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OPENSEQ.org
3a8k_F_B
Genes: A B A+B
Length: 129 364 475
Sequences: 3072 5209 1251
Seq/Len: 23.81 14.31 2.63
MirrorTree (Pazo et al. 2001) 0.54
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 0.05 2.32
2 0.06 0.06 2.41
5 0.07 0.08 2.49
10 0.07 0.13 2.51
20 0.07 0.15 2.54
100 0.07 0.17 2.66
∞ 0.10 0.24 3.65
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
47_E 345_R 1.27 0.85 0.16
25_Y 33_Q 0.96 0.56 0.06
49_G 344_N 0.91 0.49 0.05
67_A 359_N 0.90 0.49 0.05
40_M 103_Y 0.90 0.49 0.05
59_A 171_M 0.89 0.48 0.05
99_G 64_E 0.89 0.47 0.05
87_D 9_E 0.87 0.45 0.04
66_A 69_L 0.85 0.43 0.04
64_V 124_W 0.85 0.42 0.04
66_A 144_M 0.84 0.41 0.04
67_A 174_F 0.83 0.41 0.04
64_V 18_M 0.82 0.39 0.04
50_A 344_N 0.77 0.34 0.03
42_F 6_P 0.76 0.33 0.03
61_A 57_L 0.76 0.33 0.03
67_A 217_K 0.76 0.32 0.03
79_V 335_G 0.76 0.32 0.03
69_D 74_V 0.74 0.31 0.03
77_E 207_F 0.74 0.30 0.03
40_M 174_F 0.74 0.30 0.03
11_S 22_H 0.74 0.30 0.03
53_S 15_G 0.73 0.29 0.02
12_K 156_A 0.73 0.29 0.02
69_D 312_I 0.73 0.29 0.02
50_A 219_C 0.72 0.29 0.02
30_T 313_T 0.71 0.28 0.02
88_S 245_S 0.71 0.28 0.02
2_S 226_T 0.71 0.28 0.02
81_V 57_L 0.71 0.27 0.02
98_A 241_D 0.70 0.27 0.02
29_I 4_Q 0.70 0.26 0.02
41_V 50_S 0.70 0.26 0.02
34_Q 72_N 0.69 0.26 0.02
44_D 86_S 0.69 0.26 0.02
60_V 238_Q 0.68 0.25 0.02
67_A 67_R 0.68 0.25 0.02
68_S 112_V 0.68 0.25 0.02
95_E 16_A 0.68 0.24 0.02
39_D 46_M 0.68 0.24 0.02
102_I 115_S 0.67 0.24 0.02
29_I 26_M 0.67 0.24 0.02
17_L 35_D 0.67 0.24 0.02
34_Q 316_T 0.66 0.23 0.02
78_I 16_A 0.66 0.23 0.02
85_L 73_D 0.66 0.23 0.02
34_Q 291_V 0.66 0.23 0.02
34_Q 124_W 0.65 0.22 0.02
85_L 49_V 0.65 0.22 0.02
106_K 233_M 0.65 0.22 0.02
64_V 121_D 0.64 0.22 0.02
16_W 112_V 0.64 0.22 0.02
107_A 125_I 0.64 0.21 0.02
44_D 290_G 0.64 0.21 0.02
96_P 6_P 0.63 0.21 0.02
92_V 115_S 0.63 0.21 0.02
90_E 67_R 0.63 0.21 0.02
41_V 343_R 0.63 0.21 0.02
45_L 319_P 0.63 0.21 0.02
109_D 322_G 0.63 0.21 0.02
39_D 314_S 0.63 0.20 0.02
103_F 184_I 0.63 0.20 0.02
78_I 347_M 0.62 0.20 0.01
66_A 222_G 0.62 0.20 0.01
79_V 152_A 0.62 0.20 0.01
68_S 82_K 0.61 0.19 0.01
75_S 285_V 0.61 0.19 0.01
11_S 12_T 0.61 0.19 0.01
79_V 101_V 0.60 0.19 0.01
68_S 49_V 0.60 0.18 0.01
49_G 301_T 0.60 0.18 0.01
71_Y 175_F 0.60 0.18 0.01
27_V 43_D 0.60 0.18 0.01
127_E 109_F 0.60 0.18 0.01
83_D 12_T 0.60 0.18 0.01
47_E 326_A 0.60 0.18 0.01
94_S 95_V 0.60 0.18 0.01
42_F 129_A 0.60 0.18 0.01
19_K 154_A 0.60 0.18 0.01
66_A 239_E 0.59 0.18 0.01
32_H 34_I 0.59 0.18 0.01
12_K 157_A 0.59 0.18 0.01
64_V 111_L 0.59 0.18 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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