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OPENSEQ.org
YARR_AD
Genes: A B A+B
Length: 128 466 500
Sequences: 3274 2022 1093
Seq/Len: 25.58 4.34 2.19
MirrorTree (Pazo et al. 2001) 0.81
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 0.04 0.07 0.06
2 0.04 0.07 0.48
5 0.04 0.07 1.78
10 0.04 0.07 1.81
20 0.04 0.08 1.84
100 0.05 0.08 1.92
∞ 0.06 0.14 2.03
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
64_L 390_K 1.50 0.92 0.52
38_F 448_P 1.02 0.58 0.15
38_F 90_Q 0.99 0.54 0.14
40_C 85_I 0.99 0.54 0.14
107_N 345_R 0.98 0.53 0.13
18_L 321_V 0.92 0.45 0.10
56_F 452_A 0.91 0.44 0.10
110_A 132_Y 0.90 0.44 0.10
21_V 302_P 0.89 0.42 0.09
71_S 441_I 0.88 0.42 0.09
70_I 166_V 0.87 0.41 0.09
88_F 440_H 0.87 0.41 0.09
97_I 239_L 0.87 0.40 0.09
68_L 209_E 0.87 0.40 0.08
110_A 331_D 0.87 0.40 0.08
38_F 143_D 0.86 0.39 0.08
52_F 336_R 0.86 0.39 0.08
65_P 354_M 0.84 0.38 0.08
112_K 318_D 0.84 0.38 0.08
19_L 108_E 0.84 0.37 0.07
57_I 455_G 0.84 0.37 0.07
13_I 447_L 0.84 0.37 0.07
9_I 275_T 0.83 0.36 0.07
4_F 194_A 0.82 0.35 0.07
10_L 183_V 0.82 0.35 0.07
90_I 292_S 0.82 0.35 0.07
46_N 350_C 0.82 0.34 0.07
50_L 109_I 0.81 0.34 0.07
101_G 102_L 0.81 0.34 0.07
16_F 415_V 0.81 0.34 0.07
71_S 197_V 0.81 0.34 0.07
57_I 189_S 0.81 0.34 0.07
57_I 87_F 0.81 0.34 0.07
37_A 342_Q 0.80 0.33 0.06
31_Y 337_M 0.80 0.33 0.06
8_I 282_T 0.80 0.32 0.06
62_L 335_I 0.79 0.32 0.06
57_I 321_V 0.79 0.32 0.06
40_C 175_T 0.79 0.32 0.06
9_I 335_I 0.79 0.32 0.06
92_L 278_I 0.79 0.31 0.06
57_I 466_R 0.77 0.30 0.06
48_T 87_F 0.77 0.30 0.06
38_F 451_V 0.77 0.30 0.06
89_T 451_V 0.77 0.30 0.06
13_I 105_S 0.77 0.29 0.05
22_N 242_G 0.77 0.29 0.05
65_P 136_L 0.76 0.29 0.05
64_L 164_V 0.76 0.28 0.05
112_K 155_S 0.75 0.28 0.05
46_N 260_E 0.75 0.28 0.05
8_I 455_G 0.75 0.28 0.05
36_G 451_V 0.75 0.28 0.05
36_G 85_I 0.75 0.28 0.05
88_F 431_G 0.75 0.28 0.05
87_G 162_L 0.74 0.27 0.05
6_I 321_V 0.74 0.27 0.05
9_I 307_K 0.74 0.27 0.05
71_S 150_N 0.73 0.27 0.05
90_I 204_L 0.73 0.26 0.05
84_S 83_F 0.73 0.26 0.05
74_L 455_G 0.73 0.26 0.05
38_F 94_A 0.72 0.26 0.04
70_I 153_V 0.72 0.26 0.04
36_G 426_K 0.72 0.25 0.04
86_Y 320_D 0.72 0.25 0.04
40_C 277_N 0.72 0.25 0.04
109_N 143_D 0.72 0.25 0.04
77_V 395_P 0.72 0.25 0.04
19_L 173_I 0.72 0.25 0.04
64_L 347_I 0.71 0.25 0.04
93_L 225_L 0.71 0.24 0.04
107_N 301_I 0.71 0.24 0.04
11_I 444_G 0.71 0.24 0.04
87_G 216_F 0.70 0.24 0.04
114_N 323_V 0.70 0.24 0.04
80_I 130_K 0.70 0.24 0.04
100_I 116_V 0.70 0.24 0.04
56_F 160_K 0.70 0.24 0.04
62_L 209_E 0.70 0.24 0.04
13_I 206_G 0.70 0.24 0.04
34_K 134_Q 0.70 0.23 0.04
110_A 149_T 0.70 0.23 0.04
51_A 153_V 0.69 0.23 0.04
25_L 333_Y 0.69 0.23 0.04
40_C 198_G 0.69 0.23 0.04
43_T 351_C 0.69 0.23 0.04
47_Q 447_L 0.69 0.23 0.04
27_V 318_D 0.68 0.22 0.04
61_I 185_N 0.68 0.22 0.04
96_L 163_N 0.68 0.22 0.04
111_L 397_G 0.68 0.22 0.04
89_T 307_K 0.68 0.22 0.04
40_C 83_F 0.68 0.22 0.04
14_V 352_N 0.68 0.22 0.04
4_F 114_P 0.68 0.22 0.04
83_V 188_M 0.68 0.22 0.04
59_V 461_F 0.68 0.22 0.04
12_P 320_D 0.67 0.21 0.04
96_L 165_E 0.67 0.21 0.04
37_A 345_R 0.67 0.21 0.03
9_I 355_P 0.67 0.21 0.03
38_F 265_L 0.67 0.21 0.03
21_V 193_H 0.66 0.21 0.03
105_E 276_V 0.66 0.21 0.03
91_V 231_R 0.66 0.21 0.03
10_L 245_D 0.66 0.21 0.03
67_D 160_K 0.66 0.20 0.03
96_L 166_V 0.66 0.20 0.03
52_F 134_Q 0.66 0.20 0.03
52_F 235_V 0.66 0.20 0.03
11_I 351_C 0.66 0.20 0.03
93_L 318_D 0.66 0.20 0.03
71_S 138_Y 0.66 0.20 0.03
73_L 374_M 0.65 0.20 0.03
102_F 464_V 0.65 0.20 0.03
84_S 109_I 0.65 0.20 0.03
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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