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OPENSEQ.org
Thays
Genes: A B A+B
Length: 91 681 672
Sequences: 94 3168 76
Seq/Len: 1.03 4.65 0.11
MirrorTree (Pazo et al. 2001) 0.01
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 0.01 0.09
2 0.00 0.02 0.10
5 0.00 0.02 0.10
10 0.00 0.02 0.10
20 0.00 0.02 0.10
100 0.00 0.02 0.10
∞ 0.00 0.07 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
14_A 552_L 1.45 0.20 0.00
70_A 329_E 1.34 0.17 0.00
28_W 641_R 1.29 0.15 0.00
33_V 283_L 1.29 0.15 0.00
18_A 676_L 1.25 0.14 0.00
27_M 388_W 1.24 0.14 0.00
15_V 105_N 1.22 0.13 0.00
20_S 283_L 1.21 0.13 0.00
28_W 367_L 1.20 0.13 0.00
18_A 405_G 1.17 0.12 0.00
33_V 623_F 1.16 0.12 0.00
42_G 568_G 1.14 0.12 0.00
82_N 213_L 1.13 0.11 0.00
27_M 258_G 1.13 0.11 0.00
77_V 536_M 1.13 0.11 0.00
45_D 232_A 1.12 0.11 0.00
78_Q 283_L 1.12 0.11 0.00
45_D 112_Y 1.12 0.11 0.00
9_R 410_D 1.11 0.11 0.00
45_D 212_W 1.11 0.11 0.00
51_G 388_W 1.10 0.11 0.00
15_V 279_N 1.09 0.11 0.00
33_V 212_W 1.08 0.10 0.00
40_A 625_R 1.08 0.10 0.00
54_I 212_W 1.05 0.10 0.00
78_Q 96_S 1.05 0.10 0.00
63_N 96_S 1.05 0.10 0.00
42_G 78_V 1.04 0.10 0.00
43_Y 314_D 1.04 0.10 0.00
27_M 226_T 1.04 0.10 0.00
21_E 362_K 1.04 0.10 0.00
64_Q 578_I 1.03 0.10 0.00
20_S 314_D 1.03 0.10 0.00
24_K 239_A 1.03 0.10 0.00
20_S 536_M 1.03 0.10 0.00
20_S 669_A 1.02 0.09 0.00
45_D 433_A 1.02 0.09 0.00
67_P 595_N 1.02 0.09 0.00
32_G 669_A 1.01 0.09 0.00
24_K 514_G 1.01 0.09 0.00
53_S 388_W 1.01 0.09 0.00
40_A 157_V 1.00 0.09 0.00
43_Y 129_K 1.00 0.09 0.00
81_P 178_A 0.99 0.09 0.00
24_K 101_E 0.99 0.09 0.00
42_G 537_L 0.98 0.09 0.00
47_L 367_L 0.98 0.09 0.00
15_V 282_E 0.98 0.09 0.00
60_T 240_A 0.97 0.09 0.00
25_I 149_D 0.97 0.09 0.00
15_V 362_K 0.97 0.09 0.00
42_G 279_N 0.97 0.08 0.00
79_F 643_A 0.97 0.08 0.00
43_Y 394_L 0.96 0.08 0.00
6_T 519_S 0.96 0.08 0.00
20_S 112_Y 0.96 0.08 0.00
68_K 622_A 0.96 0.08 0.00
8_K 323_A 0.96 0.08 0.00
45_D 588_P 0.95 0.08 0.00
45_D 283_L 0.94 0.08 0.00
77_V 166_S 0.94 0.08 0.00
24_K 362_K 0.94 0.08 0.00
88_K 649_G 0.94 0.08 0.00
69_P 529_P 0.94 0.08 0.00
77_V 285_L 0.93 0.08 0.00
33_V 228_A 0.93 0.08 0.00
37_E 375_Y 0.93 0.08 0.00
24_K 171_Q 0.92 0.08 0.00
40_A 508_W 0.92 0.08 0.00
53_S 405_G 0.92 0.08 0.00
83_P 283_L 0.92 0.08 0.00
44_A 490_I 0.91 0.08 0.00
25_I 177_Q 0.91 0.08 0.00
8_K 237_V 0.91 0.08 0.00
45_D 375_Y 0.91 0.08 0.00
47_L 332_S 0.91 0.07 0.00
42_G 353_A 0.91 0.07 0.00
74_V 331_Q 0.91 0.07 0.00
82_N 132_L 0.90 0.07 0.00
58_L 510_W 0.90 0.07 0.00
40_A 269_Q 0.90 0.07 0.00
9_R 265_L 0.90 0.07 0.00
14_A 321_Y 0.90 0.07 0.00
31_D 228_A 0.89 0.07 0.00
74_V 294_D 0.89 0.07 0.00
54_I 560_E 0.89 0.07 0.00
4_A 633_N 0.89 0.07 0.00
85_L 172_L 0.89 0.07 0.00
32_G 644_I 0.89 0.07 0.00
43_Y 152_K 0.89 0.07 0.00
27_M 508_W 0.88 0.07 0.00
28_W 651_R 0.88 0.07 0.00
69_P 330_L 0.88 0.07 0.00
74_V 372_E 0.88 0.07 0.00
79_F 619_S 0.87 0.07 0.00
15_V 112_Y 0.87 0.07 0.00
20_S 646_A 0.87 0.07 0.00
63_N 132_L 0.86 0.07 0.00
78_Q 107_A 0.86 0.07 0.00
81_P 385_F 0.86 0.07 0.00
42_G 508_W 0.86 0.07 0.00
22_Q 413_A 0.85 0.07 0.00
68_K 399_E 0.85 0.07 0.00
79_F 310_F 0.85 0.07 0.00
18_A 560_E 0.85 0.07 0.00
69_P 606_A 0.85 0.07 0.00
58_L 531_D 0.85 0.07 0.00
45_D 213_L 0.85 0.07 0.00
18_A 73_S 0.85 0.07 0.00
24_K 658_V 0.85 0.07 0.00
47_L 148_A 0.84 0.07 0.00
81_P 512_P 0.84 0.07 0.00
9_R 476_H 0.84 0.07 0.00
63_N 354_L 0.84 0.07 0.00
43_Y 411_L 0.84 0.07 0.00
76_S 279_N 0.84 0.07 0.00
79_F 132_L 0.84 0.07 0.00
26_Q 443_Y 0.83 0.07 0.00
44_A 442_A 0.83 0.07 0.00
78_Q 643_A 0.83 0.07 0.00
20_S 546_M 0.83 0.07 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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