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OPENSEQ.org
SecE_YchJ
Genes: A B A+B
Length: 127 152 266
Sequences: 502 613 205
Seq/Len: 3.95 4.03 0.77
MirrorTree (Pazo et al. 2001) 0.66
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 0.05 0.00
2 0.01 0.05 0.00
5 0.01 0.05 0.00
10 0.01 0.05 0.00
20 0.01 0.05 0.01
100 0.01 0.05 0.11
∞ 0.01 0.05 0.73
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
25_L 80_V 1.55 0.73 0.01
17_M 146_F 1.47 0.67 0.01
50_I 20_Y 1.39 0.61 0.01
21_V 27_A 1.34 0.56 0.01
76_R 126_D 1.32 0.55 0.01
21_V 52_T 1.31 0.54 0.01
92_H 131_Q 1.31 0.54 0.01
18_K 134_R 1.30 0.54 0.01
107_I 79_T 1.28 0.51 0.00
92_H 109_I 1.27 0.51 0.00
97_V 109_I 1.25 0.49 0.00
107_I 123_Y 1.25 0.49 0.00
32_G 125_I 1.24 0.48 0.00
17_M 109_I 1.23 0.47 0.00
111_L 30_P 1.22 0.46 0.00
31_V 47_D 1.18 0.43 0.00
103_V 80_V 1.16 0.41 0.00
58_V 42_V 1.16 0.41 0.00
18_K 51_K 1.15 0.40 0.00
29_A 30_P 1.13 0.39 0.00
74_E 120_G 1.11 0.37 0.00
102_A 74_E 1.08 0.35 0.00
18_K 136_D 1.08 0.34 0.00
24_A 20_Y 1.08 0.34 0.00
48_V 71_A 1.06 0.33 0.00
105_S 120_G 1.05 0.32 0.00
104_M 148_K 1.04 0.32 0.00
47_A 42_V 1.02 0.30 0.00
36_Y 14_S 1.02 0.30 0.00
21_V 43_M 1.02 0.30 0.00
36_Y 45_D 1.00 0.29 0.00
30_I 95_S 1.00 0.29 0.00
41_L 53_W 0.99 0.28 0.00
57_G 44_Q 0.99 0.28 0.00
20_V 41_F 0.98 0.27 0.00
15_E 27_A 0.98 0.27 0.00
29_A 123_Y 0.97 0.27 0.00
60_L 136_D 0.97 0.26 0.00
122_I 151_G 0.97 0.26 0.00
98_A 49_L 0.95 0.26 0.00
119_V 82_E 0.95 0.25 0.00
90_T 141_G 0.94 0.25 0.00
74_E 81_F 0.94 0.24 0.00
50_I 15_L 0.94 0.24 0.00
106_L 136_D 0.93 0.24 0.00
76_R 41_F 0.93 0.24 0.00
115_L 49_L 0.93 0.24 0.00
72_A 93_F 0.93 0.24 0.00
24_A 83_H 0.92 0.23 0.00
36_Y 38_Y 0.92 0.23 0.00
91_L 50_I 0.91 0.23 0.00
111_L 126_D 0.91 0.23 0.00
116_V 49_L 0.91 0.23 0.00
76_R 39_C 0.91 0.23 0.00
45_A 129_R 0.91 0.23 0.00
101_T 66_L 0.91 0.22 0.00
72_A 20_Y 0.90 0.22 0.00
18_K 135_N 0.90 0.22 0.00
11_G 49_L 0.90 0.22 0.00
15_E 28_P 0.89 0.22 0.00
98_A 150_C 0.89 0.21 0.00
118_L 148_K 0.89 0.21 0.00
32_G 136_D 0.88 0.21 0.00
46_L 82_E 0.88 0.21 0.00
114_I 117_K 0.88 0.21 0.00
42_P 151_G 0.87 0.20 0.00
2_S 73_T 0.87 0.20 0.00
74_E 112_R 0.87 0.20 0.00
118_L 15_L 0.87 0.20 0.00
57_G 85_W 0.87 0.20 0.00
38_D 29_D 0.87 0.20 0.00
51_L 95_S 0.86 0.20 0.00
23_V 49_L 0.86 0.20 0.00
103_V 100_F 0.85 0.20 0.00
30_I 49_L 0.85 0.19 0.00
90_T 68_A 0.85 0.19 0.00
17_M 100_F 0.85 0.19 0.00
113_G 69_G 0.85 0.19 0.00
49_V 73_T 0.85 0.19 0.00
53_A 14_S 0.85 0.19 0.00
20_V 27_A 0.85 0.19 0.00
64_K 80_V 0.85 0.19 0.00
29_A 41_F 0.84 0.19 0.00
38_D 103_G 0.83 0.18 0.00
74_E 41_F 0.83 0.18 0.00
31_V 116_L 0.83 0.18 0.00
56_G 36_S 0.83 0.18 0.00
60_L 150_C 0.83 0.18 0.00
79_V 82_E 0.83 0.18 0.00
35_L 100_F 0.83 0.18 0.00
90_T 148_K 0.83 0.18 0.00
67_A 141_G 0.83 0.18 0.00
26_L 100_F 0.82 0.18 0.00
91_L 76_L 0.81 0.17 0.00
25_L 151_G 0.81 0.17 0.00
48_V 42_V 0.81 0.17 0.00
60_L 49_L 0.81 0.17 0.00
54_A 121_Q 0.81 0.17 0.00
77_T 41_F 0.81 0.17 0.00
11_G 100_F 0.81 0.17 0.00
66_K 129_R 0.81 0.17 0.00
72_A 127_G 0.81 0.17 0.00
75_A 72_H 0.81 0.17 0.00
56_G 52_T 0.80 0.17 0.00
77_T 82_E 0.80 0.17 0.00
3_A 21_V 0.80 0.17 0.00
15_E 151_G 0.80 0.17 0.00
68_T 52_T 0.80 0.17 0.00
58_V 100_F 0.80 0.17 0.00
83_I 56_S 0.79 0.16 0.00
104_M 80_V 0.79 0.16 0.00
24_A 18_H 0.79 0.16 0.00
66_K 68_A 0.79 0.16 0.00
57_G 152_Q 0.79 0.16 0.00
102_A 49_L 0.79 0.16 0.00
81_K 110_I 0.79 0.16 0.00
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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