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OPENSEQ.org
1kf6_D_B
Genes: A B A+B
Length: 119 243 340
Sequences: 147 2044 96
Seq/Len: 1.24 8.41 0.28
MirrorTree (Pazo et al. 2001) 0.86
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 0.07 0.01 0.01
2 0.07 0.01 0.27
5 0.07 0.01 0.27
10 0.07 0.01 0.27
20 0.07 0.01 0.27
100 0.07 0.01 0.27
∞ 0.07 0.08 0.27
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
9_S 156_A 1.59 0.46 0.00
110_V 53_Y 1.56 0.44 0.00
23_M 53_Y 1.47 0.38 0.00
79_G 95_N 1.45 0.37 0.00
77_W 99_E 1.41 0.34 0.00
92_I 98_I 1.38 0.33 0.00
24_W 33_T 1.35 0.31 0.00
69_F 95_N 1.33 0.30 0.00
78_C 36_L 1.33 0.30 0.00
75_P 152_G 1.33 0.30 0.00
117_V 90_V 1.32 0.29 0.00
93_H 8_I 1.28 0.27 0.00
29_A 225_Q 1.25 0.26 0.00
85_H 142_Y 1.24 0.25 0.00
84_H 41_G 1.24 0.25 0.00
89_D 93_L 1.24 0.25 0.00
33_I 224_I 1.23 0.24 0.00
11_E 206_F 1.23 0.24 0.00
103_G 100_R 1.23 0.24 0.00
100_V 137_A 1.20 0.23 0.00
37_G 61_I 1.19 0.23 0.00
46_P 145_F 1.19 0.22 0.00
44_L 26_Y 1.18 0.22 0.00
64_G 145_F 1.18 0.22 0.00
84_H 34_T 1.17 0.22 0.00
42_L 163_L 1.17 0.22 0.00
70_L 147_G 1.16 0.21 0.00
8_R 45_D 1.16 0.21 0.00
72_I 232_S 1.15 0.21 0.00
11_E 38_D 1.14 0.20 0.00
65_R 137_A 1.13 0.20 0.00
72_I 172_A 1.12 0.20 0.00
54_R 10_V 1.12 0.20 0.00
86_A 72_V 1.12 0.20 0.00
74_L 183_S 1.11 0.19 0.00
91_K 8_I 1.10 0.19 0.00
77_W 147_G 1.10 0.19 0.00
85_H 35_S 1.10 0.19 0.00
98_K 177_H 1.10 0.19 0.00
83_M 119_Y 1.09 0.18 0.00
70_L 225_Q 1.09 0.18 0.00
27_I 174_T 1.09 0.18 0.00
78_C 48_A 1.08 0.18 0.00
70_L 139_M 1.08 0.18 0.00
44_L 217_H 1.08 0.18 0.00
112_T 69_V 1.07 0.18 0.00
19_G 35_S 1.06 0.17 0.00
23_M 110_I 1.04 0.17 0.00
24_W 41_G 1.04 0.16 0.00
68_L 97_P 1.03 0.16 0.00
73_V 173_I 1.03 0.16 0.00
16_G 229_V 1.03 0.16 0.00
70_L 30_Y 1.03 0.16 0.00
11_E 224_I 1.03 0.16 0.00
31_V 225_Q 1.03 0.16 0.00
85_H 114_E 1.02 0.16 0.00
77_W 110_I 1.02 0.16 0.00
27_I 88_M 1.01 0.15 0.00
19_G 114_E 1.01 0.15 0.00
111_V 22_H 1.01 0.15 0.00
91_K 161_F 1.01 0.15 0.00
35_L 171_A 1.01 0.15 0.00
9_S 42_Y 1.00 0.15 0.00
40_L 195_L 1.00 0.15 0.00
71_M 92_A 0.99 0.15 0.00
79_G 85_T 0.99 0.15 0.00
84_H 161_F 0.98 0.14 0.00
91_K 199_N 0.98 0.14 0.00
107_I 70_N 0.98 0.14 0.00
100_V 146_S 0.98 0.14 0.00
8_R 58_R 0.97 0.14 0.00
101_F 14_N 0.97 0.14 0.00
13_V 98_I 0.97 0.14 0.00
36_V 199_N 0.97 0.14 0.00
55_V 173_I 0.97 0.14 0.00
16_G 232_S 0.96 0.14 0.00
9_S 234_D 0.96 0.14 0.00
93_H 120_I 0.96 0.14 0.00
20_A 96_F 0.96 0.14 0.00
36_V 130_G 0.95 0.14 0.00
33_I 121_I 0.95 0.13 0.00
78_C 50_D 0.95 0.13 0.00
23_M 72_V 0.95 0.13 0.00
58_F 162_G 0.95 0.13 0.00
11_E 105_D 0.94 0.13 0.00
7_K 43_I 0.94 0.13 0.00
23_M 100_R 0.94 0.13 0.00
100_V 67_M 0.94 0.13 0.00
57_A 26_Y 0.94 0.13 0.00
68_L 175_L 0.94 0.13 0.00
116_V 130_G 0.94 0.13 0.00
87_M 172_A 0.94 0.13 0.00
