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OPENSEQ.org
SpC-D
Genes: A B A+B
Length: 79 422 415
Sequences: 194 254 218
Seq/Len: 2.46 0.6 0.53
MirrorTree (Pazo et al. 2001) 0.79
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 0.08 0.00 0.40
2 0.08 0.00 0.41
5 0.08 0.01 0.44
10 0.08 0.01 0.44
20 0.08 0.01 0.44
100 0.08 0.02 0.44
∞ 0.09 0.05 0.44
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
49_F 340_T 1.61 0.66 0.00
43_V 359_F 1.37 0.48 0.00
50_D 281_K 1.35 0.46 0.00
3_I 313_V 1.31 0.44 0.00
29_D 344_I 1.25 0.39 0.00
77_Q 121_E 1.25 0.38 0.00
63_W 103_G 1.23 0.37 0.00
69_I 344_I 1.23 0.37 0.00
55_V 168_Y 1.23 0.37 0.00
70_I 262_N 1.18 0.34 0.00
70_I 189_L 1.17 0.33 0.00
50_D 211_E 1.17 0.33 0.00
49_F 337_Y 1.14 0.31 0.00
33_L 352_G 1.14 0.31 0.00
57_E 390_F 1.13 0.30 0.00
48_R 312_K 1.13 0.30 0.00
56_T 275_Q 1.12 0.30 0.00
28_F 132_Q 1.12 0.30 0.00
70_I 148_F 1.11 0.29 0.00
36_M 111_F 1.10 0.28 0.00
64_N 199_D 1.10 0.28 0.00
11_I 53_S 1.10 0.28 0.00
27_L 272_Y 1.09 0.28 0.00
63_W 68_P 1.09 0.28 0.00
17_E 337_Y 1.08 0.27 0.00
41_L 366_P 1.08 0.27 0.00
51_I 256_A 1.07 0.26 0.00
43_V 206_L 1.06 0.26 0.00
45_I 57_R 1.06 0.26 0.00
55_V 77_R 1.06 0.26 0.00
13_E 298_Y 1.06 0.26 0.00
7_V 117_L 1.04 0.25 0.00
69_I 131_P 1.04 0.24 0.00
42_I 66_F 1.03 0.24 0.00
55_V 87_A 1.03 0.24 0.00
43_V 357_A 1.03 0.24 0.00
42_I 243_F 1.02 0.23 0.00
51_I 244_S 1.02 0.23 0.00
9_E 362_D 1.01 0.23 0.00
46_E 177_F 1.01 0.23 0.00
6_E 259_N 1.01 0.23 0.00
53_V 109_Q 1.00 0.22 0.00
49_F 341_V 1.00 0.22 0.00
5_S 56_V 1.00 0.22 0.00
73_I 67_V 1.00 0.22 0.00
49_F 101_Q 1.00 0.22 0.00
19_V 340_T 0.99 0.22 0.00
50_D 335_D 0.99 0.22 0.00
56_T 315_P 0.99 0.22 0.00
56_T 370_K 0.99 0.22 0.00
63_W 98_L 0.98 0.21 0.00
10_I 209_F 0.98 0.21 0.00
63_W 317_F 0.98 0.21 0.00
54_P 301_L 0.97 0.21 0.00
26_D 383_F 0.96 0.20 0.00
14_L 250_D 0.96 0.20 0.00
44_E 56_V 0.96 0.20 0.00
50_D 225_Y 0.96 0.20 0.00
61_D 393_N 0.95 0.20 0.00
26_D 199_D 0.95 0.20 0.00
29_D 209_F 0.95 0.20 0.00
37_G 209_F 0.94 0.20 0.00
11_I 210_N 0.94 0.20 0.00
69_I 301_L 0.94 0.19 0.00
39_V 369_M 0.94 0.19 0.00
55_V 144_F 0.93 0.19 0.00
63_W 173_L 0.92 0.18 0.00
7_V 289_S 0.92 0.18 0.00
15_F 94_Y 0.92 0.18 0.00
36_M 114_Q 0.92 0.18 0.00
29_D 279_D 0.92 0.18 0.00
40_E 337_Y 0.92 0.18 0.00
26_D 238_I 0.91 0.18 0.00
73_I 57_R 0.91 0.18 0.00
30_A 360_S 0.91 0.18 0.00
42_I 75_W 0.91 0.18 0.00
54_P 77_R 0.90 0.18 0.00
