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OPENSEQ.org
HJ
Genes: A B A+B
Length: 170 198 346
Sequences: 472 618 440
Seq/Len: 2.78 3.12 1.27
MirrorTree (Pazo et al. 2001) 0.75
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 0.01 0.00 0.10
2 0.01 0.00 1.17
5 0.01 0.00 1.18
10 0.01 0.00 1.20
20 0.01 0.00 1.20
100 0.01 0.00 1.20
∞ 0.03 0.03 1.20
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
18_I 13_M 1.66 0.90 0.33
137_P 99_P 1.62 0.89 0.31
13_L 15_L 1.50 0.83 0.23
105_A 174_L 1.49 0.82 0.23
23_G 146_N 1.46 0.80 0.21
61_F 99_P 1.45 0.80 0.20
47_Q 93_F 1.35 0.72 0.15
11_M 38_D 1.31 0.69 0.14
19_G 173_G 1.29 0.68 0.13
12_M 3_Q 1.27 0.66 0.12
58_T 115_Y 1.27 0.66 0.12
9_L 13_M 1.27 0.66 0.12
62_F 143_M 1.24 0.63 0.11
4_R 42_R 1.18 0.57 0.09
146_L 25_V 1.18 0.57 0.09
16_L 11_V 1.18 0.57 0.09
137_P 26_A 1.17 0.56 0.09
13_L 29_T 1.12 0.52 0.07
116_H 46_G 1.12 0.51 0.07
139_G 68_R 1.11 0.50 0.07
62_F 174_L 1.11 0.50 0.07
12_M 33_N 1.10 0.49 0.07
144_F 52_Q 1.10 0.49 0.07
42_A 42_R 1.09 0.49 0.07
2_R 3_Q 1.09 0.48 0.07
19_G 34_V 1.08 0.47 0.06
64_A 31_L 1.06 0.46 0.06
63_G 106_P 1.06 0.46 0.06
11_M 29_T 1.06 0.46 0.06
138_G 24_S 1.06 0.46 0.06
37_A 178_L 1.06 0.46 0.06
148_V 15_L 1.06 0.45 0.06
146_L 123_E 1.05 0.45 0.06
144_F 60_A 1.05 0.44 0.06
71_W 88_D 1.04 0.44 0.06
11_M 151_R 1.04 0.44 0.06
53_Q 71_R 1.04 0.43 0.06
117_L 174_L 1.04 0.43 0.06
26_M 71_R 1.04 0.43 0.05
138_G 98_W 1.03 0.42 0.05
135_I 71_R 1.02 0.41 0.05
12_M 176_V 1.00 0.40 0.05
11_M 57_Q 1.00 0.40 0.05
17_L 23_L 1.00 0.40 0.05
138_G 58_M 0.99 0.39 0.04
106_T 31_L 0.99 0.39 0.04
11_M 56_S 0.98 0.38 0.04
135_I 149_A 0.98 0.38 0.04
136_F 111_Q 0.98 0.38 0.04
79_R 45_G 0.97 0.37 0.04
138_G 126_S 0.97 0.37 0.04
19_G 183_S 0.97 0.37 0.04
17_L 36_R 0.97 0.37 0.04
19_G 95_R 0.96 0.36 0.04
57_Q 193_T 0.96 0.36 0.04
13_L 155_Y 0.96 0.36 0.04
146_L 99_P 0.96 0.36 0.04
3_Q 166_Q 0.95 0.35 0.04
12_M 103_G 0.95 0.35 0.04
55_G 144_Q 0.95 0.35 0.04
11_M 18_A 0.95 0.35 0.04
13_L 30_V 0.94 0.34 0.04
67_H 66_I 0.94 0.34 0.04
24_M 177_T 0.94 0.34 0.04
98_P 108_S 0.94 0.34 0.04
138_G 100_N 0.93 0.34 0.04
70_R 58_M 0.93 0.34 0.04
52_Q 15_L 0.93 0.33 0.04
41_L 20_L 0.93 0.33 0.04
40_A 165_Q 0.93 0.33 0.04
103_R 144_Q 0.93 0.33 0.04
72_Q 119_G 0.92 0.32 0.03
34_D 115_Y 0.91 0.32 0.03
142_T 35_M 0.91 0.32 0.03
119_F 128_D 0.91 0.32 0.03
56_L 53_L 0.91 0.32 0.03
133_V 66_I 0.91 0.32 0.03
145_R 37_A 0.90 0.31 0.03
25_V 14_L 0.90 0.31 0.03
135_I 164_W 0.90 0.30 0.03
105_A 94_S 0.89 0.30 0.03
64_A 57_Q 0.89 0.30 0.03
74_L 59_A 0.89 0.30 0.03
63_G 107_R 0.89 0.30 0.03
37_A 160_W 0.89 0.30 0.03
95_R 91_I 0.89 0.30 0.03
26_M 164_W 0.89 0.29 0.03
138_G 111_Q 0.89 0.29 0.03
73_F 173_G 0.88 0.29 0.03
98_P 51_L 0.88 0.29 0.03
4_R 6_R 0.88 0.29 0.03
156_F 180_L 0.88 0.29 0.03
73_F 30_V 0.88 0.29 0.03
67_H 176_V 0.88 0.29 0.03
146_L 23_L 0.88 0.29 0.03
68_P 66_I 0.88 0.29 0.03
41_L 181_E 0.87 0.28 0.03
