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OPENSEQ.org
1JIW
Genes: A B A+B
Length: 106 470 568
Sequences: 104 159 54
Seq/Len: 0.98 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
50_L 228_G 1.47 0.19 0.00
53_W 8_Q 1.41 0.18 0.00
72_E 236_L 1.40 0.17 0.00
68_I 316_L 1.34 0.16 0.00
60_A 292_L 1.31 0.15 0.00
54_L 388_A 1.27 0.14 0.00
12_A 375_T 1.26 0.14 0.00
32_D 383_E 1.25 0.14 0.00
79_M 120_G 1.25 0.13 0.00
64_T 340_L 1.24 0.13 0.00
54_L 283_V 1.21 0.13 0.00
53_W 51_G 1.20 0.12 0.00
46_D 378_Y 1.17 0.12 0.00
74_G 266_E 1.16 0.11 0.00
53_W 292_L 1.16 0.11 0.00
99_L 139_L 1.15 0.11 0.00
80_L 254_T 1.15 0.11 0.00
1_S 6_Y 1.14 0.11 0.00
32_D 378_Y 1.14 0.11 0.00
28_L 346_A 1.13 0.11 0.00
54_L 275_S 1.13 0.11 0.00
62_R 225_D 1.13 0.11 0.00
45_G 85_F 1.13 0.11 0.00
12_A 271_S 1.12 0.11 0.00
89_Y 18_R 1.11 0.10 0.00
89_Y 164_P 1.11 0.10 0.00
89_Y 212_S 1.11 0.10 0.00
89_Y 237_D 1.11 0.10 0.00
54_L 364_A 1.11 0.10 0.00
8_A 109_I 1.11 0.10 0.00
74_G 421_D 1.11 0.10 0.00
80_L 441_G 1.09 0.10 0.00
59_R 266_E 1.09 0.10 0.00
68_I 265_T 1.08 0.10 0.00
50_L 373_A 1.07 0.10 0.00
62_R 228_G 1.07 0.10 0.00
62_R 254_T 1.07 0.10 0.00
80_L 286_A 1.07 0.10 0.00
66_A 107_T 1.06 0.10 0.00
66_A 392_L 1.06 0.10 0.00
17_L 379_G 1.06 0.10 0.00
70_L 435_D 1.06 0.10 0.00
81_L 46_W 1.06 0.10 0.00
86_E 327_T 1.03 0.09 0.00
73_R 378_Y 1.03 0.09 0.00
9_S 109_I 1.03 0.09 0.00
103_R 115_G 1.03 0.09 0.00
100_V 397_S 1.02 0.09 0.00
12_A 217_W 1.02 0.09 0.00
72_E 87_A 1.02 0.09 0.00
50_L 364_A 1.01 0.09 0.00
99_L 210_A 1.00 0.09 0.00
28_L 328_V 1.00 0.09 0.00
74_G 258_V 0.99 0.08 0.00
99_L 152_Y 0.99 0.08 0.00
62_R 459_L 0.99 0.08 0.00
16_T 433_S 0.99 0.08 0.00
8_A 307_E 0.99 0.08 0.00
78_L 429_Q 0.99 0.08 0.00
39_S 282_S 0.99 0.08 0.00
32_D 27_H 0.98 0.08 0.00
6_L 457_I 0.98 0.08 0.00
96_G 226_F 0.98 0.08 0.00
74_G 233_A 0.98 0.08 0.00
99_L 434_Y 0.98 0.08 0.00
68_I 114_A 0.97 0.08 0.00
71_L 62_L 0.97 0.08 0.00
76_L 104_S 0.97 0.08 0.00
2_S 41_R 0.97 0.08 0.00
2_S 111_F 0.97 0.08 0.00
2_S 192_A 0.97 0.08 0.00
2_S 425_G 0.97 0.08 0.00
66_A 310_L 0.96 0.08 0.00
99_L 128_S 0.96 0.08 0.00
43_L 235_L 0.96 0.08 0.00
53_W 389_P 0.96 0.08 0.00
