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OPENSEQ.org
1vs5_C_E
Genes: A B A+B
Length: 233 167 375
Sequences: 2210 2153 1364
Seq/Len: 9.48 12.89 3.64
MirrorTree (Pazo et al. 2001) 0.89
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 0.07 0.00
2 0.09 0.07 0.01
5 0.09 0.07 0.02
10 0.09 0.07 0.84
20 0.09 0.07 3.41
100 0.09 0.07 3.47
∞ 0.09 0.08 3.62
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
162_I 29_R 1.84 0.99 0.96
168_Y 55_E 1.78 0.99 0.96
158_G 31_F 1.35 0.94 0.81
158_G 22_S 1.25 0.90 0.73
135_K 31_F 1.20 0.87 0.69
124_L 25_V 1.14 0.83 0.63
153_V 17_A 1.09 0.80 0.59
134_M 132_N 1.09 0.79 0.58
72_R 54_R 1.02 0.73 0.50
130_F 149_S 0.99 0.70 0.47
176_H 30_I 0.99 0.69 0.46
123_Q 35_A 0.98 0.69 0.46
158_G 21_V 0.95 0.65 0.42
116_V 140_T 0.95 0.65 0.42
203_F 120_V 0.94 0.63 0.40
63_S 92_S 0.93 0.62 0.39
102_N 92_S 0.93 0.62 0.39
153_V 41_D 0.93 0.62 0.39
39_V 69_R 0.93 0.62 0.39
64_I 151_E 0.92 0.61 0.38
129_M 111_M 0.91 0.59 0.36
126_R 125_A 0.90 0.58 0.35
83_D 111_M 0.89 0.57 0.35
124_L 48_F 0.88 0.56 0.34
201_W 83_H 0.88 0.56 0.33
139_Q 83_H 0.86 0.53 0.31
72_R 133_P 0.85 0.52 0.30
6_H 124_L 0.84 0.51 0.29
107_R 86_K 0.84 0.51 0.29
10_I 115_L 0.83 0.49 0.28
58_E 103_T 0.83 0.49 0.28
6_H 29_R 0.83 0.49 0.28
55_I 88_V 0.82 0.48 0.27
124_L 16_I 0.82 0.48 0.27
128_V 132_N 0.81 0.47 0.27
66_V 152_M 0.81 0.47 0.26
135_K 58_A 0.80 0.46 0.25
172_R 124_L 0.80 0.45 0.25
103_I 117_V 0.79 0.45 0.24
82_E 97_Q 0.79 0.45 0.24
15_V 68_R 0.79 0.44 0.24
45_K 155_A 0.79 0.44 0.24
25_N 74_V 0.79 0.44 0.24
124_L 137_V 0.79 0.44 0.24
88_R 61_Q 0.78 0.42 0.23
37_F 30_I 0.78 0.42 0.23
150_K 70_N 0.77 0.42 0.22
173_V 29_R 0.77 0.41 0.22
99_A 92_S 0.77 0.41 0.22
151_V 32_S 0.76 0.41 0.21
100_Q 15_L 0.76 0.41 0.21
84_V 63_A 0.76 0.40 0.21
117_A 67_A 0.76 0.40 0.21
163_A 55_E 0.76 0.40 0.21
157_L 33_F 0.76 0.40 0.21
176_H 53_A 0.76 0.40 0.21
154_S 122_N 0.75 0.40 0.21
153_V 114_V 0.75 0.40 0.20
77_I 39_V 0.75 0.39 0.20
29_F 21_V 0.75 0.39 0.20
43_L 125_A 0.74 0.38 0.20
130_F 35_A 0.74 0.38 0.20
110_E 117_V 0.74 0.38 0.20
37_F 123_V 0.74 0.38 0.19
20_S 24_T 0.74 0.38 0.19
84_V 148_N 0.73 0.36 0.18
140_N 63_A 0.73 0.36 0.18
200_V 91_G 0.72 0.36 0.18
60_P 111_M 0.72 0.36 0.18
174_P 69_R 0.72 0.36 0.18
152_E 131_T 0.72 0.35 0.17
162_I 31_F 0.71 0.34 0.17
64_I 147_M 0.71 0.34 0.17
86_K 48_F 0.71 0.34 0.17
79_K 9_G 0.71 0.34 0.17
15_V 147_M 0.71 0.34 0.17
88_R 145_E 0.71 0.34 0.17
43_L 75_A 0.70 0.34 0.17
64_I 91_G 0.70 0.34 0.16
119_S 11_L 0.70 0.34 0.16
75_I 60_I 0.70 0.33 0.16
36_D 27_G 0.70 0.33 0.16
160_A 118_A 0.70 0.33 0.16
170_E 59_A 0.70 0.33 0.16
151_V 153_V 0.70 0.33 0.16
77_I 67_A 0.70 0.33 0.16
130_F 96_M 0.70 0.33 0.16
14_I 161_V 0.69 0.32 0.15
35_S 82_Q 0.69 0.32 0.15
203_F 111_M 0.69 0.32 0.15
210_G 43_N 0.69 0.32 0.15
120_I 151_E 0.69 0.31 0.15
70_T 24_T 0.68 0.31 0.15
99_A 11_L 0.68 0.31 0.15
186_T 124_L 0.68 0.31 0.14
29_F 124_L 0.68 0.31 0.14
109_P 132_N 0.68 0.31 0.14
17_P 122_N 0.68 0.30 0.14
126_R 132_N 0.68 0.30 0.14
41_Q 73_N 0.67 0.30 0.14
68_I 144_L 0.67 0.30 0.14
126_R 71_M 0.67 0.30 0.14
127_R 27_G 0.67 0.30 0.14
157_L 24_T 0.67 0.30 0.14
51_S 152_M 0.67 0.29 0.14
106_V 63_A 0.67 0.29 0.14
65_R 88_V 0.67 0.29 0.14
71_A 63_A 0.67 0.29 0.14
126_R 48_F 0.66 0.29 0.14
143_R 137_V 0.66 0.29 0.13
106_V 85_V 0.66 0.29 0.13
87_L 75_A 0.66 0.28 0.13
151_V 50_Y 0.66 0.28 0.13
152_E 143_G 0.66 0.28 0.13
146_A 77_N 0.65 0.28 0.13
153_V 63_A 0.65 0.28 0.13
30_A 122_N 0.65 0.28 0.13
83_D 48_F 0.65 0.27 0.12
144_L 117_V 0.65 0.27 0.12
112_D 120_V 0.65 0.27 0.12
166_E 107_A 0.65 0.27 0.12
121_T 18_V 0.64 0.27 0.12
44_T 132_N 0.64 0.27 0.12
124_L 30_I 0.64 0.27 0.12
213_A 93_R 0.64 0.27 0.12
75_I 56_V 0.64 0.27 0.12
70_T 135_N 0.64 0.27 0.12
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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