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OPENSEQ.org
rsfSrplT
Genes: A B A+B
Length: 118 105 219
Sequences: 1953 2543 77
Seq/Len: 16.55 24.22 0.35
MirrorTree (Pazo et al. 2001) 0.80
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 0.10 0.00 0.00
2 0.10 0.00 0.01
5 0.10 0.00 0.05
10 0.10 0.00 0.17
20 0.10 0.00 0.35
100 0.10 0.00 0.95
∞ 0.10 0.00 5.06
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
17_I 6_L 1.79 0.65 0.00
98_I 19_G 1.63 0.55 0.00
55_R 42_G 1.61 0.53 0.00
17_I 89_V 1.55 0.49 0.00
16_K 33_I 1.50 0.46 0.00
30_R 10_V 1.45 0.42 0.00
86_A 47_H 1.34 0.35 0.00
65_I 98_Y 1.32 0.34 0.00
9_I 86_I 1.30 0.33 0.00
16_K 43_T 1.26 0.30 0.00
87_S 48_V 1.26 0.30 0.00
102_D 27_V 1.25 0.29 0.00
33_R 15_D 1.24 0.29 0.00
88_V 14_I 1.24 0.29 0.00
38_A 47_H 1.21 0.27 0.00
49_D 46_R 1.21 0.27 0.00
32_Y 36_C 1.14 0.23 0.00
111_E 63_G 1.14 0.23 0.00
34_V 72_E 1.14 0.23 0.00
94_I 33_I 1.13 0.23 0.00
109_L 23_I 1.13 0.23 0.00
48_R 46_R 1.12 0.23 0.00
70_R 57_Q 1.12 0.23 0.00
68_A 86_I 1.11 0.22 0.00
90_I 80_V 1.11 0.22 0.00
75_S 51_I 1.11 0.22 0.00
103_K 12_D 1.10 0.22 0.00
88_V 22_I 1.10 0.21 0.00
39_V 48_V 1.10 0.21 0.00
16_K 42_G 1.09 0.21 0.00
98_I 97_L 1.09 0.21 0.00
56_Q 34_T 1.09 0.21 0.00
53_R 41_T 1.09 0.21 0.00
75_S 26_D 1.09 0.21 0.00
2_A 57_Q 1.08 0.21 0.00
94_I 32_S 1.07 0.20 0.00
42_A 36_C 1.07 0.20 0.00
27_A 93_E 1.06 0.20 0.00
73_G 39_I 1.05 0.20 0.00
79_F 45_S 1.05 0.19 0.00
108_A 19_G 1.05 0.19 0.00
56_Q 86_I 1.05 0.19 0.00
53_R 88_H 1.03 0.18 0.00
105_A 79_V 1.02 0.18 0.00
91_D 32_S 1.02 0.18 0.00
51_R 49_M 1.01 0.18 0.00
30_R 83_G 0.99 0.17 0.00
41_K 88_H 0.99 0.17 0.00
55_R 10_V 0.99 0.17 0.00
34_V 105_S 0.99 0.17 0.00
112_K 13_K 0.98 0.17 0.00
4_V 99_E 0.98 0.17 0.00
16_K 14_I 0.98 0.17 0.00
86_A 50_S 0.98 0.16 0.00
72_N 78_I 0.97 0.16 0.00
90_I 56_V 0.97 0.16 0.00
108_A 45_S 0.97 0.16 0.00
66_N 26_D 0.97 0.16 0.00
110_V 68_G 0.97 0.16 0.00
34_V 89_V 0.96 0.16 0.00
104_V 85_V 0.95 0.15 0.00
42_A 38_I 0.95 0.15 0.00
30_R 74_S 0.94 0.15 0.00
33_R 16_D 0.94 0.15 0.00
87_S 88_H 0.93 0.15 0.00
11_R 43_T 0.93 0.15 0.00
63_A 27_V 0.93 0.14 0.00
100_V 39_I 0.92 0.14 0.00
7_G 46_R 0.92 0.14 0.00
27_A 89_V 0.92 0.14 0.00
97_D 55_V 0.92 0.14 0.00
83_L 47_H 0.91 0.14 0.00
83_L 50_S 0.91 0.14 0.00
66_N 76_D 0.90 0.14 0.00
73_G 59_S 0.89 0.13 0.00
27_A 72_E 0.89 0.13 0.00
53_R 68_G 0.89 0.13 0.00
105_A 69_V 0.89 0.13 0.00
80_I 33_I 0.88 0.13 0.00
30_R 6_L 0.88 0.13 0.00
51_R 2_Q 0.88 0.13 0.00
25_Y 99_E 0.88 0.13 0.00
12_A 10_V 0.88 0.13 0.00
109_L 74_S 0.88 0.13 0.00
28_R 34_T 0.88 0.13 0.00
33_R 12_D 0.88 0.13 0.00
100_V 8_D 0.87 0.13 0.00
38_A 25_L 0.87 0.13 0.00
37_Q 88_H 0.87 0.12 0.00
83_L 48_V 0.86 0.12 0.00
70_R 92_E 0.86 0.12 0.00
89_E 64_L 0.86 0.12 0.00
31_V 47_H 0.86 0.12 0.00
103_K 17_L 0.85 0.12 0.00
97_D 5_A 0.85 0.12 0.00
67_A 95_R 0.84 0.12 0.00
108_A 88_H 0.84 0.12 0.00
71_Q 20_Q 0.84 0.12 0.00
96_A 40_C 0.84 0.12 0.00
60_L 34_T 0.84 0.12 0.00
27_A 87_V 0.83 0.12 0.00
47_Y 102_K 0.83 0.11 0.00
78_K 9_F 0.83 0.11 0.00
17_I 69_V 0.83 0.11 0.00
91_D 46_R 0.83 0.11 0.00
49_D 57_Q 0.83 0.11 0.00
78_K 8_D 0.83 0.11 0.00
109_L 69_V 0.83 0.11 0.00
25_Y 18_K 0.83 0.11 0.00
51_R 20_Q 0.83 0.11 0.00
31_V 72_E 0.82 0.11 0.00
89_E 6_L 0.82 0.11 0.00
75_S 55_V 0.81 0.11 0.00
51_R 59_S 0.81 0.11 0.00
7_G 82_L 0.81 0.11 0.00
100_V 17_L 0.81 0.11 0.00
14_H 33_I 0.81 0.11 0.00
79_F 25_L 0.81 0.11 0.00
18_L 59_S 0.81 0.11 0.00
41_K 49_M 0.81 0.11 0.00
81_N 51_I 0.80 0.11 0.00
42_A 15_D 0.80 0.11 0.00
55_R 41_T 0.80 0.10 0.00
82_G 83_G 0.80 0.10 0.00
53_R 82_L 0.80 0.10 0.00
47_Y 3_G 0.80 0.10 0.00
51_R 5_A 0.80 0.10 0.00
36_F 42_G 0.79 0.10 0.00
17_I 29_G 0.79 0.10 0.00
40_I 11_I 0.79 0.10 0.00
107_T 8_D 0.79 0.10 0.00
110_V 71_G 0.79 0.10 0.00
51_R 64_L 0.79 0.10 0.00
100_V 19_G 0.78 0.10 0.00
80_I 3_G 0.78 0.10 0.00
115_A 33_I 0.78 0.10 0.00
49_D 56_V 0.78 0.10 0.00
73_G 96_R 0.78 0.10 0.00
9_I 24_A 0.77 0.10 0.00
105_A 60_R 0.77 0.10 0.00
89_E 73_N 0.77 0.10 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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