58_P 19_G 0.95 0.08 0.00
99_L 3_S 0.95 0.08 0.00
26_C 293_D 0.95 0.08 0.00
26_C 296_G 0.95 0.08 0.00
42_D 38_Q 0.95 0.08 0.00
78_L 340_L 0.94 0.08 0.00
7_S 444_A 0.94 0.08 0.00
85_G 194_E 0.94 0.08 0.00
50_L 320_V 0.94 0.08 0.00
12_A 193_G 0.94 0.08 0.00
81_L 468_I 0.93 0.08 0.00
89_Y 95_Q 0.93 0.07 0.00
64_T 62_L 0.93 0.07 0.00
86_E 317_K 0.93 0.07 0.00
60_A 167_G 0.93 0.07 0.00
76_L 385_S 0.92 0.07 0.00
81_L 457_I 0.92 0.07 0.00
79_M 442_S 0.92 0.07 0.00
99_L 297_F 0.92 0.07 0.00
32_D 217_W 0.91 0.07 0.00
96_G 33_D 0.91 0.07 0.00
41_Y 188_G 0.91 0.07 0.00
9_S 33_D 0.91 0.07 0.00
35_V 325_G 0.91 0.07 0.00
101_L 443_L 0.91 0.07 0.00
3_L 293_D 0.90 0.07 0.00
3_L 296_G 0.90 0.07 0.00
101_L 95_Q 0.90 0.07 0.00
96_G 255_G 0.90 0.07 0.00
70_L 245_L 0.90 0.07 0.00
80_L 122_L 0.90 0.07 0.00
8_A 316_L 0.90 0.07 0.00
47_T 254_T 0.90 0.07 0.00
102_R 53_S 0.89 0.07 0.00
78_L 435_D 0.89 0.07 0.00
22_A 30_Y 0.89 0.07 0.00
6_L 235_L 0.89 0.07 0.00
26_C 401_K 0.88 0.07 0.00
12_A 14_H 0.88 0.07 0.00
12_A 357_I 0.88 0.07 0.00
82_G 362_L 0.88 0.07 0.00
23_P 10_D 0.88 0.07 0.00
80_L 408_D 0.88 0.07 0.00
46_D 282_S 0.88 0.07 0.00
64_T 36_A 0.88 0.07 0.00
32_D 127_F 0.88 0.07 0.00
55_P 386_A 0.88 0.07 0.00
63_P 101_Q 0.88 0.07 0.00
12_A 89_S 0.88 0.07 0.00
78_L 128_S 0.88 0.07 0.00
74_G 113_D 0.88 0.07 0.00
6_L 118_D 0.88 0.07 0.00
83_R 126_N 0.87 0.07 0.00
81_L 235_L 0.87 0.07 0.00
3_L 332_I 0.87 0.07 0.00
95_D 206_E 0.87 0.07 0.00
89_Y 364_A 0.87 0.07 0.00
43_L 125_G 0.87 0.07 0.00
62_R 122_L 0.86 0.07 0.00
28_L 34_Q 0.86 0.07 0.00
8_A 31_T 0.86 0.07 0.00
78_L 14_H 0.86 0.07 0.00
43_L 98_L 0.86 0.07 0.00
103_R 14_H 0.86 0.07 0.00
78_L 210_A 0.85 0.07 0.00
32_D 362_L 0.85 0.07 0.00
102_R 407_L 0.85 0.07 0.00
2_S 173_T 0.85 0.07 0.00
90_R 213_V 0.85 0.07 0.00
103_R 28_P 0.85 0.06 0.00
64_T 57_L 0.85 0.06 0.00
25_I 283_V 0.84 0.06 0.00
67_G 108_N 0.84 0.06 0.00
101_L 217_W 0.84 0.06 0.00
51_T 104_S 0.84 0.06 0.00
3_L 401_K 0.84 0.06 0.00
89_Y 388_A 0.84 0.06 0.00
8_A 413_G 0.84 0.06 0.00
54_L 453_A 0.84 0.06 0.00
12_A 195_G 0.84 0.06 0.00
91_V 30_Y 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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