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OPENSEQ.org
t121
Genes: A B A+B
Length: 104 432 515
Sequences: 513 980 391
Seq/Len: 4.93 2.27 0.76
MirrorTree (Pazo et al. 2001) 0.71
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 0.08 0.71
2 0.00 0.08 0.72
5 0.00 0.08 0.72
10 0.00 0.08 0.72
20 0.00 0.08 0.73
100 0.00 0.08 0.73
∞ 0.00 0.08 0.77
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
96_I 24_P 1.59 0.75 0.01
95_I 27_I 1.56 0.74 0.01
26_P 334_A 1.36 0.58 0.01
39_I 250_F 1.28 0.51 0.01
90_Y 167_V 1.24 0.47 0.01
85_T 184_S 1.23 0.46 0.01
23_W 334_A 1.22 0.46 0.01
72_V 150_F 1.22 0.46 0.01
96_I 58_I 1.16 0.41 0.00
62_D 77_I 1.15 0.40 0.00
85_T 51_P 1.15 0.40 0.00
64_S 268_E 1.15 0.40 0.00
15_I 260_V 1.13 0.39 0.00
93_R 22_A 1.13 0.39 0.00
71_N 97_N 1.13 0.38 0.00
94_R 24_P 1.12 0.37 0.00
75_I 221_K 1.11 0.37 0.00
43_P 421_D 1.11 0.36 0.00
85_T 164_M 1.10 0.36 0.00
8_T 384_A 1.10 0.36 0.00
64_S 267_P 1.09 0.35 0.00
61_F 332_Y 1.09 0.35 0.00
13_D 318_V 1.06 0.33 0.00
19_V 164_M 1.06 0.33 0.00
48_T 230_V 1.05 0.32 0.00
75_I 153_L 1.05 0.32 0.00
38_L 22_A 1.04 0.32 0.00
23_W 267_P 1.04 0.32 0.00
69_V 96_V 1.04 0.31 0.00
64_S 75_N 1.03 0.30 0.00
62_D 332_Y 1.02 0.29 0.00
37_V 357_F 1.01 0.29 0.00
52_V 357_F 1.01 0.29 0.00
20_S 29_S 1.01 0.29 0.00
16_V 17_G 1.01 0.29 0.00
19_V 58_I 1.00 0.29 0.00
43_P 247_A 0.99 0.28 0.00
59_K 60_N 0.99 0.28 0.00
26_P 231_D 0.99 0.28 0.00
39_I 57_I 0.98 0.27 0.00
37_V 167_V 0.98 0.27 0.00
57_G 304_T 0.98 0.27 0.00
33_M 35_I 0.98 0.27 0.00
69_V 164_M 0.97 0.27 0.00
75_I 223_P 0.97 0.26 0.00
20_S 383_V 0.97 0.26 0.00
50_A 92_K 0.96 0.26 0.00
35_V 246_G 0.96 0.26 0.00
8_T 115_Y 0.96 0.26 0.00
23_W 268_E 0.96 0.26 0.00
23_W 276_S 0.96 0.26 0.00
77_E 69_E 0.96 0.26 0.00
87_D 149_S 0.95 0.25 0.00
65_A 375_T 0.94 0.24 0.00
39_I 163_K 0.94 0.24 0.00
11_L 282_L 0.94 0.24 0.00
36_E 24_P 0.94 0.24 0.00
26_P 92_K 0.94 0.24 0.00
19_V 27_I 0.93 0.24 0.00
39_I 99_V 0.93 0.24 0.00
74_R 383_V 0.93 0.24 0.00
71_N 359_I 0.92 0.23 0.00
67_A 153_L 0.92 0.23 0.00
60_P 119_D 0.92 0.23 0.00
61_F 125_Q 0.92 0.23 0.00
10_S 161_S 0.92 0.23 0.00
61_F 311_P 0.92 0.23 0.00
35_V 213_I 0.91 0.23 0.00
65_A 100_M 0.91 0.22 0.00
11_L 390_L 0.91 0.22 0.00
58_D 242_E 0.90 0.22 0.00
