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OPENSEQ.org
aa
Genes: A B A+B
Length: 116 182 263
Sequences: 15797 4709 213
Seq/Len: 136.18 25.87 0.81
MirrorTree (Pazo et al. 2001) 0.36
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 0.03 0.10
2 0.03 0.03 0.14
5 0.03 0.04 0.23
10 0.03 0.04 0.42
20 0.04 0.04 0.71
100 0.09 0.06 2.82
∞ 0.19 0.12 8.21
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
66_D 6_K 1.38 0.62 0.00
92_V 62_V 1.22 0.48 0.00
88_D 58_F 1.20 0.46 0.00
47_L 34_Y 1.13 0.40 0.00
99_K 68_L 1.12 0.40 0.00
58_L 24_Q 1.07 0.35 0.00
30_V 8_I 1.04 0.33 0.00
64_D 100_D 0.97 0.27 0.00
21_V 64_D 0.96 0.27 0.00
34_A 69_L 0.94 0.26 0.00
94_R 124_V 0.93 0.25 0.00
100_G 45_R 0.93 0.25 0.00
88_D 106_I 0.93 0.25 0.00
32_F 88_R 0.91 0.23 0.00
45_P 88_R 0.91 0.23 0.00
72_A 59_D 0.89 0.22 0.00
109_S 100_D 0.88 0.21 0.00
94_R 96_I 0.87 0.21 0.00
38_G 128_V 0.85 0.20 0.00
64_D 31_R 0.84 0.19 0.00
47_L 54_V 0.84 0.19 0.00
28_V 45_R 0.83 0.19 0.00
62_K 30_T 0.83 0.19 0.00
77_V 148_Y 0.83 0.19 0.00
64_D 55_E 0.83 0.19 0.00
95_I 139_P 0.83 0.19 0.00
64_D 38_N 0.83 0.19 0.00
60_V 6_K 0.83 0.19 0.00
61_A 56_I 0.82 0.18 0.00
63_L 41_N 0.82 0.18 0.00
41_K 139_P 0.81 0.18 0.00
43_V 73_F 0.81 0.18 0.00
50_I 114_V 0.80 0.17 0.00
30_V 135_W 0.80 0.17 0.00
94_R 21_I 0.80 0.17 0.00
110_D 58_F 0.80 0.17 0.00
110_D 124_V 0.80 0.17 0.00
82_T 96_I 0.79 0.17 0.00
65_V 31_R 0.79 0.17 0.00
88_D 102_Q 0.79 0.17 0.00
52_T 40_P 0.79 0.17 0.00
38_G 108_L 0.78 0.16 0.00
86_F 47_H 0.78 0.16 0.00
39_P 79_T 0.78 0.16 0.00
27_P 27_V 0.77 0.16 0.00
30_V 30_T 0.77 0.16 0.00
87_K 98_Y 0.77 0.16 0.00
41_K 144_Y 0.76 0.15 0.00
109_S 109_D 0.76 0.15 0.00
80_I 19_D 0.76 0.15 0.00
75_F 56_I 0.75 0.15 0.00
83_L 29_S 0.75 0.15 0.00
102_A 20_L 0.75 0.15 0.00
75_F 81_K 0.75 0.15 0.00
15_A 127_E 0.74 0.15 0.00
77_V 62_V 0.74 0.14 0.00
63_L 60_P 0.74 0.14 0.00
109_S 128_V 0.74 0.14 0.00
45_P 128_V 0.74 0.14 0.00
88_D 113_D 0.74 0.14 0.00
29_L 68_L 0.73 0.14 0.00
16_S 54_V 0.73 0.14 0.00
104_L 28_V 0.72 0.14 0.00
59_T 69_L 0.72 0.14 0.00
25_N 39_I 0.72 0.14 0.00
88_D 135_W 0.72 0.14 0.00
104_L 108_L 0.72 0.14 0.00
20_D 139_P 0.72 0.14 0.00
77_V 125_V 0.72 0.14 0.00
84_I 116_A 0.72 0.13 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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