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OPENSEQ.org
S6_S18
Genes: A B A+B
Length: 135 75 184
Sequences: 689 1779 519
Seq/Len: 5.1 23.72 2.82
MirrorTree (Pazo et al. 2001) 0.85
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 0.06 0.09 1.81
2 0.06 0.09 2.46
5 0.06 0.09 2.47
10 0.06 0.09 2.47
20 0.06 0.09 2.47
100 0.06 0.09 2.45
∞ 0.06 0.10 2.57
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
7_V 65_L 2.55 1.00 1.00
9_M 66_S 2.14 1.00 0.99
88_M 65_L 1.91 0.99 0.97
57_A 66_S 1.52 0.96 0.90
86_R 65_L 1.34 0.90 0.81
86_R 64_Y 1.34 0.90 0.80
79_R 40_V 1.31 0.88 0.78
6_I 32_Y 1.29 0.88 0.77
57_A 73_R 1.22 0.83 0.71
59_Y 66_S 1.17 0.79 0.66
90_M 61_R 1.16 0.79 0.65
91_R 6_R 1.16 0.78 0.65
88_M 64_Y 1.14 0.77 0.64
76_T 36_S 1.11 0.74 0.60
39_L 71_T 1.09 0.72 0.58
55_H 31_N 1.07 0.70 0.55
94_H 36_S 1.03 0.66 0.51
68_Q 44_I 1.03 0.66 0.51
9_M 32_Y 1.01 0.64 0.49
79_R 21_I 0.99 0.62 0.47
27_A 33_I 0.96 0.59 0.43
51_I 65_L 0.95 0.57 0.41
38_R 20_E 0.94 0.56 0.40
52_N 33_I 0.94 0.55 0.39
42_W 53_R 0.94 0.55 0.39
18_V 65_L 0.92 0.53 0.37
37_H 32_Y 0.90 0.51 0.35
55_H 25_D 0.90 0.51 0.35
61_L 58_A 0.90 0.51 0.35
92_T 32_Y 0.90 0.51 0.35
86_R 58_A 0.90 0.50 0.35
60_V 49_A 0.88 0.48 0.32
61_L 55_L 0.86 0.47 0.31
67_P 50_K 0.85 0.45 0.30
64_V 42_S 0.85 0.44 0.29
71_I 57_R 0.84 0.43 0.28
82_D 13_F 0.83 0.43 0.28
51_I 66_S 0.83 0.43 0.28
17_Q 48_R 0.83 0.42 0.27
86_R 22_D 0.82 0.42 0.27
12_P 12_R 0.82 0.42 0.27
90_M 32_Y 0.81 0.40 0.26
114_D 57_R 0.81 0.39 0.25
51_I 45_T 0.80 0.38 0.24
52_N 27_A 0.80 0.38 0.24
91_R 4_Y 0.79 0.38 0.23
8_F 35_E 0.79 0.37 0.23
66_A 50_K 0.78 0.37 0.23
52_N 56_A 0.78 0.37 0.23
94_H 68_L 0.77 0.36 0.21
23_E 7_R 0.77 0.35 0.21
8_F 11_C 0.77 0.35 0.21
73_E 44_I 0.77 0.35 0.21
68_Q 33_I 0.77 0.35 0.21
78_F 46_G 0.76 0.34 0.20
32_A 73_R 0.76 0.34 0.20
44_R 45_T 0.76 0.34 0.20
2_R 46_G 0.76 0.34 0.20
45_R 13_F 0.76 0.34 0.20
88_M 17_G 0.75 0.33 0.20
42_W 67_L 0.75 0.33 0.19
23_E 5_F 0.74 0.32 0.19
27_A 7_R 0.74 0.32 0.19
32_A 8_R 0.74 0.32 0.19
90_M 38_K 0.74 0.32 0.18
99_A 34_T 0.74 0.32 0.18
29_I 54_Q 0.74 0.32 0.18
42_W 37_G 0.73 0.31 0.18
88_M 61_R 0.73 0.31 0.17
28_A 59_I 0.72 0.30 0.17
53_K 8_R 0.72 0.30 0.17
95_A 30_K 0.72 0.30 0.17
54_L 47_T 0.72 0.30 0.17
86_R 56_A 0.72 0.30 0.17
75_E 43_R 0.72 0.30 0.17
53_K 44_I 0.72 0.30 0.17
101_P 64_Y 0.72 0.30 0.17
98_E 16_E 0.72 0.30 0.17
67_P 25_D 0.72 0.30 0.17
33_E 60_K 0.72 0.30 0.17
8_F 33_I 0.72 0.30 0.17
3_H 51_Y 0.72 0.30 0.17
80_F 36_S 0.72 0.30 0.17
70_V 42_S 0.72 0.29 0.17
56_K 42_S 0.71 0.29 0.17
2_R 12_R 0.71 0.29 0.16
86_R 19_Q 0.71 0.29 0.16
12_P 46_G 0.71 0.29 0.16
99_A 61_R 0.70 0.28 0.16
84_V 58_A 0.70 0.28 0.15
46_Q 10_F 0.70 0.28 0.15
96_V 70_Y 0.69 0.27 0.15
60_V 11_C 0.69 0.27 0.15
4_Y 38_K 0.69 0.27 0.15
20_G 70_Y 0.69 0.27 0.15
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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