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OPENSEQ.org
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Genes: A B A+B
Length: 62 519 562
Sequences: 50 141 56
Seq/Len: 0.81 0.27 0.1
MirrorTree (Pazo et al. 2001) 0.92
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 0.09
2 0.00 0.00 0.09
5 0.00 0.00 0.10
10 0.00 0.00 0.10
20 0.00 0.00 0.10
100 0.00 0.00 0.10
∞ 0.00 0.00 0.09
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
58_F 468_V 1.39 0.17 0.00
30_S 91_L 1.34 0.16 0.00
60_Q 250_L 1.32 0.15 0.00
41_Q 81_M 1.26 0.14 0.00
20_N 444_P 1.24 0.13 0.00
19_Q 279_I 1.23 0.13 0.00
49_L 39_A 1.23 0.13 0.00
22_I 429_F 1.18 0.12 0.00
19_Q 221_E 1.15 0.11 0.00
31_L 28_N 1.13 0.11 0.00
6_P 122_R 1.13 0.11 0.00
46_A 459_E 1.12 0.11 0.00
44_Q 355_Q 1.10 0.10 0.00
37_A 441_H 1.08 0.10 0.00
40_S 253_E 1.07 0.10 0.00
29_F 325_S 1.07 0.10 0.00
34_I 418_I 1.06 0.10 0.00
43_E 434_D 1.06 0.10 0.00
58_F 273_E 1.06 0.10 0.00
40_S 399_R 1.06 0.10 0.00
28_A 382_P 1.06 0.10 0.00
46_A 98_S 1.05 0.09 0.00
6_P 349_T 1.05 0.09 0.00
44_Q 182_A 1.04 0.09 0.00
61_Q 190_V 1.04 0.09 0.00
29_F 393_R 1.04 0.09 0.00
47_A 409_P 1.04 0.09 0.00
19_Q 218_R 1.03 0.09 0.00
22_I 415_I 1.02 0.09 0.00
37_A 183_F 1.02 0.09 0.00
45_L 357_L 1.02 0.09 0.00
34_I 118_I 1.01 0.09 0.00
49_L 56_S 1.01 0.09 0.00
27_Q 43_I 1.00 0.09 0.00
40_S 137_N 1.00 0.09 0.00
51_R 235_P 1.00 0.09 0.00
23_V 127_L 0.99 0.08 0.00
42_R 400_V 0.99 0.08 0.00
24_A 107_I 0.99 0.08 0.00
41_Q 343_V 0.99 0.08 0.00
11_D 349_T 0.99 0.08 0.00
58_F 416_M 0.99 0.08 0.00
59_A 289_A 0.98 0.08 0.00
44_Q 358_K 0.98 0.08 0.00
27_Q 511_L 0.98 0.08 0.00
33_D 511_L 0.97 0.08 0.00
27_Q 274_P 0.97 0.08 0.00
58_F 467_L 0.97 0.08 0.00
11_D 161_Y 0.97 0.08 0.00
24_A 376_M 0.96 0.08 0.00
13_A 48_E 0.96 0.08 0.00
56_A 142_L 0.96 0.08 0.00
14_I 222_K 0.96 0.08 0.00
9_L 374_N 0.96 0.08 0.00
28_A 422_R 0.94 0.08 0.00
4_N 386_K 0.94 0.08 0.00
59_A 495_E 0.94 0.08 0.00
27_Q 500_H 0.93 0.08 0.00
20_N 365_W 0.93 0.07 0.00
34_I 509_R 0.93 0.07 0.00
56_A 268_Q 0.93 0.07 0.00
22_I 186_N 0.93 0.07 0.00
34_I 117_N 0.92 0.07 0.00
40_S 494_A 0.92 0.07 0.00
60_Q 473_L 0.92 0.07 0.00
6_P 161_Y 0.92 0.07 0.00
44_Q 421_N 0.92 0.07 0.00
61_Q 211_E 0.92 0.07 0.00
27_Q 187_E 0.91 0.07 0.00
20_N 65_F 0.91 0.07 0.00
56_A 517_R 0.91 0.07 0.00
42_R 355_Q 0.91 0.07 0.00
59_A 259_A 0.91 0.07 0.00
60_Q 469_Q 0.90 0.07 0.00
7_D 379_P 0.90 0.07 0.00
43_E 341_R 0.90 0.07 0.00
31_L 503_R 0.89 0.07 0.00
50_K 68_D 0.89 0.07 0.00
5_E 87_G 0.89 0.07 0.00
24_A 342_Y 0.89 0.07 0.00
37_A 42_T 0.89 0.07 0.00
20_N 251_F 0.88 0.07 0.00
6_P 345_E 0.88 0.07 0.00
32_P 452_S 0.88 0.07 0.00
2_N 412_T 0.88 0.07 0.00
20_N 180_D 0.88 0.07 0.00
20_N 410_N 0.88 0.07 0.00
9_L 206_T 0.88 0.07 0.00
28_A 284_R 0.88 0.07 0.00
45_L 390_V 0.88 0.07 0.00
10_P 83_N 0.88 0.07 0.00
41_Q 155_S 0.87 0.07 0.00
20_N 81_M 0.87 0.07 0.00
26_K 52_V 0.87 0.07 0.00
58_F 243_L 0.87 0.07 0.00
6_P 447_T 0.87 0.07 0.00
58_F 340_S 0.87 0.07 0.00
41_Q 196_L 0.86 0.07 0.00
14_I 440_N 0.86 0.07 0.00
28_A 64_I 0.86 0.07 0.00
60_Q 269_N 0.86 0.07 0.00
32_P 397_G 0.86 0.07 0.00
16_Y 481_P 0.86 0.07 0.00
17_I 509_R 0.85 0.07 0.00
51_R 286_R 0.85 0.07 0.00
51_R 301_L 0.85 0.07 0.00
10_P 85_E 0.85 0.07 0.00
9_L 215_I 0.85 0.07 0.00
50_K 449_D 0.85 0.07 0.00
48_A 408_R 0.85 0.07 0.00
30_S 428_S 0.85 0.07 0.00
49_L 29_V 0.85 0.06 0.00
26_K 169_S 0.85 0.06 0.00
27_Q 454_R 0.85 0.06 0.00
24_A 98_S 0.84 0.06 0.00
14_I 515_V 0.84 0.06 0.00
24_A 477_Q 0.84 0.06 0.00
28_A 383_A 0.84 0.06 0.00
33_D 209_Q 0.84 0.06 0.00
2_N 84_H 0.84 0.06 0.00
20_N 303_A 0.84 0.06 0.00
14_I 163_S 0.84 0.06 0.00
6_P 278_S 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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