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OPENSEQ.org
L20-vs-S10
Genes: A B A+B
Length: 118 103 215
Sequences: 1984 1460 740
Seq/Len: 16.81 14.17 3.44
MirrorTree (Pazo et al. 2001) 0.62
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 0.10 0.09 0.01
2 0.10 0.09 0.01
5 0.10 0.09 0.02
10 0.10 0.09 0.05
20 0.10 0.09 0.09
100 0.10 0.09 0.75
∞ 0.10 0.09 3.35
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
90_I 11_K 1.29 0.91 0.34
40_I 60_D 1.28 0.90 0.33
44_Q 18_I 1.27 0.90 0.32
36_F 18_I 1.23 0.88 0.29
98_I 40_I 1.16 0.83 0.24
13_R 57_V 1.11 0.79 0.21
27_A 13_F 1.08 0.77 0.19
24_Y 90_L 1.04 0.73 0.17
96_A 12_A 0.99 0.68 0.14
59_Q 52_L 0.99 0.67 0.14
110_V 73_L 0.96 0.64 0.13
36_F 60_D 0.96 0.64 0.13
88_V 16_R 0.95 0.63 0.12
72_N 11_K 0.90 0.56 0.10
40_I 98_V 0.89 0.56 0.10
91_D 37_R 0.88 0.54 0.10
97_D 49_F 0.87 0.52 0.09
47_Y 55_P 0.86 0.52 0.09
12_A 49_F 0.86 0.51 0.09
14_H 18_I 0.85 0.51 0.09
17_I 91_D 0.85 0.50 0.09
91_D 82_K 0.85 0.50 0.09
94_I 31_R 0.85 0.50 0.09
38_A 94_A 0.84 0.49 0.08
73_G 94_A 0.83 0.48 0.08
59_Q 58_N 0.82 0.47 0.08
12_A 22_T 0.81 0.46 0.07
109_L 102_L 0.81 0.45 0.07
30_R 5_R 0.80 0.44 0.07
18_L 21_A 0.80 0.44 0.07
18_L 29_A 0.78 0.42 0.07
53_R 90_L 0.78 0.41 0.06
4_V 68_R 0.78 0.41 0.06
88_V 47_E 0.77 0.41 0.06
74_I 5_R 0.77 0.40 0.06
35_A 59_K 0.77 0.40 0.06
91_D 51_V 0.77 0.40 0.06
49_D 13_F 0.75 0.38 0.06
59_Q 35_Q 0.75 0.38 0.06
19_K 58_N 0.75 0.37 0.06
7_G 66_E 0.75 0.37 0.06
40_I 64_Q 0.74 0.37 0.06
49_D 89_R 0.74 0.37 0.06
65_I 6_I 0.74 0.37 0.06
63_A 52_L 0.74 0.36 0.05
38_A 91_D 0.74 0.36 0.05
6_R 50_T 0.73 0.35 0.05
100_V 40_I 0.72 0.35 0.05
80_I 28_T 0.71 0.33 0.05
4_V 66_E 0.71 0.33 0.05
86_A 80_T 0.70 0.32 0.04
5_K 66_E 0.70 0.31 0.04
110_V 29_A 0.68 0.30 0.04
24_Y 15_H 0.68 0.30 0.04
70_R 4_Q 0.68 0.30 0.04
41_K 23_A 0.68 0.30 0.04
94_I 71_L 0.68 0.29 0.04
74_I 86_A 0.68 0.29 0.04
102_D 79_P 0.67 0.29 0.04
55_R 17_L 0.67 0.29 0.04
108_A 22_T 0.67 0.28 0.04
102_D 74_V 0.67 0.28 0.04
7_G 18_I 0.67 0.28 0.04
79_F 81_E 0.67 0.28 0.04
103_K 61_A 0.67 0.28 0.04
70_R 96_V 0.67 0.28 0.04
28_R 19_D 0.66 0.28 0.04
15_K 18_I 0.66 0.28 0.04
25_Y 50_T 0.66 0.28 0.04
25_Y 74_V 0.66 0.28 0.04
5_K 60_D 0.66 0.28 0.04
10_A 17_L 0.66 0.28 0.04
32_Y 60_D 0.65 0.27 0.04
51_R 3_N 0.65 0.27 0.04
82_G 12_A 0.65 0.27 0.04
7_G 13_F 0.65 0.26 0.04
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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