84_A 313_I 0.90 0.22 0.00
86_F 128_T 0.89 0.21 0.00
99_P 28_S 0.89 0.21 0.00
58_D 313_I 0.89 0.21 0.00
69_V 313_I 0.89 0.21 0.00
64_S 55_S 0.89 0.21 0.00
37_V 240_N 0.88 0.21 0.00
23_W 262_S 0.88 0.21 0.00
62_D 335_N 0.88 0.21 0.00
70_R 316_M 0.88 0.20 0.00
55_S 335_N 0.87 0.20 0.00
56_S 311_P 0.87 0.20 0.00
55_S 92_K 0.87 0.20 0.00
41_M 91_W 0.87 0.20 0.00
35_V 201_I 0.87 0.20 0.00
78_M 165_L 0.87 0.20 0.00
62_D 411_V 0.87 0.20 0.00
58_D 246_G 0.87 0.20 0.00
48_T 366_R 0.86 0.20 0.00
49_N 55_S 0.86 0.20 0.00
21_Q 225_I 0.86 0.20 0.00
97_F 358_Q 0.86 0.20 0.00
65_A 430_Y 0.86 0.19 0.00
89_L 113_V 0.85 0.19 0.00
69_V 227_I 0.84 0.19 0.00
64_S 334_A 0.84 0.19 0.00
72_V 296_K 0.84 0.19 0.00
93_R 25_L 0.84 0.18 0.00
33_M 98_Y 0.84 0.18 0.00
27_P 198_R 0.84 0.18 0.00
5_S 313_I 0.84 0.18 0.00
43_P 393_A 0.84 0.18 0.00
18_L 301_L 0.83 0.18 0.00
39_I 65_S 0.83 0.18 0.00
6_E 375_T 0.83 0.18 0.00
39_I 271_V 0.83 0.18 0.00
29_A 266_N 0.83 0.18 0.00
72_V 25_L 0.82 0.18 0.00
7_V 373_S 0.82 0.18 0.00
54_R 348_V 0.82 0.18 0.00
39_I 423_R 0.82 0.18 0.00
84_A 110_R 0.82 0.18 0.00
35_V 348_V 0.82 0.17 0.00
54_R 26_V 0.82 0.17 0.00
50_A 392_Y 0.82 0.17 0.00
76_P 209_D 0.82 0.17 0.00
28_S 237_Q 0.81 0.17 0.00
65_A 195_L 0.81 0.17 0.00
68_A 379_D 0.81 0.17 0.00
48_T 343_K 0.81 0.17 0.00
19_V 273_D 0.81 0.17 0.00
64_S 84_S 0.81 0.17 0.00
95_I 362_Q 0.81 0.17 0.00
77_E 225_I 0.81 0.17 0.00
49_N 146_A 0.81 0.17 0.00
44_D 337_K 0.81 0.17 0.00
98_K 39_V 0.81 0.17 0.00
37_V 276_S 0.80 0.17 0.00
65_A 276_S 0.80 0.17 0.00
79_Q 191_P 0.80 0.17 0.00
82_P 57_I 0.80 0.17 0.00
83_R 115_Y 0.80 0.17 0.00
87_D 358_Q 0.80 0.17 0.00
72_V 226_F 0.80 0.16 0.00
75_I 244_L 0.80 0.16 0.00
54_R 211_R 0.79 0.16 0.00
64_S 121_G 0.79 0.16 0.00
91_R 167_V 0.79 0.16 0.00
19_V 113_V 0.79 0.16 0.00
36_E 417_T 0.79 0.16 0.00
97_F 331_N 0.79 0.16 0.00
44_D 359_I 0.79 0.16 0.00
14_L 274_L 0.79 0.16 0.00
94_R 22_A 0.79 0.16 0.00
52_V 388_T 0.79 0.16 0.00
15_I 25_L 0.79 0.16 0.00
61_F 294_W 0.79 0.16 0.00
63_S 60_N 0.79 0.16 0.00
19_V 51_P 0.79 0.16 0.00
66_V 403_M 0.78 0.16 0.00
13_D 24_P 0.78 0.16 0.00
50_A 357_F 0.78 0.16 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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