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OPENSEQ.org
BP2924_BP2926 (A, 20-95)
Genes: A B A+B
Length: 76 251 315
Sequences: 357 915 438
Seq/Len: 4.7 3.65 1.39
MirrorTree (Pazo et al. 2001) 0.56
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 0.02 0.00 0.07
2 0.02 0.00 1.21
5 0.03 0.00 1.34
10 0.04 0.01 1.34
20 0.04 0.01 1.35
100 0.05 0.01 1.35
∞ 0.06 0.07 1.35
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
50_P 64_F 1.54 0.87 0.18
38_K 210_V 1.44 0.81 0.14
38_K 220_G 1.40 0.78 0.12
18_A 150_L 1.37 0.77 0.11
51_K 63_D 1.36 0.76 0.11
27_A 78_P 1.16 0.58 0.06
11_M 70_H 1.16 0.58 0.06
32_T 245_A 1.16 0.58 0.06
28_G 78_P 1.12 0.54 0.05
29_A 153_A 1.08 0.50 0.04
18_A 199_A 1.08 0.50 0.04
39_V 244_G 1.07 0.49 0.04
50_P 105_Y 1.03 0.45 0.04
20_K 94_V 1.02 0.44 0.04
29_A 117_V 1.02 0.44 0.04
37_S 5_A 1.00 0.42 0.03
53_T 170_H 0.98 0.40 0.03
59_S 162_A 0.97 0.40 0.03
28_G 48_A 0.97 0.39 0.03
12_E 90_F 0.96 0.38 0.03
15_Y 79_R 0.95 0.38 0.03
11_M 72_Y 0.94 0.37 0.03
50_P 60_V 0.91 0.34 0.03
20_K 59_L 0.90 0.32 0.02
15_Y 212_A 0.89 0.32 0.02
34_A 105_Y 0.89 0.32 0.02
34_A 60_V 0.89 0.31 0.02
20_K 151_H 0.89 0.31 0.02
39_V 12_L 0.88 0.31 0.02
22_K 81_P 0.88 0.31 0.02
36_T 44_S 0.88 0.31 0.02
27_A 82_V 0.87 0.30 0.02
42_Q 108_D 0.87 0.30 0.02
31_T 47_Q 0.87 0.30 0.02
4_P 150_L 0.87 0.30 0.02
51_K 13_D 0.86 0.29 0.02
34_A 97_H 0.85 0.29 0.02
38_K 19_P 0.85 0.28 0.02
73_K 174_L 0.84 0.27 0.02
18_A 79_R 0.83 0.27 0.02
67_G 45_L 0.83 0.27 0.02
73_K 187_A 0.83 0.27 0.02
19_L 114_Y 0.83 0.27 0.02
41_Y 34_Y 0.82 0.26 0.02
10_D 166_L 0.82 0.26 0.02
8_A 95_A 0.82 0.26 0.02
19_L 176_I 0.82 0.26 0.02
19_L 117_V 0.82 0.26 0.02
30_G 41_V 0.82 0.26 0.02
70_E 208_A 0.81 0.25 0.02
60_P 51_D 0.80 0.25 0.02
10_D 90_F 0.80 0.24 0.01
31_T 44_S 0.80 0.24 0.01
18_A 145_S 0.80 0.24 0.01
31_T 41_V 0.79 0.24 0.01
50_P 163_I 0.79 0.24 0.01
26_K 228_D 0.79 0.24 0.01
71_A 247_I 0.78 0.23 0.01
72_F 162_A 0.78 0.23 0.01
10_D 56_C 0.78 0.23 0.01
10_D 101_A 0.78 0.23 0.01
26_K 189_V 0.78 0.23 0.01
22_K 52_T 0.77 0.23 0.01
55_E 144_A 0.77 0.22 0.01
4_P 135_A 0.77 0.22 0.01
19_L 82_V 0.77 0.22 0.01
67_G 36_I 0.76 0.22 0.01
57_T 169_A 0.76 0.22 0.01
20_K 210_V 0.76 0.21 0.01
48_Q 45_L 0.76 0.21 0.01
17_V 107_A 0.76 0.21 0.01
42_Q 40_N 0.76 0.21 0.01
31_T 78_P 0.76 0.21 0.01
67_G 39_N 0.76 0.21 0.01
12_E 11_L 0.76 0.21 0.01
32_T 82_V 0.75 0.21 0.01
22_K 174_L 0.75 0.21 0.01
8_A 107_A 0.75 0.21 0.01
68_Q 119_A 0.74 0.20 0.01
20_K 198_L 0.74 0.20 0.01
37_S 211_R 0.73 0.20 0.01
43_G 115_L 0.73 0.20 0.01
20_K 199_A 0.73 0.20 0.01
55_E 118_R 0.73 0.20 0.01
19_L 34_Y 0.73 0.19 0.01
34_A 99_P 0.73 0.19 0.01
48_Q 121_Y 0.73 0.19 0.01
8_A 15_L 0.73 0.19 0.01
39_V 134_G 0.72 0.19 0.01
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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