 14_G 1.04 0.31 0.05
90_C 92_S 1.04 0.30 0.04
53_T 160_R 1.03 0.30 0.04
107_G 176_K 1.03 0.29 0.04
118_A 38_E 1.02 0.29 0.04
16_V 17_Q 1.02 0.29 0.04
71_S 152_V 1.02 0.29 0.04
65_T 81_S 1.01 0.28 0.04
4_F 33_I 1.01 0.28 0.04
57_E 14_G 1.00 0.27 0.04
110_R 131_L 0.99 0.27 0.04
3_Y 89_A 0.99 0.27 0.04
28_L 54_L 0.98 0.27 0.04
4_F 30_T 0.98 0.27 0.04
10_A 88_K 0.98 0.26 0.04
51_F 128_A 0.98 0.26 0.04
107_G 61_K 0.98 0.26 0.04
124_A 87_V 0.98 0.26 0.04
49_V 9_V 0.97 0.26 0.03
68_Q 39_N 0.97 0.25 0.03
119_F 54_L 0.97 0.25 0.03
28_L 63_N 0.96 0.25 0.03
45_A 46_G 0.95 0.24 0.03
26_Q 114_Y 0.95 0.24 0.03
109_Q 61_K 0.94 0.23 0.03
62_P 132_R 0.93 0.23 0.03
92_P 59_G 0.93 0.23 0.03
120_M 171_G 0.93 0.23 0.03
95_T 50_V 0.93 0.23 0.03
60_I 57_M 0.93 0.23 0.03
109_Q 113_L 0.93 0.23 0.03
24_N 146_T 0.93 0.23 0.03
13_P 62_E 0.92 0.23 0.03
10_A 108_I 0.92 0.23 0.03
30_P 50_V 0.92 0.23 0.03
41_N 107_I 0.92 0.23 0.03
49_V 190_I 0.92 0.22 0.03
98_Q 70_A 0.92 0.22 0.03
99_D 101_N 0.91 0.22 0.03
46_T 79_R 0.91 0.22 0.03
28_L 55_F 0.91 0.22 0.03
39_L 119_K 0.90 0.22 0.03
104_L 103_L 0.90 0.21 0.03
23_E 92_S 0.89 0.21 0.02
53_T 77_Q 0.89 0.21 0.02
46_T 92_S 0.89 0.21 0.02
19_L 54_L 0.87 0.20 0.02
96_M 19_Q 0.87 0.20 0.02
49_V 87_V 0.87 0.20 0.02
101_T 145_P 0.86 0.19 0.02
9_L 104_Q 0.86 0.19 0.02
4_F 90_I 0.86 0.19 0.02
21_R 88_K 0.86 0.19 0.02
8_F 89_A 0.86 0.19 0.02
45_A 63_N 0.86 0.19 0.02
39_L 58_K 0.85 0.19 0.02
26_Q 166_L 0.85 0.19 0.02
104_L 3_A 0.85 0.19 0.02
89_A 79_R 0.85 0.18 0.02
5_N 13_A 0.85 0.18 0.02
91_V 57_M 0.85 0.18 0.02
35_V 95_K 0.85 0.18 0.02
36_D 155_L 0.84 0.18 0.02
61_V 152_V 0.84 0.18 0.02
20_S 20_L 0.84 0.18 0.02
46_T 63_N 0.84 0.18 0.02
16_V 62_E 0.84 0.18 0.02
18_D 67_I 0.84 0.18 0.02
113_L 149_Y 0.84 0.18 0.02
63_C 20_L 0.84 0.18 0.02
69_L 55_F 0.83 0.18 0.02
6_P 92_S 0.83 0.18 0.02
105_D 36_W 0.83 0.18 0.02
2_L 83_F 0.83 0.18 0.02
124_A 171_G 0.83 0.18 0.02
31_G 52_P 0.83 0.18 0.02
31_G 80_E 0.83 0.18 0.02
31_G 116_R 0.83 0.18 0.02
31_G 144_N 0.83 0.18 0.02
62_P 49_I 0.83 0.18 0.02
49_V 201_T 0.83 0.17 0.02
24_N 155_L 0.82 0.17 0.02
28_L 18_E 0.82 0.17 0.02
112_N 37_V 0.82 0.17 0.02
49_V 4_L 0.82 0.17 0.02
113_L 54_L 0.82 0.17 0.02
104_L 66_R 0.82 0.17 0.02
16_V 189_T 0.82 0.17 0.02
46_T 5_G 0.82 0.17 0.02
19_L 1_G 0.81 0.17 0.02
125_R 66_R 0.81 0.17 0.02
37_I 170_M 0.81 0.17 0.02
21_R 15_Q 0.81 0.17 0.02
115_I 22_V 0.81 0.17 0.02
49_V 2_V 0.81 0.17 0.02
109_Q 66_R 0.81 0.17 0.02
99_D 90_I 0.81 0.17 0.02
29_P 49_I 0.81 0.17 0.02
17_A 54_L 0.80 0.16 0.02
98_Q 129_E 0.80 0.16 0.02
28_L 15_Q 0.80 0.16 0.02
113_L 166_L 0.80 0.16 0.02
119_F 148_Y 0.80 0.16 0.02
60_I 89_A 0.80 0.16 0.02
124_A 151_T 0.80 0.16 0.02
6_P 1_G 0.80 0.16 0.01
114_T 118_A 0.80 0.16 0.01
41_N 153_T 0.79 0.16 0.01
3_Y 31_Y 0.79 0.16 0.01
37_I 3_A 0.79 0.16 0.01
68_Q 57_M 0.79 0.16 0.01
87_D 19_Q 0.79 0.16 0.01
70_A 170_M 0.79 0.16 0.01
16_V 195_A 0.79 0.16 0.01
86_A 131_L 0.79 0.16 0.01
14_Q 105_L 0.79 0.16 0.01
111_L 91_P 0.79 0.16 0.01
50_T 49_I 0.79 0.15 0.01
74_L 200_M 0.79 0.15 0.01
99_D 20_L 0.79 0.15 0.01
59_G 143_I 0.78 0.15 0.01
64_L 130_K 0.78 0.15 0.01
125_R 71_T 0.78 0.15 0.01
22_F 145_P 0.78 0.15 0.01
71_S 181_A 0.78 0.15 0.01
69_L 195_A 0.78 0.15 0.01
120_M 74_Q 0.78 0.15 0.01
99_D 83_F 0.78 0.15 0.01
80_A 75_L 0.78 0.15 0.01
6_P 89_A 0.78 0.15 0.01
5_N 102_T 0.78 0.15 0.01
17_A 30_T 0.77 0.15 0.01
65_T 155_L 0.77 0.15 0.01
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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