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OPENSEQ.org
Hs_BCL6_BTB vs Hs_TLE1_WD
Genes: A B A+B
Length: 125 300 402
Sequences: 3014 12077 176
Seq/Len: 24.11 40.26 0.44
MirrorTree (Pazo et al. 2001) 0.14
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 0.09 0.09 0.04
2 0.10 0.10 0.05
5 0.10 0.11 0.12
10 0.11 0.12 0.22
20 0.12 0.14 0.41
100 0.14 0.18 1.18
∞ 0.17 0.24 2.09
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
59_D 133_V 1.53 0.55 0.00
83_L 87_L 1.37 0.43 0.00
86_M 119_S 1.20 0.31 0.00
42_H 176_W 1.19 0.30 0.00
70_L 33_Y 1.17 0.29 0.00
47_M 174_R 1.10 0.25 0.00
117_C 32_V 1.09 0.25 0.00
85_F 80_V 1.09 0.25 0.00
32_I 185_Q 1.09 0.24 0.00
78_G 87_L 1.09 0.24 0.00
39_F 216_V 1.09 0.24 0.00
68_I 122_C 1.06 0.23 0.00
43_K 23_V 1.04 0.22 0.00
85_F 124_S 1.00 0.20 0.00
45_V 193_I 1.00 0.20 0.00
32_I 24_T 0.98 0.19 0.00
47_M 23_V 0.98 0.19 0.00
54_Y 262_Y 0.98 0.19 0.00
118_R 81_G 0.98 0.19 0.00
35_S 158_S 0.97 0.19 0.00
88_T 83_E 0.96 0.18 0.00
45_V 224_K 0.96 0.18 0.00
74_I 244_K 0.94 0.17 0.00
88_T 129_G 0.93 0.17 0.00
88_T 125_C 0.93 0.17 0.00
94_R 208_G 0.93 0.17 0.00
121_I 197_G 0.93 0.17 0.00
113_V 87_L 0.92 0.16 0.00
45_V 40_V 0.92 0.16 0.00
46_L 122_C 0.91 0.16 0.00
102_M 214_V 0.90 0.15 0.00
120_F 89_I 0.89 0.15 0.00
64_N 43_W 0.89 0.15 0.00
89_S 138_N 0.88 0.15 0.00
43_K 187_H 0.88 0.15 0.00
18_L 135_D 0.88 0.15 0.00
23_S 194_F 0.87 0.15 0.00
48_A 80_V 0.87 0.15 0.00
39_F 98_R 0.87 0.14 0.00
81_I 207_V 0.86 0.14 0.00
51_G 193_I 0.86 0.14 0.00
85_F 142_V 0.86 0.14 0.00
110_M 191_S 0.86 0.14 0.00
22_R 135_D 0.85 0.14 0.00
30_V 255_L 0.85 0.14 0.00
82_L 122_C 0.85 0.14 0.00
83_L 218_H 0.85 0.14 0.00
91_L 262_Y 0.84 0.14 0.00
49_C 209_M 0.84 0.13 0.00
43_K 101_A 0.84 0.13 0.00
54_Y 156_D 0.84 0.13 0.00
45_V 32_V 0.84 0.13 0.00
32_I 135_D 0.83 0.13 0.00
54_Y 211_S 0.83 0.13 0.00
45_V 138_N 0.83 0.13 0.00
54_Y 82_G 0.83 0.13 0.00
36_R 165_W 0.83 0.13 0.00
47_M 57_L 0.83 0.13 0.00
108_L 243_G 0.83 0.13 0.00
57_F 241_Y 0.82 0.13 0.00
88_T 198_Y 0.82 0.13 0.00
75_N 107_A 0.82 0.13 0.00
111_E 216_V 0.81 0.12 0.00
26_I 69_C 0.81 0.12 0.00
50_S 41_K 0.81 0.12 0.00
43_K 112_A 0.81 0.12 0.00
86_M 157_I 0.80 0.12 0.00
89_S 82_G 0.80 0.12 0.00
112_H 155_I 0.80 0.12 0.00
38_Q 137_H 0.80 0.12 0.00
56_I 242_C 0.80 0.12 0.00
38_Q 195_S 0.80 0.12 0.00
64_N 168_G 0.80 0.12 0.00
21_L 118_D 0.80 0.12 0.00
47_M 40_V 0.80 0.12 0.00
38_Q 254_L 0.79 0.12 0.00
12_S 173_V 0.79 0.12 0.00
21_L 234_V 0.79 0.12 0.00
91_L 78_L 0.79 0.12 0.00
91_L 249_T 0.78 0.12 0.00
36_R 246_F 0.78 0.12 0.00
85_F 163_K 0.78 0.11 0.00
76_P 158_S 0.78 0.11 0.00
83_L 119_S 0.78 0.11 0.00
32_I 277_S 0.78 0.11 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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