16_G 233_K 0.94 0.13 0.00
34_L 173_I 0.94 0.13 0.00
24_W 6_L 0.94 0.13 0.00
16_G 10_V 0.94 0.13 0.00
28_I 174_T 0.93 0.13 0.00
11_E 84_Y 0.93 0.13 0.00
38_I 84_Y 0.93 0.13 0.00
69_F 100_R 0.93 0.13 0.00
79_G 147_G 0.93 0.13 0.00
113_L 189_K 0.93 0.13 0.00
111_V 224_I 0.93 0.13 0.00
16_G 225_Q 0.93 0.13 0.00
19_G 58_R 0.92 0.13 0.00
48_D 7_K 0.92 0.12 0.00
92_I 225_Q 0.92 0.12 0.00
59_A 137_A 0.92 0.12 0.00
109_T 117_K 0.92 0.12 0.00
16_G 106_M 0.91 0.12 0.00
9_S 68_M 0.91 0.12 0.00
83_M 192_M 0.91 0.12 0.00
110_V 74_K 0.91 0.12 0.00
31_V 147_G 0.90 0.12 0.00
58_F 190_E 0.90 0.12 0.00
71_M 50_D 0.90 0.12 0.00
60_Q 137_A 0.89 0.12 0.00
66_V 212_E 0.89 0.12 0.00
81_H 113_L 0.89 0.12 0.00
78_C 6_L 0.89 0.12 0.00
115_G 226_Q 0.89 0.12 0.00
8_R 81_L 0.89 0.12 0.00
108_L 196_N 0.89 0.12 0.00
30_P 100_R 0.89 0.12 0.00
17_L 135_T 0.89 0.12 0.00
35_L 139_M 0.88 0.12 0.00
71_M 125_R 0.88 0.11 0.00
8_R 42_Y 0.88 0.11 0.00
8_R 35_S 0.88 0.11 0.00
115_G 92_A 0.88 0.11 0.00
58_F 168_I 0.88 0.11 0.00
89_D 160_Q 0.88 0.11 0.00
108_L 90_V 0.88 0.11 0.00
69_F 197_S 0.87 0.11 0.00
11_E 202_W 0.87 0.11 0.00
27_I 31_D 0.87 0.11 0.00
48_D 90_V 0.87 0.11 0.00
95_P 41_G 0.86 0.11 0.00
99_W 189_K 0.86 0.11 0.00
49_A 124_S 0.86 0.11 0.00
69_F 168_I 0.86 0.11 0.00
23_M 225_Q 0.86 0.11 0.00
80_L 95_N 0.86 0.11 0.00
62_F 110_I 0.86 0.11 0.00
64_G 60_A 0.86 0.11 0.00
104_L 199_N 0.86 0.11 0.00
11_E 43_I 0.86 0.11 0.00
110_V 92_A 0.86 0.11 0.00
78_C 133_I 0.86 0.11 0.00
32_M 232_S 0.85 0.11 0.00
103_G 29_P 0.85 0.11 0.00
41_P 61_I 0.85 0.11 0.00
38_I 5_N 0.85 0.11 0.00
69_F 145_F 0.84 0.10 0.00
94_V 90_V 0.84 0.10 0.00
78_C 14_N 0.84 0.10 0.00
110_V 212_E 0.84 0.10 0.00
25_S 145_F 0.84 0.10 0.00
71_M 112_S 0.84 0.10 0.00
112_T 152_G 0.84 0.10 0.00
9_S 122_G 0.84 0.10 0.00
109_T 168_I 0.84 0.10 0.00
99_W 2_E 0.84 0.10 0.00
77_W 116_I 0.84 0.10 0.00
91_K 112_S 0.84 0.10 0.00
63_I 121_I 0.83 0.10 0.00
65_R 193_A 0.83 0.10 0.00
43_G 26_Y 0.83 0.10 0.00
45_F 168_I 0.83 0.10 0.00
54_R 133_I 0.83 0.10 0.00
16_G 222_A 0.83 0.10 0.00
110_V 89_K 0.83 0.10 0.00
20_A 117_K 0.82 0.10 0.00
16_G 78_K 0.82 0.10 0.00
84_H 176_A 0.82 0.10 0.00
56_L 47_L 0.82 0.10 0.00
74_L 131_T 0.82 0.10 0.00
117_V 187_G 0.82 0.10 0.00
77_W 206_F 0.82 0.10 0.00
56_L 225_Q 0.82 0.10 0.00
95_P 203_S 0.82 0.10 0.00
19_G 156_A 0.82 0.10 0.00
19_G 139_M 0.82 0.10 0.00
96_A 53_Y 0.82 0.10 0.00
85_H 58_R 0.81 0.10 0.00
110_V 171_A 0.81 0.10 0.00
74_L 68_M 0.81 0.10 0.00
87_M 142_Y 0.81 0.10 0.00
16_G 147_G 0.81 0.10 0.00
101_F 120_I 0.81 0.10 0.00
25_S 224_I 0.81 0.10 0.00
11_E 123_N 0.81 0.10 0.00
88_H 82_R 0.81 0.10 0.00
28_I 195_L 0.81 0.10 0.00
64_G 160_Q 0.81 0.10 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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