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OPENSEQ.org
3i1m_C_N
Genes: A B A+B
Length: 233 101 313
Sequences: 2210 1732 603
Seq/Len: 9.48 17.15 1.93
MirrorTree (Pazo et al. 2001) 0.75
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 0.09 0.09 0.00
2 0.09 0.09 0.00
5 0.09 0.09 0.10
10 0.09 0.09 1.62
20 0.09 0.09 1.81
100 0.09 0.09 2.32
∞ 0.09 0.09 2.87
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
29_F 93_I 2.29 1.00 0.99
29_F 74_L 1.62 0.94 0.87
88_R 55_S 1.50 0.91 0.81
43_L 99_A 1.50 0.91 0.81
10_I 71_H 1.39 0.85 0.73
23_F 54_D 1.35 0.83 0.70
23_F 51_L 1.26 0.77 0.62
33_L 93_I 1.23 0.75 0.59
101_I 28_K 1.22 0.73 0.57
181_D 54_D 1.18 0.70 0.53
9_G 89_M 1.17 0.69 0.52
64_I 77_F 1.15 0.67 0.50
8_N 91_G 1.07 0.59 0.41
31_D 65_R 1.05 0.57 0.39
37_F 87_A 1.03 0.55 0.36
153_V 6_M 1.03 0.55 0.36
147_K 4_Q 1.03 0.54 0.36
113_A 81_R 1.03 0.54 0.36
30_A 77_F 1.01 0.53 0.34
61_A 77_F 1.01 0.53 0.34
14_I 96_L 1.00 0.51 0.33
165_T 6_M 0.99 0.50 0.32
84_V 8_A 0.99 0.50 0.32
13_G 97_K 0.99 0.50 0.32
99_A 22_A 0.98 0.49 0.30
5_V 35_N 0.97 0.48 0.30
153_V 57_P 0.97 0.48 0.30
145_G 91_G 0.97 0.48 0.30
213_A 99_A 0.96 0.47 0.28
29_F 42_W 0.94 0.45 0.27
19_N 92_E 0.94 0.45 0.27
138_V 54_D 0.94 0.45 0.27
182_I 23_K 0.93 0.44 0.26
208_L 72_G 0.93 0.43 0.26
165_T 53_R 0.93 0.43 0.26
198_V 7_K 0.93 0.43 0.25
57_I 23_K 0.92 0.43 0.25
16_K 91_G 0.92 0.42 0.24
52_V 73_F 0.91 0.42 0.24
154_S 54_D 0.91 0.41 0.24
140_N 89_M 0.91 0.41 0.23
160_A 20_Y 0.91 0.41 0.23
18_W 93_I 0.91 0.41 0.23
3_Q 86_E 0.90 0.41 0.23
55_I 11_V 0.90 0.40 0.23
28_E 80_S 0.90 0.40 0.23
32_N 80_S 0.89 0.40 0.22
57_I 61_R 0.89 0.39 0.22
117_A 19_K 0.89 0.39 0.22
31_D 55_S 0.89 0.39 0.22
75_I 4_Q 0.89 0.39 0.22
41_Q 15_A 0.89 0.39 0.22
5_V 89_M 0.88 0.38 0.21
63_S 92_E 0.88 0.38 0.21
6_H 90_R 0.87 0.38 0.20
173_V 79_L 0.87 0.37 0.20
68_I 37_S 0.87 0.37 0.20
114_K 80_S 0.86 0.37 0.20
23_F 16_L 0.86 0.36 0.19
193_Y 83_K 0.85 0.36 0.19
80_K 44_A 0.85 0.35 0.18
85_E 97_K 0.84 0.34 0.18
119_S 99_A 0.84 0.34 0.18
151_V 37_S 0.84 0.34 0.18
129_M 89_M 0.84 0.34 0.18
202_I 75_R 0.83 0.33 0.17
154_S 23_K 0.83 0.33 0.17
55_I 41_R 0.82 0.33 0.17
89_K 73_F 0.82 0.32 0.17
97_V 84_V 0.82 0.32 0.17
35_S 60_Q 0.82 0.32 0.16
24_A 44_A 0.82 0.32 0.16
158_G 42_W 0.82 0.32 0.16
198_V 75_R 0.81 0.32 0.16
84_V 42_W 0.81 0.32 0.16
23_F 56_S 0.81 0.31 0.16
152_E 9_R 0.81 0.31 0.16
149_I 54_D 0.81 0.31 0.16
66_V 40_D 0.81 0.31 0.15
60_P 93_I 0.81 0.31 0.15
35_S 89_M 0.81 0.31 0.15
38_K 56_S 0.80 0.31 0.15
120_I 73_F 0.80 0.30 0.15
83_D 84_V 0.80 0.30 0.15
152_E 49_Q 0.80 0.30 0.15
116_V 71_H 0.79 0.29 0.14
115_L 62_N 0.79 0.29 0.14
16_K 54_D 0.79 0.29 0.14
153_V 60_Q 0.78 0.29 0.14
25_N 20_Y 0.78 0.28 0.14
82_E 83_K 0.78 0.28 0.14
192_T 83_K 0.78 0.28 0.14
144_L 73_F 0.78 0.28 0.14
188_E 86_E 0.78 0.28 0.13
195_V 58_S 0.77 0.28 0.13
41_Q 25_A 0.77 0.28 0.13
182_I 28_K 0.77 0.27 0.13
21_T 58_S 0.77 0.27 0.13
153_V 10_E 0.77 0.27 0.13
50_A 77_F 0.76 0.27 0.13
150_K 11_V 0.76 0.27 0.12
10_I 92_E 0.76 0.27 0.12
8_N 82_I 0.76 0.27 0.12
162_I 84_V 0.76 0.27 0.12
23_F 37_S 0.76 0.26 0.12
15_V 78_G 0.76 0.26 0.12
200_V 51_L 0.76 0.26 0.12
44_T 51_L 0.75 0.26 0.12
152_E 45_V 0.75 0.26 0.12
146_A 27_L 0.75 0.26 0.12
9_G 70_P 0.75 0.26 0.12
158_G 10_E 0.75 0.26 0.12
14_I 8_A 0.75 0.26 0.12
6_H 65_R 0.75 0.26 0.12
8_N 58_S 0.75 0.26 0.12
75_I 6_M 0.74 0.25 0.11
178_L 22_A 0.74 0.25 0.11
54_R 11_V 0.74 0.25 0.11
141_A 99_A 0.74 0.25 0.11
85_E 16_L 0.74 0.25 0.11
196_I 55_S 0.74 0.25 0.11
75_I 97_K 0.74 0.25 0.11
99_A 31_I 0.73 0.24 0.11
147_K 71_H 0.73 0.24 0.11
134_M 73_F 0.73 0.24 0.11
27_K 66_Q 0.73 0.24 0.11
158_G 78_G 0.73 0.24 0.11
109_P 49_Q 0.73 0.24 0.11
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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