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OPENSEQ.org
6078
Genes: A B A+B
Length: 113 216 314
Sequences: 10421 1961 126
Seq/Len: 92.22 9.08 0.4
MirrorTree (Pazo et al. 2001) 0.65
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 0.04 0.01 0.38
2 0.05 0.01 0.42
5 0.08 0.01 0.48
10 0.09 0.02 0.60
20 0.10 0.02 0.71
100 0.14 0.03 1.04
∞ 0.18 0.10 1.91
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
8_K 171_A 1.59 0.56 0.00
87_L 135_N 1.51 0.51 0.00
13_E 161_I 1.38 0.41 0.00
98_E 137_F 1.38 0.41 0.00
32_I 53_I 1.31 0.36 0.00
45_L 172_L 1.28 0.34 0.00
10_L 133_R 1.23 0.31 0.00
80_F 138_A 1.22 0.30 0.00
53_N 50_N 1.21 0.30 0.00
82_V 99_A 1.21 0.30 0.00
87_L 73_F 1.18 0.28 0.00
81_R 148_L 1.16 0.27 0.00
64_D 58_F 1.15 0.26 0.00
90_S 80_S 1.11 0.24 0.00
87_L 93_S 1.10 0.23 0.00
26_G 20_I 1.10 0.23 0.00
90_S 141_A 1.10 0.23 0.00
6_K 79_I 1.09 0.23 0.00
32_I 55_P 1.07 0.22 0.00
1_M 176_L 1.06 0.22 0.00
80_F 49_E 1.05 0.21 0.00
95_L 116_D 1.04 0.21 0.00
15_K 81_Y 1.03 0.20 0.00
56_V 75_D 1.02 0.20 0.00
11_A 162_C 1.00 0.19 0.00
76_I 138_A 1.00 0.19 0.00
100_K 195_I 0.99 0.18 0.00
52_F 84_T 0.99 0.18 0.00
99_L 115_S 0.99 0.18 0.00
103_L 18_T 0.99 0.18 0.00
11_A 143_I 0.98 0.18 0.00
27_F 144_N 0.97 0.17 0.00
102_Y 80_S 0.96 0.17 0.00
8_K 175_R 0.96 0.17 0.00
43_D 87_K 0.96 0.17 0.00
7_I 186_L 0.95 0.17 0.00
103_L 81_Y 0.95 0.17 0.00
100_K 58_F 0.95 0.16 0.00
38_N 142_L 0.93 0.16 0.00
6_K 83_P 0.93 0.16 0.00
7_I 89_R 0.93 0.16 0.00
89_E 23_E 0.92 0.15 0.00
48_V 181_T 0.91 0.15 0.00
80_F 104_D 0.91 0.15 0.00
105_F 142_L 0.91 0.15 0.00
48_V 92_F 0.91 0.15 0.00
22_E 40_H 0.91 0.15 0.00
90_S 27_N 0.91 0.15 0.00
64_D 32_E 0.91 0.15 0.00
103_L 142_L 0.90 0.15 0.00
26_G 181_T 0.90 0.15 0.00
6_K 108_E 0.90 0.15 0.00
30_G 179_F 0.90 0.14 0.00
97_E 161_I 0.90 0.14 0.00
36_R 143_I 0.89 0.14 0.00
4_Y 133_R 0.89 0.14 0.00
105_F 137_F 0.89 0.14 0.00
95_L 124_T 0.89 0.14 0.00
45_L 158_F 0.88 0.14 0.00
52_F 53_I 0.88 0.14 0.00
54_I 158_F 0.87 0.14 0.00
81_R 89_R 0.87 0.14 0.00
97_E 101_Y 0.87 0.14 0.00
8_K 114_F 0.87 0.14 0.00
82_V 105_M 0.87 0.14 0.00
8_K 166_E 0.87 0.14 0.00
17_S 166_E 0.87 0.14 0.00
104_E 167_M 0.86 0.13 0.00
48_V 179_F 0.86 0.13 0.00
21_L 41_Y 0.86 0.13 0.00
54_I 163_E 0.85 0.13 0.00
60_L 152_L 0.85 0.13 0.00
52_F 82_N 0.85 0.13 0.00
43_D 53_I 0.85 0.13 0.00
82_V 172_L 0.85 0.13 0.00
13_E 128_E 0.84 0.13 0.00
45_L 40_H 0.84 0.13 0.00
33_N 78_G 0.84 0.13 0.00
95_L 139_S 0.84 0.13 0.00
7_I 55_P 0.84 0.13 0.00
106_M 137_F 0.84 0.13 0.00
94_Q 53_I 0.83 0.12 0.00
104_E 176_L 0.83 0.12 0.00
35_W 135_N 0.83 0.12 0.00
14_K 176_L 0.83 0.12 0.00
67_N 185_L 0.83 0.12 0.00
80_F 129_P 0.83 0.12 0.00
59_L 97_E 0.83 0.12 0.00
14_K 24_K 0.83 0.12 0.00
59_L 53_I 0.83 0.12 0.00
53_N 77_C 0.82 0.12 0.00
82_V 176_L 0.82 0.12 0.00
26_G 30_G 0.82 0.12 0.00
52_F 167_M 0.81 0.12 0.00
46_K 138_A 0.81 0.12 0.00
42_S 138_A 0.81 0.12 0.00
86_D 101_Y 0.81 0.12 0.00
17_S 41_Y 0.81 0.12 0.00
25_L 139_S 0.81 0.12 0.00
77_T 141_A 0.81 0.12 0.00
15_K 70_I 0.81 0.12 0.00
78_T 143_I 0.81 0.12 0.00
49_A 27_N 0.81 0.12 0.00
82_V 95_L 0.80 0.12 0.00
79_F 68_G 0.80 0.11 0.00
45_L 126_E 0.80 0.11 0.00
50_D 182_K 0.80 0.11 0.00
94_Q 25_V 0.80 0.11 0.00
23_E 160_Q 0.80 0.11 0.00
45_L 67_S 0.80 0.11 0.00
4_Y 158_F 0.80 0.11 0.00
40_P 26_A 0.79 0.11 0.00
54_I 114_F 0.79 0.11 0.00
77_T 71_I 0.79 0.11 0.00
16_M 90_Q 0.79 0.11 0.00
48_V 65_I 0.79 0.11 0.00
32_I 198_Y 0.79 0.11 0.00
47_K 171_A 0.79 0.11 0.00
102_Y 66_F 0.79 0.11 0.00
50_D 172_L 0.79 0.11 0.00
104_E 143_I 0.78 0.11 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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