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OPENSEQ.org
A_c
Genes: A B A+B
Length: 124 226 333
Sequences: 64 132 65
Seq/Len: 0.52 0.58 0.2
MirrorTree (Pazo et al. 2001) 0.68
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.01
2 0.00 0.00 0.19
5 0.00 0.00 0.19
10 0.00 0.00 0.19
20 0.00 0.00 0.19
100 0.00 0.00 0.19
∞ 0.00 0.00 0.19
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
2_D 157_N 1.54 0.34 0.00
30_A 78_A 1.45 0.30 0.00
110_L 195_V 1.37 0.26 0.00
110_L 23_T 1.31 0.23 0.00
100_G 160_L 1.28 0.22 0.00
75_N 43_N 1.28 0.22 0.00
94_S 113_N 1.24 0.20 0.00
66_P 154_S 1.21 0.19 0.00
98_L 175_V 1.18 0.18 0.00
97_S 156_D 1.18 0.18 0.00
32_A 62_G 1.17 0.18 0.00
83_G 126_Q 1.17 0.17 0.00
34_P 136_I 1.14 0.17 0.00
30_A 49_S 1.14 0.17 0.00
110_L 156_D 1.14 0.16 0.00
96_N 85_A 1.13 0.16 0.00
32_A 136_I 1.12 0.16 0.00
67_N 174_V 1.11 0.15 0.00
58_S 114_S 1.10 0.15 0.00
77_L 50_K 1.10 0.15 0.00
117_G 110_S 1.09 0.15 0.00
92_H 12_P 1.09 0.15 0.00
97_S 110_S 1.08 0.15 0.00
98_L 114_S 1.06 0.14 0.00
115_N 110_S 1.06 0.14 0.00
19_P 158_H 1.04 0.13 0.00
55_S 101_T 1.04 0.13 0.00
102_I 124_A 1.04 0.13 0.00
99_G 100_G 1.04 0.13 0.00
108_R 111_A 1.03 0.13 0.00
110_L 27_K 1.03 0.13 0.00
94_S 151_E 1.02 0.13 0.00
26_Y 86_D 1.02 0.13 0.00
99_G 101_T 1.02 0.13 0.00
116_I 19_A 1.01 0.12 0.00
98_L 120_V 1.00 0.12 0.00
60_I 43_N 1.00 0.12 0.00
70_L 192_G 1.00 0.12 0.00
34_P 66_D 1.00 0.12 0.00
93_A 209_L 0.99 0.12 0.00
23_K 186_N 0.99 0.12 0.00
17_G 134_L 0.98 0.12 0.00
97_S 134_L 0.98 0.12 0.00
82_A 53_L 0.98 0.12 0.00
5_I 101_T 0.97 0.12 0.00
64_I 43_N 0.97 0.12 0.00
102_I 44_G 0.96 0.11 0.00
72_G 45_S 0.96 0.11 0.00
34_P 133_N 0.96 0.11 0.00
44_G 110_S 0.95 0.11 0.00
108_R 28_D 0.95 0.11 0.00
16_V 9_T 0.95 0.11 0.00
55_S 28_D 0.94 0.11 0.00
40_R 76_G 0.94 0.11 0.00
101_Q 91_S 0.94 0.11 0.00
53_G 32_D 0.94 0.11 0.00
59_T 37_L 0.94 0.11 0.00
64_I 37_L 0.93 0.11 0.00
6_V 103_N 0.93 0.11 0.00
7_T 14_G 0.93 0.11 0.00
88_A 101_T 0.92 0.10 0.00
19_P 25_V 0.92 0.10 0.00
60_I 177_N 0.92 0.10 0.00
117_G 7_K 0.92 0.10 0.00
38_I 62_G 0.91 0.10 0.00
59_T 183_S 0.90 0.10 0.00
20_S 181_L 0.90 0.10 0.00
4_I 123_A 0.90 0.10 0.00
103_S 33_D 0.89 0.10 0.00
32_A 26_S 0.89 0.10 0.00
18_R 36_T 0.89 0.10 0.00
69_D 48_N 0.89 0.10 0.00
51_F 105_A 0.89 0.10 0.00
54_V 55_A 0.89 0.10 0.00
50_D 185_N 0.89 0.10 0.00
85_G 134_L 0.88 0.10 0.00
33_N 36_T 0.88 0.10 0.00
55_S 12_P 0.88 0.10 0.00
120_M 74_S 0.88 0.10 0.00
111_A 104_N 0.88 0.10 0.00
107_E 30_K 0.88 0.10 0.00
47_S 184_A 0.88 0.10 0.00
110_L 186_N 0.88 0.09 0.00
53_G 169_Y 0.87 0.09 0.00
117_G 156_D 0.87 0.09 0.00
59_T 184_A 0.87 0.09 0.00
16_V 163_A 0.87 0.09 0.00
66_P 180_L 0.87 0.09 0.00
61_T 86_D 0.87 0.09 0.00
39_L 155_L 0.87 0.09 0.00
4_I 47_S 0.87 0.09 0.00
90_A 138_T 0.87 0.09 0.00
85_G 124_A 0.86 0.09 0.00
96_N 11_A 0.86 0.09 0.00
65_L 188_S 0.86 0.09 0.00
5_I 61_S 0.86 0.09 0.00
6_V 172_Q 0.86 0.09 0.00
29_T 189_G 0.85 0.09 0.00
20_S 84_V 0.85 0.09 0.00
13_G 153_V 0.85 0.09 0.00
22_G 103_N 0.85 0.09 0.00
47_S 166_K 0.84 0.09 0.00
64_I 183_S 0.84 0.09 0.00
54_V 172_Q 0.84 0.09 0.00
58_S 93_D 0.84 0.09 0.00
60_I 90_E 0.84 0.09 0.00
99_G 33_D 0.84 0.09 0.00
104_G 71_I 0.84 0.09 0.00
58_S 126_Q 0.84 0.09 0.00
28_S 28_D 0.84 0.09 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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