20_V 17_L 0.87 0.28 0.03
52_Q 132_P 0.87 0.28 0.03
22_A 52_Q 0.87 0.28 0.03
3_Q 103_G 0.86 0.28 0.03
118_T 46_G 0.86 0.28 0.03
19_G 89_W 0.86 0.28 0.03
17_L 98_W 0.86 0.28 0.03
47_Q 44_K 0.86 0.28 0.03
43_R 173_G 0.86 0.28 0.03
96_W 68_R 0.85 0.27 0.03
131_P 124_R 0.85 0.27 0.03
59_G 150_F 0.85 0.27 0.03
100_R 108_S 0.85 0.27 0.03
19_G 190_F 0.85 0.27 0.03
36_S 58_M 0.85 0.27 0.03
132_D 173_G 0.85 0.27 0.03
103_R 23_L 0.85 0.26 0.03
136_F 173_G 0.84 0.26 0.03
23_G 147_V 0.84 0.26 0.03
54_R 23_L 0.84 0.26 0.03
17_L 159_R 0.84 0.26 0.03
112_G 106_P 0.84 0.26 0.03
19_G 5_A 0.84 0.26 0.03
137_P 126_S 0.84 0.26 0.03
41_L 174_L 0.84 0.26 0.03
10_E 12_E 0.84 0.26 0.03
112_G 174_L 0.84 0.26 0.03
30_P 21_A 0.84 0.26 0.02
107_S 178_L 0.84 0.26 0.02
19_G 59_A 0.84 0.26 0.02
74_L 150_F 0.84 0.26 0.02
44_F 91_I 0.84 0.26 0.02
48_L 42_R 0.83 0.26 0.02
109_S 41_T 0.83 0.25 0.02
38_A 114_S 0.83 0.25 0.02
7_T 52_Q 0.83 0.25 0.02
22_A 24_S 0.83 0.25 0.02
45_E 24_S 0.83 0.25 0.02
146_L 171_P 0.83 0.25 0.02
102_G 179_T 0.83 0.25 0.02
131_P 108_S 0.82 0.25 0.02
4_R 118_R 0.82 0.25 0.02
37_A 16_A 0.82 0.25 0.02
62_F 108_S 0.82 0.25 0.02
25_V 39_T 0.82 0.24 0.02
16_L 16_A 0.82 0.24 0.02
145_R 139_T 0.82 0.24 0.02
7_T 17_L 0.82 0.24 0.02
120_P 131_D 0.82 0.24 0.02
25_V 115_Y 0.82 0.24 0.02
67_H 17_L 0.82 0.24 0.02
25_V 93_F 0.81 0.24 0.02
46_A 11_V 0.81 0.24 0.02
21_S 72_D 0.81 0.24 0.02
12_M 6_R 0.81 0.24 0.02
15_L 91_I 0.81 0.24 0.02
13_L 105_L 0.81 0.24 0.02
60_Q 182_Q 0.81 0.24 0.02
20_V 175_E 0.81 0.23 0.02
36_S 143_M 0.81 0.23 0.02
53_Q 53_L 0.81 0.23 0.02
111_A 151_R 0.81 0.23 0.02
16_L 163_E 0.81 0.23 0.02
12_M 31_L 0.81 0.23 0.02
19_G 116_R 0.80 0.23 0.02
118_T 17_L 0.80 0.23 0.02
137_P 112_N 0.80 0.23 0.02
162_S 8_F 0.80 0.23 0.02
73_F 46_G 0.80 0.23 0.02
68_P 148_Q 0.80 0.23 0.02
18_I 138_P 0.80 0.23 0.02
51_V 110_I 0.80 0.23 0.02
40_A 21_A 0.80 0.23 0.02
74_L 166_Q 0.80 0.23 0.02
138_G 107_R 0.79 0.22 0.02
17_L 123_E 0.79 0.22 0.02
53_Q 180_L 0.79 0.22 0.02
48_L 151_R 0.79 0.22 0.02
4_R 119_G 0.79 0.22 0.02
109_S 145_R 0.79 0.22 0.02
63_G 100_N 0.79 0.22 0.02
24_M 114_S 0.78 0.22 0.02
147_T 52_Q 0.78 0.22 0.02
138_G 22_A 0.78 0.22 0.02
32_S 142_V 0.78 0.22 0.02
110_V 156_A 0.78 0.22 0.02
15_L 33_N 0.78 0.22 0.02
71_W 20_L 0.78 0.21 0.02
51_V 190_F 0.78 0.21 0.02
141_M 36_R 0.78 0.21 0.02
140_E 107_R 0.78 0.21 0.02
115_L 15_L 0.77 0.21 0.02
143_P 17_L 0.77 0.21 0.02
52_Q 112_N 0.77 0.21 0.02
79_R 117_L 0.77 0.21 0.02
116_H 176_V 0.77 0.21 0.02
98_P 44_K 0.77 0.21 0.02
66_V 177_T 0.77 0.21 0.02
12_M 14_L 0.77 0.21 0.02
77_Q 15_L 0.77 0.21 0.02
11_M 13_M 0.77 0.21 0.02
147_T 185_E 0.77 0.21 0.02
141_M 115_Y 0.76 0.20 0.02
13_L 48_M 0.76 0.20 0.02
154_I 186_I 0.76 0.20 0.02
165_E 116_R 0.76 0.20 0.02
56_L 20_L 0.76 0.20 0.02
119_F 119_G 0.76 0.20 0.02
12_M 49_Q 0.76 0.20 0.02
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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