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OPENSEQ.org
IK
Genes: A B A+B
Length: 121 326 443
Sequences: 694 874 635
Seq/Len: 5.74 2.68 1.43
MirrorTree (Pazo et al. 2001) 0.82
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 0.00 0.04
2 0.00 0.00 1.34
5 0.00 0.00 1.36
10 0.00 0.00 1.40
20 0.00 0.00 1.42
100 0.00 0.00 1.43
∞ 0.04 0.04 1.45
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
19_F 13_V 1.64 0.91 0.41
20_A 27_M 1.61 0.90 0.38
36_Q 208_A 1.57 0.88 0.35
23_G 13_V 1.42 0.81 0.25
117_Y 53_G 1.39 0.79 0.23
71_T 107_N 1.31 0.72 0.18
48_W 102_A 1.26 0.69 0.16
20_A 21_M 1.26 0.68 0.16
51_D 49_W 1.25 0.68 0.15
26_V 21_M 1.25 0.67 0.15
38_G 206_V 1.25 0.67 0.15
34_T 86_F 1.24 0.66 0.15
25_A 216_V 1.23 0.66 0.15
94_L 313_V 1.21 0.64 0.14
18_V 295_S 1.20 0.63 0.13
40_M 36_Q 1.18 0.61 0.12
116_T 49_W 1.18 0.60 0.12
13_M 58_A 1.15 0.58 0.11
79_S 185_V 1.14 0.57 0.11
80_W 55_E 1.13 0.56 0.10
10_I 278_L 1.11 0.54 0.10
33_Q 27_M 1.11 0.54 0.10
89_T 97_I 1.10 0.53 0.10
45_L 15_L 1.10 0.53 0.09
17_A 282_S 1.10 0.53 0.09
36_Q 127_F 1.10 0.53 0.09
13_M 97_I 1.09 0.52 0.09
22_A 95_A 1.06 0.49 0.08
96_A 77_Q 1.05 0.48 0.08
76_A 295_S 1.03 0.46 0.07
116_T 27_M 1.03 0.46 0.07
55_V 177_T 1.03 0.46 0.07
14_V 296_A 1.02 0.45 0.07
55_V 313_V 1.02 0.45 0.07
51_D 216_V 1.02 0.45 0.07
93_Q 287_A 1.02 0.44 0.07
14_V 311_F 1.01 0.44 0.07
37_L 294_G 1.01 0.44 0.07
49_L 55_E 1.01 0.43 0.07
111_V 124_A 1.00 0.43 0.07
19_F 21_M 0.99 0.42 0.06
47_G 45_L 0.99 0.41 0.06
90_D 294_G 0.97 0.40 0.06
17_A 8_V 0.97 0.40 0.06
22_A 17_L 0.97 0.40 0.06
18_V 97_I 0.97 0.40 0.06
14_V 176_L 0.97 0.40 0.06
21_L 245_L 0.96 0.39 0.06
115_R 182_L 0.96 0.39 0.06
7_M 15_L 0.94 0.37 0.05
94_L 56_T 0.94 0.37 0.05
98_D 11_L 0.93 0.36 0.05
71_T 153_D 0.93 0.36 0.05
49_L 37_Q 0.93 0.36 0.05
79_S 177_T 0.93 0.36 0.05
18_V 130_L 0.93 0.36 0.05
41_E 47_A 0.93 0.36 0.05
84_W 109_I 0.93 0.35 0.05
56_Q 47_A 0.92 0.35 0.05
49_L 210_A 0.92 0.35 0.05
17_A 131_L 0.92 0.35 0.05
46_A 79_W 0.92 0.35 0.05
5_A 3_T 0.92 0.35 0.05
13_M 13_V 0.91 0.34 0.05
88_E 4_R 0.91 0.34 0.05
42_E 20_M 0.91 0.34 0.05
71_T 187_E 0.91 0.34 0.05
72_T 125_Q 0.91 0.34 0.04
59_L 210_A 0.91 0.34 0.04
20_A 97_I 0.90 0.34 0.04
111_V 294_G 0.90 0.34 0.04
28_Q 303_L 0.90 0.34 0.04
80_W 186_S 0.90 0.33 0.04
102_R 134_L 0.90 0.33 0.04
78_V 216_V 0.90 0.33 0.04
77_G 146_A 0.89 0.33 0.04
4_Q 145_T 0.89 0.33 0.04
16_L 152_V 0.89 0.33 0.04
5_A 272_A 0.89 0.32 0.04
97_L 93_I 0.89 0.32 0.04
114_L 54_A 0.88 0.32 0.04
13_M 315_Q 0.88 0.32 0.04
18_V 133_N 0.88 0.32 0.04
43_K 16_I 0.88 0.31 0.04
22_A 259_A 0.87 0.31 0.04
10_I 93_I 0.87 0.31 0.04
81_H 23_L 0.87 0.31 0.04
