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OPENSEQ.org
24
Genes: A B A+B
Length: 76 294 362
Sequences: 299 61566 95
Seq/Len: 3.93 209.41 0.26
MirrorTree (Pazo et al. 2001) 0.16
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 0.10 0.03
2 0.04 0.12 0.04
5 0.04 0.16 0.09
10 0.04 0.20 0.15
20 0.04 0.24 0.26
100 0.06 0.31 0.64
∞ 0.06 0.34 0.78
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
65_I 110_G 1.45 0.35 0.00
35_H 259_L 1.25 0.24 0.00
14_E 77_E 1.21 0.23 0.00
72_L 110_G 1.20 0.22 0.00
17_E 142_F 1.17 0.21 0.00
47_V 14_T 1.17 0.20 0.00
72_L 63_L 1.10 0.18 0.00
14_E 164_Y 1.08 0.17 0.00
3_K 59_I 1.08 0.17 0.00
65_I 4_F 1.07 0.17 0.00
66_L 211_I 1.07 0.17 0.00
17_E 47_E 1.07 0.17 0.00
66_L 166_A 1.06 0.16 0.00
69_R 263_L 1.04 0.16 0.00
22_M 112_A 1.04 0.16 0.00
14_E 12_E 1.04 0.15 0.00
14_E 126_P 1.04 0.15 0.00
14_E 56_H 1.03 0.15 0.00
36_L 182_I 1.02 0.15 0.00
72_L 11_G 1.01 0.15 0.00
45_L 165_R 1.01 0.15 0.00
44_N 16_G 0.99 0.14 0.00
33_K 199_F 0.99 0.14 0.00
21_V 51_L 0.98 0.14 0.00
29_K 23_N 0.97 0.14 0.00
49_Q 18_V 0.96 0.13 0.00
47_V 194_T 0.96 0.13 0.00
51_Q 131_I 0.95 0.13 0.00
50_S 47_E 0.95 0.13 0.00
41_E 166_A 0.94 0.12 0.00
70_R 142_F 0.94 0.12 0.00
65_I 48_I 0.93 0.12 0.00
32_P 183_W 0.93 0.12 0.00
47_V 79_L 0.92 0.12 0.00
27_I 169_I 0.92 0.12 0.00
25_K 111_L 0.92 0.12 0.00
4_Q 170_L 0.92 0.12 0.00
49_Q 78_F 0.92 0.12 0.00
51_Q 194_T 0.90 0.12 0.00
65_I 58_N 0.90 0.12 0.00
10_K 192_M 0.90 0.12 0.00
43_R 168_E 0.90 0.11 0.00
43_R 181_D 0.90 0.11 0.00
43_R 270_R 0.90 0.11 0.00
47_V 182_I 0.90 0.11 0.00
11_Y 183_W 0.90 0.11 0.00
54_V 170_L 0.89 0.11 0.00
47_V 200_P 0.89 0.11 0.00
31_V 269_K 0.89 0.11 0.00
73_P 271_I 0.89 0.11 0.00
66_L 233_K 0.89 0.11 0.00
45_L 237_P 0.89 0.11 0.00
72_L 246_K 0.89 0.11 0.00
29_K 177_S 0.88 0.11 0.00
37_M 254_D 0.88 0.11 0.00
38_S 118_R 0.87 0.11 0.00
37_M 86_F 0.87 0.11 0.00
24_P 30_V 0.86 0.10 0.00
26_D 191_E 0.85 0.10 0.00
36_L 81_Q 0.85 0.10 0.00
58_I 23_N 0.85 0.10 0.00
24_P 283_Q 0.85 0.10 0.00
27_I 154_T 0.84 0.10 0.00
9_D 53_E 0.84 0.10 0.00
16_F 161_T 0.84 0.10 0.00
37_M 265_Y 0.83 0.10 0.00
26_D 118_R 0.83 0.10 0.00
12_D 58_N 0.82 0.10 0.00
43_R 128_N 0.82 0.10 0.00
35_H 126_P 0.82 0.10 0.00
32_P 72_L 0.82 0.10 0.00
69_R 198_L 0.82 0.09 0.00
46_G 47_E 0.81 0.09 0.00
35_H 106_Q 0.81 0.09 0.00
65_I 187_C 0.81 0.09 0.00
68_F 115_H 0.81 0.09 0.00
52_G 168_E 0.81 0.09 0.00
52_G 181_D 0.81 0.09 0.00
52_G 270_R 0.81 0.09 0.00
68_F 16_G 0.81 0.09 0.00
72_L 194_T 0.81 0.09 0.00
26_D 29_V 0.81 0.09 0.00
17_E 121_H 0.81 0.09 0.00
10_K 144_L 0.80 0.09 0.00
58_I 95_I 0.80 0.09 0.00
57_M 265_Y 0.80 0.09 0.00
57_M 196_R 0.80 0.09 0.00
64_H 137_I 0.79 0.09 0.00
61_P 167_P 0.79 0.09 0.00
16_F 193_V 0.79 0.09 0.00
30_L 267_P 0.78 0.09 0.00
36_L 10_I 0.78 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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