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OPENSEQ.org
L14-vs-S7
Genes: A B A+B
Length: 123 179 278
Sequences: 1778 1685 1043
Seq/Len: 14.46 9.41 3.75
MirrorTree (Pazo et al. 2001) 0.80
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 0.09 0.11 0.01
2 0.09 0.11 0.04
5 0.09 0.11 0.07
10 0.09 0.11 0.29
20 0.09 0.11 2.42
100 0.09 0.11 2.88
∞ 0.10 0.11 3.45
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
51_K 131_K 1.35 0.94 0.53
95_I 131_K 1.35 0.94 0.53
86_L 22_L 1.19 0.87 0.38
27_G 62_F 1.08 0.79 0.29
55_G 156_W 1.01 0.73 0.23
111_K 12_I 1.00 0.71 0.22
78_R 109_R 0.98 0.70 0.21
17_R 152_A 0.97 0.68 0.20
123_L 104_I 0.97 0.68 0.20
93_Q 131_K 0.95 0.66 0.19
17_R 70_R 0.90 0.60 0.16
19_V 27_V 0.89 0.58 0.15
109_S 131_K 0.88 0.57 0.15
45_E 69_V 0.88 0.57 0.15
110_E 38_T 0.87 0.55 0.14
40_K 129_E 0.86 0.55 0.14
95_I 106_E 0.86 0.54 0.14
83_A 107_A 0.86 0.54 0.14
110_E 143_R 0.83 0.51 0.12
93_Q 20_S 0.83 0.50 0.12
121_E 15_D 0.83 0.50 0.12
32_Y 59_L 0.82 0.48 0.12
114_K 9_Q 0.82 0.48 0.12
42_T 25_K 0.80 0.47 0.11
52_V 64_V 0.80 0.47 0.11
49_R 119_R 0.80 0.46 0.11
71_R 71_P 0.80 0.46 0.11
112_F 100_A 0.79 0.45 0.10
114_K 36_K 0.79 0.45 0.10
47_I 77_S 0.79 0.45 0.10
17_R 119_R 0.79 0.45 0.10
78_R 84_T 0.78 0.44 0.10
39_I 122_N 0.78 0.43 0.10
19_V 24_A 0.78 0.43 0.10
30_R 31_M 0.77 0.42 0.10
53_K 14_P 0.77 0.42 0.09
28_S 37_S 0.77 0.42 0.09
55_G 25_K 0.76 0.41 0.09
40_K 29_I 0.76 0.41 0.09
86_L 115_S 0.75 0.40 0.09
121_E 44_Y 0.75 0.40 0.09
123_L 61_A 0.75 0.40 0.09
20_M 4_R 0.75 0.39 0.09
102_P 136_K 0.75 0.39 0.09
90_N 26_F 0.74 0.39 0.09
87_L 154_Y 0.74 0.39 0.08
42_T 30_L 0.74 0.38 0.08
121_E 78_R 0.74 0.38 0.08
23_K 113_D 0.73 0.38 0.08
66_K 59_L 0.73 0.38 0.08
62_V 8_G 0.73 0.37 0.08
5_Q 66_L 0.73 0.37 0.08
99_I 72_T 0.73 0.37 0.08
108_R 79_R 0.72 0.36 0.08
90_N 22_L 0.72 0.36 0.07
50_G 156_W 0.72 0.36 0.07
103_V 57_S 0.71 0.35 0.07
19_V 72_T 0.70 0.34 0.07
91_S 21_E 0.70 0.34 0.07
74_G 123_E 0.70 0.34 0.07
55_G 67_E 0.70 0.33 0.07
95_I 25_K 0.70 0.33 0.07
72_P 51_A 0.70 0.33 0.07
100_F 78_R 0.69 0.33 0.07
91_S 143_R 0.69 0.33 0.07
89_N 52_Q 0.69 0.33 0.07
77_I 38_T 0.69 0.33 0.07
43_I 133_T 0.69 0.33 0.07
46_A 136_K 0.69 0.33 0.07
35_V 134_A 0.69 0.33 0.07
14_S 75_V 0.69 0.32 0.07
119_A 147_A 0.69 0.32 0.07
62_V 92_R 0.68 0.32 0.06
67_K 138_R 0.68 0.32 0.06
104_T 76_K 0.68 0.32 0.06
111_K 67_E 0.68 0.31 0.06
104_T 23_L 0.68 0.31 0.06
123_L 98_A 0.67 0.31 0.06
55_G 42_I 0.67 0.30 0.06
78_R 73_V 0.67 0.30 0.06
4_E 77_S 0.67 0.30 0.06
108_R 145_A 0.67 0.30 0.06
38_I 67_E 0.67 0.30 0.06
104_T 110_K 0.66 0.30 0.06
43_I 125_S 0.66 0.30 0.06
84_C 91_V 0.66 0.29 0.06
40_K 101_M 0.66 0.29 0.06
5_Q 2_P 0.66 0.29 0.06
86_L 24_A 0.66 0.29 0.06
81_G 125_S 0.66 0.29 0.06
109_S 19_G 0.65 0.28 0.06
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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