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OPENSEQ.org
jean-Pierre
Genes: A B A+B
Length: 144 117 251
Sequences: 453 53363 175
Seq/Len: 3.15 456.09 0.7
MirrorTree (Pazo et al. 2001) 0.84
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 0.00 0.03 0.61
2 0.00 0.05 0.61
5 0.00 0.08 0.64
10 0.00 0.10 0.65
20 0.00 0.13 0.67
100 0.00 0.22 1.06
∞ 0.00 0.27 1.61
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
103_G 75_G 1.41 0.60 0.00
109_G 97_R 1.40 0.59 0.00
57_E 40_R 1.39 0.58 0.00
119_R 82_R 1.38 0.57 0.00
142_E 45_A 1.37 0.56 0.00
59_F 52_L 1.36 0.55 0.00
78_Y 56_A 1.36 0.55 0.00
47_I 108_L 1.35 0.54 0.00
127_G 32_N 1.33 0.53 0.00
76_L 43_R 1.23 0.44 0.00
36_V 32_N 1.22 0.44 0.00
44_R 43_R 1.18 0.41 0.00
35_V 11_L 1.18 0.40 0.00
118_V 37_S 1.18 0.40 0.00
95_S 28_S 1.18 0.40 0.00
123_N 51_V 1.17 0.39 0.00
28_F 70_Q 1.15 0.38 0.00
109_G 105_G 1.15 0.38 0.00
65_S 65_A 1.13 0.36 0.00
142_E 89_L 1.12 0.35 0.00
50_K 51_V 1.10 0.34 0.00
140_R 90_W 1.10 0.34 0.00
90_V 99_K 1.09 0.33 0.00
51_V 41_A 1.08 0.32 0.00
140_R 109_A 1.08 0.32 0.00
25_L 73_R 1.05 0.30 0.00
36_V 30_D 1.05 0.30 0.00
79_R 67_Q 1.05 0.30 0.00
42_G 44_I 1.04 0.29 0.00
26_A 9_E 1.03 0.29 0.00
44_R 55_L 1.02 0.28 0.00
62_L 42_Q 1.02 0.28 0.00
79_R 39_E 1.00 0.27 0.00
111_E 61_A 1.00 0.27 0.00
44_R 80_N 1.00 0.27 0.00
87_P 64_D 0.99 0.27 0.00
28_F 89_L 0.99 0.26 0.00
141_L 93_I 0.98 0.26 0.00
114_Q 92_L 0.98 0.25 0.00
28_F 35_A 0.97 0.25 0.00
41_S 43_R 0.97 0.25 0.00
41_S 13_G 0.97 0.25 0.00
92_V 63_G 0.97 0.25 0.00
88_G 46_P 0.97 0.25 0.00
41_S 14_P 0.96 0.25 0.00
101_T 55_L 0.95 0.23 0.00
61_G 22_A 0.94 0.23 0.00
114_Q 71_V 0.94 0.23 0.00
42_G 43_R 0.94 0.23 0.00
116_V 37_S 0.94 0.23 0.00
24_L 57_Q 0.93 0.23 0.00
103_G 89_L 0.93 0.22 0.00
43_R 49_P 0.92 0.22 0.00
64_L 59_R 0.92 0.22 0.00
144_L 85_L 0.92 0.22 0.00
144_L 88_G 0.92 0.22 0.00
33_D 45_A 0.91 0.21 0.00
117_R 87_A 0.91 0.21 0.00
144_L 9_E 0.91 0.21 0.00
106_F 43_R 0.90 0.21 0.00
99_L 84_A 0.90 0.21 0.00
140_R 18_M 0.90 0.21 0.00
109_G 22_A 0.90 0.21 0.00
55_P 90_W 0.89 0.20 0.00
33_D 96_A 0.89 0.20 0.00
79_R 101_G 0.89 0.20 0.00
36_V 110_R 0.89 0.20 0.00
51_V 109_A 0.87 0.19 0.00
51_V 90_W 0.87 0.19 0.00
52_Y 66_A 0.87 0.19 0.00
64_L 38_L 0.86 0.19 0.00
18_G 39_E 0.86 0.18 0.00
40_F 109_A 0.86 0.18 0.00
60_N 24_Q 0.85 0.18 0.00
57_E 76_L 0.85 0.18 0.00
126_S 65_A 0.85 0.18 0.00
23_V 52_L 0.85 0.18 0.00
128_L 84_A 0.85 0.18 0.00
55_P 46_P 0.85 0.18 0.00
59_F 14_P 0.84 0.18 0.00
11_L 60_L 0.84 0.18 0.00
143_P 69_E 0.84 0.18 0.00
48_P 109_A 0.84 0.18 0.00
45_W 60_L 0.84 0.17 0.00
49_A 59_R 0.84 0.17 0.00
54_R 42_Q 0.83 0.17 0.00
44_R 87_A 0.83 0.17 0.00
118_V 36_A 0.83 0.17 0.00
39_K 48_E 0.83 0.17 0.00
86_G 93_I 0.83 0.17 0.00
45_W 48_E 0.83 0.17 0.00
56_L 93_I 0.83 0.17 0.00
65_S 92_L 0.83 0.17 0.00
130_Q 106_A 0.82 0.17 0.00
143_P 41_A 0.82 0.17 0.00
129_S 36_A 0.82 0.17 0.00
36_V 114_K 0.82 0.17 0.00
36_V 25_Q 0.82 0.17 0.00
119_R 44_I 0.82 0.17 0.00
90_V 116_S 0.82 0.17 0.00
44_R 14_P 0.82 0.17 0.00
79_R 106_A 0.82 0.17 0.00
61_G 97_R 0.82 0.17 0.00
121_N 24_Q 0.81 0.17 0.00
70_L 49_P 0.81 0.16 0.00
27_G 92_L 0.81 0.16 0.00
99_L 66_A 0.81 0.16 0.00
103_G 96_A 0.81 0.16 0.00
78_Y 72_A 0.81 0.16 0.00
38_E 63_G 0.81 0.16 0.00
53_A 38_L 0.81 0.16 0.00
97_V 44_I 0.81 0.16 0.00
41_S 75_G 0.80 0.16 0.00
99_L 13_G 0.80 0.16 0.00
141_L 113_A 0.80 0.16 0.00
61_G 51_V 0.80 0.15 0.00
107_Y 88_G 0.79 0.15 0.00
24_L 55_L 0.79 0.15 0.00
21_G 112_K 0.79 0.15 0.00
91_S 91_E 0.79 0.15 0.00
89_T 25_Q 0.79 0.15 0.00
102_R 46_P 0.79 0.15 0.00
58_L 95_Q 0.78 0.15 0.00
91_S 36_A 0.78 0.15 0.00
33_D 55_L 0.78 0.15 0.00
96_A 111_Q 0.78 0.15 0.00
35_V 86_Q 0.78 0.15 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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