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OPENSEQ.org
1c17_M_K
Genes: A B A+B
Length: 177 79 239
Sequences: 3494 1098 1308
Seq/Len: 19.74 13.9 5.47
MirrorTree (Pazo et al. 2001) 0.72
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 0.04 0.08 4.93
2 0.04 0.08 5.04
5 0.04 0.08 5.05
10 0.04 0.08 5.09
20 0.04 0.08 5.11
100 0.04 0.08 5.12
∞ 0.04 0.09 5.21
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
119_G 65_M 2.58 1.00 1.00
110_P 42_Q 1.46 0.98 0.92
112_S 66_I 1.39 0.98 0.89
168_V 54_F 1.33 0.97 0.86
73_K 11_M 1.32 0.97 0.86
52_D 71_G 1.18 0.93 0.77
169_Y 62_A 1.13 0.91 0.73
13_T 33_G 1.05 0.86 0.65
60_A 55_I 1.03 0.84 0.63
156_T 26_I 1.03 0.84 0.62
112_S 62_A 0.99 0.80 0.57
57_L 42_Q 0.97 0.78 0.55
106_L 24_A 0.96 0.78 0.54
151_H 28_I 0.96 0.77 0.54
153_L 23_G 0.94 0.75 0.51
169_Y 20_A 0.93 0.75 0.50
110_P 27_G 0.92 0.73 0.48
70_Y 25_A 0.90 0.71 0.46
119_G 62_A 0.90 0.71 0.46
102_E 63_I 0.90 0.71 0.46
161_I 9_L 0.90 0.70 0.46
103_G 14_A 0.89 0.70 0.45
154_I 66_I 0.89 0.70 0.45
105_S 17_M 0.89 0.69 0.45
102_E 42_Q 0.87 0.67 0.42
115_L 69_G 0.85 0.65 0.40
123_A 57_M 0.85 0.64 0.40
136_P 44_D 0.85 0.64 0.40
51_A 24_A 0.83 0.62 0.38
128_F 39_A 0.83 0.62 0.38
154_I 24_A 0.82 0.61 0.37
72_I 11_M 0.82 0.60 0.36
113_L 57_M 0.82 0.60 0.36
133_G 72_L 0.80 0.58 0.34
89_F 58_G 0.80 0.57 0.34
107_L 70_L 0.80 0.57 0.33
12_L 36_L 0.80 0.57 0.33
24_M 21_A 0.79 0.56 0.33
98_N 58_G 0.79 0.55 0.32
97_V 26_I 0.79 0.55 0.32
100_I 69_G 0.78 0.55 0.32
166_T 29_G 0.78 0.54 0.31
114_G 59_L 0.78 0.54 0.31
131_I 73_Y 0.77 0.54 0.30
88_P 49_L 0.77 0.53 0.30
21_M 11_M 0.76 0.51 0.29
152_I 44_D 0.76 0.51 0.28
124_G 63_I 0.75 0.51 0.28
107_L 29_G 0.75 0.51 0.28
80_F 16_M 0.75 0.51 0.28
161_I 59_L 0.75 0.50 0.28
124_G 28_I 0.75 0.50 0.28
25_D 54_F 0.74 0.49 0.27
153_L 36_L 0.74 0.48 0.26
169_Y 69_G 0.74 0.48 0.26
74_M 38_G 0.73 0.48 0.26
123_A 62_A 0.73 0.48 0.26
124_G 64_P 0.73 0.48 0.26
101_L 69_G 0.72 0.46 0.25
171_S 21_A 0.72 0.46 0.24
146_P 58_G 0.72 0.46 0.24
58_S 19_L 0.72 0.45 0.24
110_P 20_A 0.72 0.45 0.24
121_M 14_A 0.72 0.45 0.24
105_S 42_Q 0.71 0.45 0.24
49_P 31_L 0.71 0.44 0.23
157_L 59_L 0.71 0.44 0.23
168_V 56_V 0.70 0.43 0.23
154_I 53_F 0.70 0.43 0.23
115_L 72_L 0.70 0.43 0.23
87_Q 18_G 0.70 0.43 0.23
123_A 22_I 0.70 0.43 0.22
134_L 46_I 0.69 0.42 0.22
157_L 50_R 0.69 0.42 0.22
123_A 24_A 0.69 0.42 0.21
161_I 54_F 0.68 0.41 0.21
7_I 46_I 0.68 0.41 0.21
65_I 26_I 0.68 0.40 0.21
126_L 40_A 0.68 0.40 0.20
50_S 30_I 0.68 0.40 0.20
166_T 48_L 0.68 0.40 0.20
174_S 17_M 0.68 0.39 0.20
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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