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OPENSEQ.org
101
Genes: A B A+B
Length: 99 470 561
Sequences: 105 159 54
Seq/Len: 1.06 0.34 0.1
MirrorTree (Pazo et al. 2001) 0.67
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 0.03 0.07 0.09
2 0.03 0.07 0.09
5 0.03 0.07 0.09
10 0.03 0.07 0.09
20 0.03 0.07 0.09
100 0.06 0.09 0.10
∞ 0.08 0.17 0.10
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
5_A 375_T 1.46 0.19 0.00
1_A 307_E 1.42 0.18 0.00
43_L 228_G 1.40 0.17 0.00
47_L 388_A 1.38 0.17 0.00
61_I 316_L 1.32 0.15 0.00
46_W 8_Q 1.32 0.15 0.00
73_L 254_T 1.31 0.15 0.00
61_I 265_T 1.30 0.14 0.00
25_D 383_E 1.29 0.14 0.00
67_G 266_E 1.25 0.14 0.00
57_T 340_L 1.24 0.13 0.00
53_A 292_L 1.22 0.13 0.00
67_G 421_D 1.22 0.13 0.00
72_M 120_G 1.21 0.12 0.00
47_L 364_A 1.18 0.12 0.00
93_V 397_S 1.18 0.12 0.00
65_E 236_L 1.18 0.12 0.00
21_L 346_A 1.17 0.12 0.00
92_L 139_L 1.15 0.11 0.00
46_W 292_L 1.14 0.11 0.00
25_D 378_Y 1.13 0.11 0.00
5_A 271_S 1.13 0.11 0.00
55_R 225_D 1.13 0.11 0.00
55_R 254_T 1.12 0.11 0.00
43_L 373_A 1.12 0.11 0.00
82_Y 164_P 1.12 0.11 0.00
82_Y 212_S 1.12 0.11 0.00
82_Y 237_D 1.12 0.11 0.00
73_L 441_G 1.11 0.10 0.00
10_L 379_G 1.10 0.10 0.00
65_E 87_A 1.09 0.10 0.00
46_W 51_G 1.09 0.10 0.00
47_L 283_V 1.09 0.10 0.00
55_R 228_G 1.08 0.10 0.00
92_L 152_Y 1.08 0.10 0.00
59_A 107_T 1.07 0.10 0.00
59_A 392_L 1.07 0.10 0.00
73_L 286_A 1.07 0.10 0.00
2_S 109_I 1.06 0.10 0.00
71_L 340_L 1.05 0.10 0.00
66_R 378_Y 1.05 0.09 0.00
9_T 433_S 1.05 0.09 0.00
71_L 429_Q 1.03 0.09 0.00
69_L 104_S 1.02 0.09 0.00
5_A 217_W 1.02 0.09 0.00
82_Y 18_R 1.01 0.09 0.00
55_R 459_L 1.00 0.09 0.00
94_L 443_L 1.00 0.09 0.00
21_L 328_V 1.00 0.09 0.00
79_E 327_T 0.99 0.08 0.00
38_G 85_F 0.98 0.08 0.00
63_L 435_D 0.98 0.08 0.00
43_L 364_A 0.98 0.08 0.00
73_L 108_N 0.98 0.08 0.00
40_T 254_T 0.98 0.08 0.00
27_E 424_A 0.98 0.08 0.00
5_A 193_G 0.97 0.08 0.00
89_G 226_F 0.97 0.08 0.00
67_G 258_V 0.97 0.08 0.00
59_A 310_L 0.97 0.08 0.00
19_C 293_D 0.96 0.08 0.00
19_C 296_G 0.96 0.08 0.00
74_L 457_I 0.96 0.08 0.00
92_L 210_A 0.96 0.08 0.00
43_L 320_V 0.95 0.08 0.00
39_D 378_Y 0.95 0.08 0.00
63_L 245_L 0.95 0.08 0.00
5_A 14_H 0.95 0.08 0.00
92_L 434_Y 0.94 0.08 0.00
71_L 128_S 0.94 0.08 0.00
67_G 97_K 0.94 0.08 0.00
92_L 128_S 0.94 0.08 0.00
74_L 235_L 0.93 0.08 0.00
46_W 389_P 0.93 0.07 0.00
25_D 27_H 0.93 0.07 0.00
22_E 433_S 0.92 0.07 0.00
93_V 181_T 0.92 0.07 0.00
69_L 424_A 0.92 0.07 0.00
82_Y 388_A 0.92 0.07 0.00
44_T 104_S 0.92 0.07 0.00
63_L 332_I 0.92 0.07 0.00
80_G 38_Q 0.92 0.07 0.00
56_P 101_Q 0.91 0.07 0.00
7_Q 327_T 0.91 0.07 0.00
92_L 297_F 0.91 0.07 0.00
95_R 53_S 0.91 0.07 0.00
69_L 142_V 0.91 0.07 0.00
5_A 383_E 0.91 0.07 0.00
36_L 235_L 0.91 0.07 0.00
82_Y 364_A 0.90 0.07 0.00
12_Q 359_Y 0.90 0.07 0.00
73_L 122_L 0.90 0.07 0.00
19_C 401_K 0.90 0.07 0.00
25_D 127_F 0.90 0.07 0.00
73_L 408_D 0.90 0.07 0.00
83_R 213_V 0.90 0.07 0.00
74_L 46_W 0.90 0.07 0.00
76_R 29_S 0.90 0.07 0.00
69_L 110_H 0.89 0.07 0.00
3_D 226_F 0.89 0.07 0.00
69_L 385_S 0.89 0.07 0.00
48_P 59_Y 0.89 0.07 0.00
25_D 217_W 0.89 0.07 0.00
34_Y 188_G 0.89 0.07 0.00
80_G 277_S 0.89 0.07 0.00
48_P 393_R 0.89 0.07 0.00
67_G 233_A 0.88 0.07 0.00
1_A 109_I 0.88 0.07 0.00
91_Q 36_A 0.88 0.07 0.00
28_V 325_G 0.88 0.07 0.00
75_G 362_L 0.87 0.07 0.00
72_M 442_S 0.87 0.07 0.00
57_T 62_L 0.87 0.07 0.00
43_L 344_D 0.87 0.07 0.00
51_P 240_A 0.87 0.07 0.00
75_G 383_E 0.87 0.07 0.00
52_R 266_E 0.87 0.07 0.00
85_Q 251_T 0.87 0.07 0.00
73_L 339_L 0.87 0.07 0.00
55_R 122_L 0.86 0.07 0.00
94_L 217_W 0.86 0.07 0.00
5_A 195_G 0.86 0.07 0.00
39_D 282_S 0.86 0.07 0.00
43_L 223_G 0.86 0.07 0.00
46_W 452_H 0.85 0.07 0.00
88_D 404_L 0.85 0.07 0.00
39_D 272_A 0.85 0.07 0.00
73_L 459_L 0.85 0.07 0.00
61_I 100_L 0.85 0.07 0.00
32_S 282_S 0.85 0.07 0.00
5_A 89_S 0.84 0.06 0.00
7_Q 138_F 0.84 0.06 0.00
71_L 14_H 0.84 0.06 0.00
60_G 108_N 0.84 0.06 0.00
4_L 303_I 0.84 0.06 0.00
2_S 272_A 0.84 0.06 0.00
82_Y 95_Q 0.84 0.06 0.00
67_G 114_A 0.84 0.06 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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