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OPENSEQ.org
GK
Genes: A B A+B
Length: 140 326 458
Sequences: 1248 874 701
Seq/Len: 8.91 2.68 1.53
MirrorTree (Pazo et al. 2001) 0.69
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 0.08 0.00 0.09
2 0.09 0.00 0.11
5 0.09 0.00 1.39
10 0.09 0.00 1.50
20 0.09 0.00 1.50
100 0.09 0.00 1.51
∞ 0.13 0.04 1.56
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
16_I 23_L 1.37 0.79 0.04
46_L 14_L 1.11 0.56 0.02
19_L 71_N 1.11 0.56 0.02
77_P 219_N 1.10 0.55 0.02
49_L 231_A 1.07 0.52 0.02
31_M 22_V 1.06 0.51 0.02
136_T 191_L 1.01 0.46 0.01
129_N 298_Y 1.00 0.45 0.01
38_D 21_M 1.00 0.45 0.01
63_Y 233_F 0.99 0.43 0.01
130_D 103_C 0.97 0.42 0.01
67_E 208_A 0.97 0.42 0.01
119_S 21_M 0.97 0.41 0.01
129_N 72_Q 0.97 0.41 0.01
65_T 288_T 0.97 0.41 0.01
92_I 108_A 0.97 0.41 0.01
45_D 105_N 0.96 0.40 0.01
124_G 222_Q 0.94 0.39 0.01
30_L 19_L 0.94 0.39 0.01
50_E 13_V 0.93 0.37 0.01
22_L 9_A 0.92 0.37 0.01
74_V 206_V 0.92 0.37 0.01
54_D 17_L 0.92 0.36 0.01
8_T 170_A 0.92 0.36 0.01
57_K 250_A 0.92 0.36 0.01
19_L 52_L 0.92 0.36 0.01
61_S 208_A 0.91 0.36 0.01
134_N 227_A 0.90 0.35 0.01
65_T 20_M 0.90 0.34 0.01
56_Y 104_F 0.90 0.34 0.01
19_L 291_V 0.89 0.34 0.01
125_V 287_A 0.89 0.34 0.01
120_L 148_L 0.89 0.34 0.01
107_L 134_L 0.89 0.33 0.01
13_M 209_L 0.88 0.33 0.01
65_T 37_Q 0.88 0.33 0.01
32_G 102_A 0.88 0.33 0.01
36_K 103_C 0.87 0.32 0.01
104_Y 293_M 0.87 0.32 0.01
17_V 96_T 0.86 0.31 0.01
116_D 231_A 0.86 0.31 0.01
87_P 19_L 0.86 0.31 0.01
54_D 13_V 0.85 0.30 0.01
107_L 220_T 0.85 0.30 0.01
54_D 20_M 0.84 0.30 0.01
75_S 11_L 0.84 0.29 0.01
93_R 147_A 0.84 0.29 0.01
117_I 49_W 0.83 0.29 0.01
46_L 23_L 0.83 0.29 0.01
24_S 177_T 0.83 0.28 0.01
26_V 31_S 0.83 0.28 0.01
42_V 283_E 0.82 0.28 0.01
13_M 280_V 0.82 0.28 0.01
4_Q 295_S 0.82 0.28 0.01
65_T 240_A 0.82 0.28 0.01
27_V 242_A 0.82 0.28 0.01
75_S 312_S 0.82 0.28 0.01
17_V 44_N 0.82 0.27 0.01
76_A 39_A 0.82 0.27 0.01
120_L 70_P 0.82 0.27 0.01
120_L 43_D 0.82 0.27 0.01
106_L 235_A 0.81 0.27 0.01
19_L 102_A 0.81 0.27 0.01
120_L 235_A 0.81 0.27 0.01
62_R 231_A 0.81 0.27 0.01
25_L 135_G 0.81 0.27 0.01
49_L 103_C 0.80 0.26 0.01
25_L 148_L 0.80 0.26 0.01
13_M 109_I 0.80 0.26 0.01
50_E 10_L 0.80 0.26 0.01
30_L 190_L 0.80 0.26 0.01
96_P 46_Q 0.79 0.25 0.01
5_R 135_G 0.79 0.25 0.01
106_L 169_M 0.79 0.25 0.01
117_I 121_P 0.78 0.25 0.01
66_T 187_E 0.78 0.24 0.01
12_I 270_D 0.78 0.24 0.01
21_V 25_S 0.78 0.24 0.01
120_L 144_L 0.78 0.24 0.01
56_Y 177_T 0.77 0.24 0.01
78_S 177_T 0.77 0.24 0.01
46_L 46_Q 0.77 0.24 0.01
24_S 260_F 0.77 0.24 0.01
26_V 139_L 0.77 0.24 0.01
93_R 129_R 0.77 0.24 0.01
74_V 132_E 0.77 0.24 0.01
67_E 274_A 0.77 0.24 0.01
38_D 306_K 0.77 0.23 0.01
131_D 79_W 0.77 0.23 0.01
33_N 13_V 0.77 0.23 0.01
82_H 2_N 0.77 0.23 0.01
67_E 144_L 0.77 0.23 0.01
1_M 4_R 0.76 0.23 0.01
13_M 210_A 0.76 0.23 0.01
60_N 109_I 0.76 0.23 0.01
36_K 47_A 0.76 0.23 0.01
124_G 103_C 0.76 0.23 0.01
49_L 34_M 0.76 0.23 0.01
67_E 54_A 0.76 0.23 0.01
133_G 206_V 0.76 0.23 0.01
119_S 95_A 0.76 0.23 0.01
3_R 6_R 0.76 0.23 0.01
5_R 200_Q 0.76 0.23 0.01
57_K 89_N 0.76 0.23 0.01
65_T 181_P 0.76 0.23 0.01
48_A 20_M 0.75 0.22 0.01
65_T 241_E 0.75 0.22 0.01
134_N 16_I 0.75 0.22 0.01
115_V 196_A 0.75 0.22 0.01
8_T 165_D 0.75 0.22 0.01
51_G 38_T 0.75 0.22 0.01
80_E 25_S 0.75 0.22 0.01
105_Q 206_V 0.74 0.22 0.01
16_I 16_I 0.74 0.22 0.01
51_G 64_R 0.74 0.22 0.01
62_R 289_F 0.74 0.22 0.01
4_Q 282_S 0.74 0.22 0.01
3_R 59_A 0.74 0.21 0.01
16_I 28_T 0.74 0.21 0.01
8_T 147_A 0.74 0.21 0.01
56_Y 275_R 0.74 0.21 0.01
12_I 10_L 0.74 0.21 0.01
120_L 136_S 0.74 0.21 0.01
19_L 149_R 0.74 0.21 0.01
19_L 191_L 0.73 0.21 0.01
102_S 53_G 0.73 0.21 0.01
105_Q 144_L 0.73 0.21 0.01
24_S 50_Y 0.73 0.21 0.01
78_S 102_A 0.73 0.21 0.01
50_E 182_L 0.73 0.21 0.01
12_I 82_Q 0.73 0.21 0.01
106_L 291_V 0.73 0.21 0.01
57_K 287_A 0.72 0.20 0.01
25_L 266_L 0.72 0.20 0.01
115_V 259_A 0.72 0.20 0.01
29_N 16_I 0.72 0.20 0.01
49_L 130_L 0.72 0.20 0.01
39_R 216_V 0.72 0.20 0.01
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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