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OPENSEQ.org
2804
Genes: A B A+B
Length: 94 290 364
Sequences: 11035 558 73
Seq/Len: 117.39 1.92 0.2
MirrorTree (Pazo et al. 2001) 0.82
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.03 0.00 0.19
2 0.03 0.00 0.20
5 0.05 0.01 0.22
10 0.06 0.01 0.23
20 0.07 0.01 0.24
100 0.11 0.02 0.38
∞ 0.17 0.05 0.86
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
63_F 204_M 1.62 0.39 0.00
20_A 101_V 1.55 0.35 0.00
62_T 141_D 1.53 0.34 0.00
93_E 184_I 1.48 0.31 0.00
52_E 181_Y 1.47 0.30 0.00
69_S 228_A 1.32 0.23 0.00
84_P 170_Q 1.28 0.22 0.00
66_I 88_D 1.23 0.20 0.00
74_M 149_Q 1.21 0.19 0.00
19_L 54_S 1.21 0.19 0.00
66_I 64_L 1.20 0.18 0.00
54_N 148_F 1.20 0.18 0.00
66_I 143_Y 1.20 0.18 0.00
83_S 167_V 1.19 0.18 0.00
43_I 229_K 1.19 0.18 0.00
66_I 245_F 1.19 0.18 0.00
85_E 6_T 1.18 0.18 0.00
27_R 161_H 1.15 0.17 0.00
27_R 164_N 1.15 0.17 0.00
27_R 179_P 1.15 0.17 0.00
27_R 182_D 1.15 0.17 0.00
67_L 75_I 1.14 0.17 0.00
66_I 150_V 1.11 0.16 0.00
74_M 80_H 1.09 0.15 0.00
83_S 258_T 1.08 0.14 0.00
18_Q 158_T 1.07 0.14 0.00
49_S 165_F 1.07 0.14 0.00
81_N 230_V 1.06 0.14 0.00
33_T 169_I 1.06 0.14 0.00
72_L 141_D 1.05 0.14 0.00
83_S 257_K 1.05 0.14 0.00
43_I 271_A 1.04 0.14 0.00
37_L 82_K 1.03 0.13 0.00
20_A 223_H 1.03 0.13 0.00
43_I 225_L 1.03 0.13 0.00
48_I 165_F 1.03 0.13 0.00
64_F 39_R 1.03 0.13 0.00
24_K 166_S 1.02 0.13 0.00
41_I 25_T 1.02 0.13 0.00
52_E 165_F 1.02 0.13 0.00
27_R 159_D 1.02 0.13 0.00
27_R 163_K 1.02 0.13 0.00
93_E 167_V 1.01 0.13 0.00
40_K 84_R 1.00 0.12 0.00
36_E 156_G 0.99 0.12 0.00
82_A 262_T 0.99 0.12 0.00
18_Q 202_L 0.98 0.12 0.00
23_M 261_P 0.98 0.12 0.00
81_N 183_I 0.97 0.12 0.00
59_S 101_V 0.97 0.12 0.00
78_D 172_G 0.97 0.12 0.00
23_M 47_L 0.97 0.12 0.00
33_T 23_A 0.96 0.11 0.00
76_L 268_V 0.96 0.11 0.00
19_L 219_I 0.95 0.11 0.00
79_A 97_S 0.95 0.11 0.00
70_L 159_D 0.95 0.11 0.00
70_L 163_K 0.95 0.11 0.00
49_S 88_D 0.94 0.11 0.00
62_T 224_F 0.94 0.11 0.00
55_P 260_L 0.94 0.11 0.00
38_A 111_T 0.94 0.11 0.00
48_I 158_T 0.94 0.11 0.00
73_S 27_K 0.94 0.11 0.00
60_L 108_E 0.94 0.11 0.00
27_R 181_Y 0.94 0.11 0.00
13_I 229_K 0.94 0.11 0.00
37_L 13_V 0.93 0.11 0.00
42_G 36_R 0.93 0.11 0.00
24_K 107_D 0.93 0.11 0.00
34_Q 150_V 0.93 0.11 0.00
42_G 219_I 0.92 0.10 0.00
91_D 274_T 0.92 0.10 0.00
37_L 235_E 0.92 0.10 0.00
23_M 270_T 0.92 0.10 0.00
66_I 267_N 0.92 0.10 0.00
74_M 223_H 0.91 0.10 0.00
37_L 120_L 0.91 0.10 0.00
43_I 213_K 0.91 0.10 0.00
49_S 69_P 0.91 0.10 0.00
51_F 183_I 0.90 0.10 0.00
93_E 196_H 0.90 0.10 0.00
23_M 92_E 0.90 0.10 0.00
74_M 55_D 0.90 0.10 0.00
92_L 280_H 0.90 0.10 0.00
37_L 280_H 0.89 0.10 0.00
54_N 280_H 0.89 0.10 0.00
74_M 15_E 0.89 0.10 0.00
45_Q 216_I 0.89 0.10 0.00
78_D 92_E 0.89 0.10 0.00
18_Q 241_I 0.89 0.10 0.00
54_N 214_T 0.89 0.10 0.00
20_A 155_I 0.89 0.10 0.00
71_E 177_L 0.88 0.10 0.00
92_L 195_I 0.88 0.09 0.00
52_E 228_A 0.88 0.09 0.00
65_K 145_F 0.88 0.09 0.00
91_D 278_R 0.88 0.09 0.00
90_Q 281_G 0.87 0.09 0.00
90_Q 278_R 0.87 0.09 0.00
49_S 104_I 0.87 0.09 0.00
76_L 68_S 0.87 0.09 0.00
75_T 195_I 0.87 0.09 0.00
74_M 53_T 0.86 0.09 0.00
81_N 269_V 0.86 0.09 0.00
12_K 25_T 0.86 0.09 0.00
40_K 74_R 0.86 0.09 0.00
36_E 239_H 0.86 0.09 0.00
63_F 183_I 0.86 0.09 0.00
73_S 131_F 0.85 0.09 0.00
66_I 241_I 0.85 0.09 0.00
92_L 284_S 0.85 0.09 0.00
72_L 203_A 0.85 0.09 0.00
51_F 204_M 0.85 0.09 0.00
56_D 175_Y 0.85 0.09 0.00
17_T 270_T 0.85 0.09 0.00
44_K 101_V 0.85 0.09 0.00
82_A 249_I 0.85 0.09 0.00
35_S 184_I 0.85 0.09 0.00
12_K 8_M 0.85 0.09 0.00
30_N 78_R 0.84 0.09 0.00
51_F 64_L 0.84 0.09 0.00
33_T 248_M 0.84 0.09 0.00
66_I 85_Q 0.84 0.09 0.00
50_N 209_S 0.84 0.09 0.00
76_L 38_A 0.84 0.09 0.00
62_T 51_N 0.84 0.09 0.00
52_E 161_H 0.84 0.09 0.00
52_E 164_N 0.84 0.09 0.00
52_E 179_P 0.84 0.09 0.00
52_E 182_D 0.84 0.09 0.00
13_I 154_L 0.84 0.09 0.00
21_N 51_N 0.84 0.09 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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