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OPENSEQ.org
5161
Genes: A B A+B
Length: 109 128 218
Sequences: 1100 552 59
Seq/Len: 10.09 4.31 0.27
MirrorTree (Pazo et al. 2001) 0.79
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 0.25
2 0.01 0.00 0.26
5 0.01 0.01 0.26
10 0.01 0.01 0.26
20 0.01 0.01 0.26
100 0.01 0.03 0.28
∞ 0.04 0.07 0.47
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
56_I 126_N 1.67 0.50 0.00
20_L 100_M 1.61 0.46 0.00
16_N 97_Y 1.57 0.44 0.00
51_E 116_I 1.54 0.42 0.00
74_S 7_R 1.46 0.36 0.00
48_M 92_D 1.41 0.33 0.00
73_M 46_K 1.41 0.33 0.00
26_V 11_Q 1.37 0.31 0.00
53_I 33_G 1.34 0.30 0.00
64_Q 40_G 1.30 0.28 0.00
21_M 30_V 1.29 0.27 0.00
54_K 65_K 1.28 0.27 0.00
52_E 115_L 1.24 0.24 0.00
89_S 29_E 1.22 0.23 0.00
15_L 8_R 1.21 0.23 0.00
80_K 30_V 1.20 0.22 0.00
55_A 114_D 1.18 0.21 0.00
42_I 14_K 1.17 0.21 0.00
29_I 107_F 1.17 0.21 0.00
83_R 57_G 1.15 0.20 0.00
47_S 14_K 1.15 0.20 0.00
51_E 25_A 1.15 0.20 0.00
29_I 120_F 1.14 0.20 0.00
45_V 115_L 1.13 0.20 0.00
27_D 76_W 1.13 0.20 0.00
80_K 62_I 1.13 0.19 0.00
50_G 82_S 1.13 0.19 0.00
79_S 44_I 1.13 0.19 0.00
73_M 70_V 1.10 0.18 0.00
77_S 46_K 1.10 0.18 0.00
91_P 44_I 1.09 0.18 0.00
75_K 24_M 1.08 0.18 0.00
74_S 111_Q 1.07 0.17 0.00
55_A 112_I 1.07 0.17 0.00
66_V 36_E 1.04 0.16 0.00
79_S 57_G 1.04 0.16 0.00
51_E 121_L 1.04 0.16 0.00
27_D 34_I 1.03 0.16 0.00
22_S 120_F 1.03 0.16 0.00
45_V 106_A 1.03 0.16 0.00
25_E 121_L 1.03 0.16 0.00
67_L 87_K 1.03 0.16 0.00
29_I 3_V 1.02 0.15 0.00
78_V 106_A 1.02 0.15 0.00
62_M 60_T 1.01 0.15 0.00
95_I 104_F 1.01 0.15 0.00
48_M 90_E 1.00 0.15 0.00
61_G 56_G 0.98 0.14 0.00
49_T 109_N 0.98 0.14 0.00
63_S 40_G 0.98 0.14 0.00
88_P 40_G 0.98 0.14 0.00
33_V 13_T 0.98 0.14 0.00
61_G 6_A 0.97 0.14 0.00
25_E 3_V 0.97 0.14 0.00
59_R 57_G 0.97 0.14 0.00
53_I 65_K 0.96 0.14 0.00
25_E 21_K 0.96 0.14 0.00
87_K 38_D 0.96 0.13 0.00
25_E 64_F 0.95 0.13 0.00
79_S 46_K 0.95 0.13 0.00
83_R 64_F 0.94 0.13 0.00
89_S 70_V 0.94 0.13 0.00
35_A 77_S 0.94 0.13 0.00
25_E 110_K 0.94 0.13 0.00
80_K 46_K 0.94 0.13 0.00
25_E 103_A 0.93 0.12 0.00
18_L 21_K 0.93 0.12 0.00
83_R 75_G 0.92 0.12 0.00
56_I 112_I 0.92 0.12 0.00
45_V 79_S 0.91 0.12 0.00
11_D 74_D 0.91 0.12 0.00
96_L 15_K 0.91 0.12 0.00
76_E 2_G 0.90 0.12 0.00
54_K 118_T 0.90 0.12 0.00
89_S 65_K 0.90 0.12 0.00
54_K 15_K 0.89 0.12 0.00
57_R 45_K 0.89 0.12 0.00
57_R 47_R 0.89 0.12 0.00
57_R 59_R 0.89 0.12 0.00
68_A 45_K 0.89 0.12 0.00
68_A 47_R 0.89 0.12 0.00
68_A 59_R 0.89 0.12 0.00
82_E 47_R 0.89 0.12 0.00
82_E 59_R 0.89 0.12 0.00
82_E 45_K 0.89 0.12 0.00
80_K 44_I 0.89 0.12 0.00
86_I 36_E 0.89 0.11 0.00
36_R 92_D 0.89 0.11 0.00
14_E 46_K 0.89 0.11 0.00
91_P 121_L 0.88 0.11 0.00
90_G 40_G 0.88 0.11 0.00
74_S 107_F 0.88 0.11 0.00
77_S 29_E 0.88 0.11 0.00
44_K 90_E 0.87 0.11 0.00
60_Y 97_Y 0.87 0.11 0.00
76_E 80_G 0.86 0.11 0.00
97_N 24_M 0.86 0.11 0.00
51_E 112_I 0.86 0.11 0.00
50_G 1_M 0.85 0.10 0.00
22_S 121_L 0.85 0.10 0.00
11_D 24_M 0.85 0.10 0.00
40_A 30_V 0.85 0.10 0.00
31_V 23_L 0.84 0.10 0.00
21_M 95_A 0.84 0.10 0.00
15_L 105_L 0.83 0.10 0.00
85_E 67_A 0.83 0.10 0.00
83_R 12_S 0.83 0.10 0.00
73_M 50_L 0.83 0.10 0.00
10_E 85_G 0.83 0.10 0.00
9_L 86_T 0.83 0.10 0.00
36_R 99_K 0.83 0.10 0.00
71_M 101_A 0.83 0.10 0.00
56_I 106_A 0.82 0.10 0.00
16_N 18_I 0.82 0.10 0.00
42_I 79_S 0.82 0.10 0.00
94_R 100_M 0.82 0.10 0.00
61_G 111_Q 0.82 0.10 0.00
51_E 32_Q 0.82 0.10 0.00
95_I 95_A 0.82 0.10 0.00
84_N 88_E 0.82 0.10 0.00
53_I 123_E 0.81 0.10 0.00
32_M 1_M 0.81 0.10 0.00
53_I 9_F 0.81 0.09 0.00
45_V 96_A 0.81 0.09 0.00
79_S 31_M 0.81 0.09 0.00
36_R 118_T 0.81 0.09 0.00
74_S 2_G 0.81 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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