29_D 63_N 0.90 0.18 0.00
9_E 289_S 0.90 0.17 0.00
67_N 338_Q 0.90 0.17 0.00
61_D 277_K 0.90 0.17 0.00
27_L 124_Q 0.90 0.17 0.00
30_A 195_L 0.90 0.17 0.00
67_N 298_Y 0.89 0.17 0.00
11_I 101_Q 0.89 0.17 0.00
63_W 308_F 0.89 0.17 0.00
70_I 86_L 0.89 0.17 0.00
5_S 298_Y 0.89 0.17 0.00
14_L 293_L 0.89 0.17 0.00
53_V 182_M 0.89 0.17 0.00
76_L 96_P 0.89 0.17 0.00
58_F 77_R 0.89 0.17 0.00
77_Q 273_N 0.88 0.17 0.00
56_T 126_V 0.88 0.17 0.00
51_I 79_D 0.88 0.17 0.00
66_A 149_N 0.88 0.17 0.00
67_N 62_P 0.88 0.17 0.00
7_V 328_D 0.88 0.17 0.00
61_D 261_S 0.88 0.16 0.00
23_M 313_V 0.88 0.16 0.00
43_V 204_E 0.88 0.16 0.00
49_F 306_T 0.87 0.16 0.00
62_D 205_L 0.87 0.16 0.00
31_G 377_W 0.87 0.16 0.00
36_M 146_Q 0.87 0.16 0.00
46_E 212_R 0.86 0.16 0.00
14_L 169_A 0.86 0.16 0.00
46_E 230_K 0.86 0.16 0.00
37_G 289_S 0.86 0.16 0.00
49_F 146_Q 0.86 0.16 0.00
26_D 105_A 0.86 0.16 0.00
3_I 253_K 0.86 0.16 0.00
11_I 255_D 0.86 0.15 0.00
10_I 148_F 0.86 0.15 0.00
9_E 236_L 0.86 0.15 0.00
43_V 150_G 0.85 0.15 0.00
42_I 105_A 0.85 0.15 0.00
66_A 53_S 0.85 0.15 0.00
50_D 55_K 0.85 0.15 0.00
24_D 310_K 0.85 0.15 0.00
53_V 360_S 0.85 0.15 0.00
29_D 392_S 0.85 0.15 0.00
29_D 178_P 0.85 0.15 0.00
46_E 146_Q 0.85 0.15 0.00
36_M 308_F 0.85 0.15 0.00
22_M 86_L 0.84 0.15 0.00
73_I 168_Y 0.84 0.15 0.00
28_F 103_G 0.84 0.15 0.00
29_D 232_V 0.84 0.15 0.00
26_D 302_Q 0.84 0.15 0.00
41_L 277_K 0.84 0.15 0.00
37_G 391_L 0.84 0.15 0.00
33_L 317_F 0.84 0.15 0.00
30_A 141_P 0.84 0.15 0.00
17_E 169_A 0.84 0.15 0.00
63_W 97_Y 0.83 0.15 0.00
4_K 129_I 0.83 0.15 0.00
42_I 383_F 0.83 0.14 0.00
57_E 106_S 0.83 0.14 0.00
51_I 171_T 0.83 0.14 0.00
16_M 69_F 0.83 0.14 0.00
44_E 251_V 0.83 0.14 0.00
42_I 124_Q 0.82 0.14 0.00
64_N 93_S 0.82 0.14 0.00
6_E 364_G 0.82 0.14 0.00
56_T 213_Q 0.82 0.14 0.00
31_G 77_R 0.82 0.14 0.00
65_T 267_M 0.82 0.14 0.00
71_A 335_D 0.82 0.14 0.00
15_F 75_W 0.82 0.14 0.00
66_A 127_Y 0.82 0.14 0.00
37_G 75_W 0.82 0.14 0.00
28_F 60_S 0.82 0.14 0.00
41_L 274_E 0.82 0.14 0.00
50_D 140_D 0.82 0.14 0.00
3_I 324_K 0.82 0.14 0.00
44_E 338_Q 0.81 0.14 0.00
40_E 76_L 0.81 0.14 0.00
38_T 77_R 0.81 0.14 0.00
54_P 373_I 0.81 0.14 0.00
51_I 314_N 0.81 0.14 0.00
46_E 225_Y 0.81 0.14 0.00
54_P 239_L 0.81 0.14 0.00
74_V 191_S 0.81 0.14 0.00
13_E 308_F 0.80 0.13 0.00
43_V 151_D 0.80 0.13 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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