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OPENSEQ.org
1a2k_a_c
Genes: A B A+B
Length: 121 202 290
Sequences: 923 9108 50
Seq/Len: 7.63 45.09 0.17
MirrorTree (Pazo et al. 2001) 0.21
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 0.05 0.04 0.02
2 0.05 0.05 0.02
5 0.05 0.06 0.05
10 0.05 0.08 0.10
20 0.05 0.10 0.15
100 0.05 0.18 0.61
∞ 0.07 0.25 1.33
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
53_L 128_A 1.49 0.28 0.00
80_S 102_D 1.43 0.26 0.00
78_I 28_G 1.38 0.23 0.00
80_S 26_L 1.34 0.22 0.00
80_S 9_V 1.32 0.21 0.00
80_S 149_N 1.25 0.18 0.00
92_P 21_F 1.23 0.18 0.00
114_D 75_Y 1.22 0.17 0.00
84_G 120_D 1.20 0.17 0.00
80_S 154_K 1.15 0.15 0.00
80_S 65_E 1.14 0.15 0.00
109_W 24_R 1.14 0.15 0.00
84_G 118_K 1.11 0.14 0.00
104_N 73_G 1.11 0.14 0.00
102_L 146_A 1.11 0.14 0.00
36_L 82_I 1.10 0.14 0.00
55_S 113_V 1.09 0.14 0.00
102_L 61_T 1.08 0.13 0.00
45_G 120_D 1.07 0.13 0.00
93_I 21_F 1.06 0.13 0.00
84_G 12_G 1.05 0.13 0.00
84_G 17_G 1.05 0.13 0.00
84_G 18_K 1.05 0.13 0.00
11_F 120_D 1.05 0.12 0.00
16_Y 120_D 1.05 0.12 0.00
73_T 102_D 1.04 0.12 0.00
84_G 145_S 1.04 0.12 0.00
84_G 60_D 1.02 0.12 0.00
90_E 106_V 1.02 0.12 0.00
69_D 120_D 1.01 0.12 0.00
23_R 114_L 1.01 0.12 0.00
53_L 109_N 1.00 0.11 0.00
75_D 19_T 0.99 0.11 0.00
90_E 65_E 0.98 0.11 0.00
40_G 117_N 0.98 0.11 0.00
96_F 146_A 0.98 0.11 0.00
90_E 32_K 0.97 0.11 0.00
45_G 146_A 0.96 0.10 0.00
84_G 146_A 0.96 0.10 0.00
56_L 86_D 0.96 0.10 0.00
96_F 154_K 0.96 0.10 0.00
45_G 118_K 0.94 0.10 0.00
32_D 93_Y 0.94 0.10 0.00
26_L 154_K 0.94 0.10 0.00
30_Y 63_G 0.94 0.10 0.00
65_I 149_N 0.93 0.10 0.00
111_C 61_T 0.93 0.10 0.00
100_F 120_D 0.92 0.10 0.00
27_G 10_L 0.92 0.10 0.00
98_Q 115_C 0.92 0.10 0.00
117_R 145_S 0.91 0.09 0.00
45_G 12_G 0.91 0.09 0.00
45_G 17_G 0.91 0.09 0.00
45_G 18_K 0.91 0.09 0.00
69_D 118_K 0.91 0.09 0.00
51_E 85_F 0.90 0.09 0.00
117_R 115_C 0.90 0.09 0.00
12_I 11_V 0.90 0.09 0.00
11_F 118_K 0.90 0.09 0.00
15_Y 120_D 0.90 0.09 0.00
16_Y 118_K 0.90 0.09 0.00
45_G 145_S 0.90 0.09 0.00
110_V 114_L 0.90 0.09 0.00
21_N 92_T 0.90 0.09 0.00
11_F 12_G 0.89 0.09 0.00
11_F 17_G 0.89 0.09 0.00
11_F 18_K 0.89 0.09 0.00
16_Y 12_G 0.89 0.09 0.00
16_Y 17_G 0.89 0.09 0.00
16_Y 18_K 0.89 0.09 0.00
62_Q 25_H 0.89 0.09 0.00
100_F 63_G 0.89 0.09 0.00
29_I 96_V 0.89 0.09 0.00
91_D 54_I 0.89 0.09 0.00
30_Y 120_D 0.89 0.09 0.00
62_Q 147_K 0.89 0.09 0.00
13_Q 45_L 0.88 0.09 0.00
36_L 22_V 0.88 0.09 0.00
98_Q 75_Y 0.88 0.09 0.00
78_I 159_L 0.88 0.09 0.00
30_Y 37_T 0.88 0.09 0.00
11_F 145_S 0.88 0.09 0.00
16_Y 145_S 0.88 0.09 0.00
45_G 60_D 0.87 0.09 0.00
110_V 20_T 0.87 0.09 0.00
101_L 92_T 0.87 0.09 0.00
47_A 159_L 0.87 0.09 0.00
100_F 19_T 0.86 0.09 0.00
11_F 60_D 0.86 0.08 0.00
16_Y 60_D 0.86 0.08 0.00
29_I 83_I 0.86 0.08 0.00
69_D 12_G 0.86 0.08 0.00
69_D 17_G 0.86 0.08 0.00
69_D 18_K 0.86 0.08 0.00
117_R 12_G 0.85 0.08 0.00
117_R 17_G 0.85 0.08 0.00
117_R 18_K 0.85 0.08 0.00
115_M 47_F 0.85 0.08 0.00
29_I 92_T 0.85 0.08 0.00
30_Y 19_T 0.85 0.08 0.00
72_P 56_F 0.85 0.08 0.00
68_Q 121_I 0.85 0.08 0.00
65_I 126_V 0.85 0.08 0.00
69_D 145_S 0.84 0.08 0.00
102_L 120_D 0.84 0.08 0.00
55_S 20_T 0.84 0.08 0.00
96_F 55_K 0.83 0.08 0.00
79_I 105_R 0.83 0.08 0.00
49_I 120_D 0.82 0.08 0.00
71_Q 120_D 0.82 0.08 0.00
102_L 37_T 0.82 0.08 0.00
69_D 60_D 0.82 0.08 0.00
75_D 54_I 0.82 0.08 0.00
40_G 67_Y 0.82 0.08 0.00
18_L 96_V 0.82 0.08 0.00
90_E 115_C 0.82 0.08 0.00
82_V 120_D 0.81 0.08 0.00
96_F 148_S 0.81 0.07 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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