112_S 11_L 0.87 0.30 0.04
16_L 89_N 0.87 0.30 0.04
64_P 167_V 0.87 0.30 0.04
80_W 199_Y 0.86 0.30 0.04
121_P 95_A 0.86 0.30 0.04
114_L 156_R 0.86 0.30 0.04
20_A 77_Q 0.86 0.30 0.04
63_W 151_W 0.85 0.29 0.04
31_L 9_A 0.85 0.29 0.04
10_I 250_A 0.85 0.29 0.04
101_V 242_A 0.85 0.29 0.04
47_G 42_L 0.85 0.29 0.04
13_M 251_A 0.85 0.29 0.04
27_M 135_G 0.84 0.28 0.04
80_W 13_V 0.84 0.28 0.04
24_L 281_H 0.84 0.28 0.03
91_L 182_L 0.84 0.28 0.03
18_V 147_A 0.84 0.28 0.03
59_L 306_K 0.84 0.28 0.03
92_P 97_I 0.84 0.28 0.03
115_R 17_L 0.83 0.28 0.03
49_L 40_T 0.83 0.27 0.03
94_L 95_A 0.83 0.27 0.03
18_V 25_S 0.83 0.27 0.03
99_V 314_V 0.83 0.27 0.03
8_T 186_S 0.83 0.27 0.03
49_L 87_A 0.83 0.27 0.03
10_I 273_A 0.83 0.27 0.03
18_V 6_R 0.83 0.27 0.03
99_V 68_D 0.82 0.27 0.03
86_G 38_T 0.82 0.27 0.03
44_T 206_V 0.82 0.27 0.03
20_A 207_C 0.82 0.27 0.03
85_Q 259_A 0.82 0.27 0.03
13_M 95_A 0.82 0.26 0.03
27_M 256_S 0.82 0.26 0.03
29_A 60_A 0.82 0.26 0.03
55_V 103_C 0.82 0.26 0.03
10_I 255_N 0.81 0.26 0.03
48_W 100_A 0.81 0.25 0.03
23_G 109_I 0.81 0.25 0.03
92_P 236_E 0.80 0.25 0.03
120_P 88_V 0.80 0.25 0.03
63_W 232_L 0.80 0.25 0.03
67_S 142_L 0.80 0.25 0.03
97_L 61_L 0.80 0.25 0.03
71_T 179_N 0.80 0.25 0.03
80_W 50_Y 0.80 0.25 0.03
43_K 241_E 0.80 0.24 0.03
52_N 254_W 0.79 0.24 0.03
99_V 284_R 0.79 0.24 0.03
49_L 194_M 0.79 0.24 0.03
59_L 88_V 0.79 0.24 0.03
18_V 67_L 0.79 0.24 0.03
119_T 194_M 0.79 0.24 0.03
94_L 60_A 0.79 0.24 0.03
100_E 174_G 0.79 0.24 0.03
111_V 54_A 0.79 0.24 0.03
13_M 231_A 0.79 0.24 0.03
95_R 227_A 0.79 0.24 0.03
10_I 228_L 0.79 0.24 0.03
56_Q 194_M 0.78 0.23 0.03
70_E 136_S 0.78 0.23 0.03
34_T 193_G 0.78 0.23 0.03
6_G 7_G 0.78 0.23 0.03
98_D 250_A 0.78 0.23 0.03
117_Y 216_V 0.78 0.23 0.03
32_Q 11_L 0.78 0.23 0.03
21_L 151_W 0.78 0.23 0.03
103_R 291_V 0.77 0.23 0.03
110_P 11_L 0.77 0.23 0.03
19_F 55_E 0.77 0.23 0.03
83_R 135_G 0.77 0.23 0.03
33_Q 31_S 0.77 0.23 0.03
47_G 100_A 0.77 0.23 0.03
27_M 47_A 0.77 0.23 0.03
18_V 112_L 0.77 0.22 0.03
46_A 97_I 0.77 0.22 0.03
41_E 210_A 0.77 0.22 0.03
99_V 305_Q 0.77 0.22 0.02
18_V 10_L 0.76 0.22 0.02
99_V 121_P 0.76 0.22 0.02
13_M 25_S 0.76 0.22 0.02
94_L 227_A 0.76 0.22 0.02
10_I 90_D 0.76 0.22 0.02
21_L 305_Q 0.76 0.22 0.02
97_L 245_L 0.76 0.22 0.02
76_A 134_L 0.75 0.21 0.02
74_Q 315_Q 0.75 0.21 0.02
25_A 143_Q 0.75 0.21 0.02
5_A 228_L 0.74 0.21 0.02
28_Q 25_S 0.74 0.21 0.02
77_G 178_G 0.74 0.21 0.02
82_I 107_N 0.74 0.20 0.02
27_M 13_V 0.74 0.20 0.02
64_P 200_Q 0.74 0.20 0.02
114_L 283_E 0.74 0.20 0.02
5_A 306_K 0.73 0.20 0.02
28_Q 22_V 0.73 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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