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OPENSEQ.org
3A8K
Genes: A B A+B
Length: 364 129 475
Sequences: 5209 3072 1244
Seq/Len: 14.31 23.81 2.62
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 0.05 0.06 2.31
2 0.06 0.06 2.40
5 0.08 0.07 2.49
10 0.13 0.07 2.51
20 0.15 0.07 2.52
100 0.17 0.07 2.67
∞ 0.24 0.10 3.67
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
345_R 47_E 1.23 0.82 0.09
33_Q 25_Y 0.96 0.56 0.04
171_M 59_A 0.89 0.47 0.03
103_Y 40_M 0.88 0.47 0.03
344_N 49_G 0.88 0.46 0.03
359_N 67_A 0.88 0.46 0.03
69_L 66_A 0.86 0.44 0.03
124_W 64_V 0.84 0.42 0.03
335_G 79_V 0.84 0.41 0.03
144_M 66_A 0.83 0.41 0.03
174_F 67_A 0.83 0.41 0.03
18_M 64_V 0.81 0.38 0.02
16_A 78_I 0.78 0.35 0.02
64_E 99_G 0.76 0.33 0.02
344_N 50_A 0.76 0.33 0.02
217_K 67_A 0.75 0.31 0.02
57_L 61_A 0.74 0.31 0.02
6_P 42_F 0.74 0.30 0.02
156_A 12_K 0.74 0.30 0.02
245_S 88_S 0.72 0.29 0.02
238_Q 60_V 0.72 0.29 0.02
226_T 2_S 0.72 0.28 0.02
174_F 40_M 0.72 0.28 0.02
50_S 41_V 0.72 0.28 0.02
15_G 53_S 0.71 0.28 0.02
219_C 50_A 0.71 0.28 0.02
207_F 77_E 0.70 0.27 0.01
22_H 11_S 0.70 0.27 0.01
313_T 30_T 0.70 0.27 0.01
72_N 34_Q 0.69 0.26 0.01
74_V 69_D 0.69 0.26 0.01
112_V 68_S 0.69 0.26 0.01
115_S 102_I 0.68 0.25 0.01
46_M 39_D 0.68 0.24 0.01
9_E 87_D 0.68 0.24 0.01
26_M 29_I 0.67 0.24 0.01
79_K 78_I 0.67 0.24 0.01
35_D 17_L 0.67 0.24 0.01
16_A 95_E 0.67 0.23 0.01
86_S 44_D 0.66 0.23 0.01
67_R 67_A 0.66 0.23 0.01
241_D 98_A 0.66 0.23 0.01
325_I 124_A 0.66 0.23 0.01
73_D 85_L 0.66 0.23 0.01
291_V 34_Q 0.65 0.22 0.01
49_V 85_L 0.65 0.22 0.01
42_T 51_T 0.65 0.22 0.01
121_D 64_V 0.65 0.22 0.01
290_G 44_D 0.64 0.22 0.01
233_M 106_K 0.64 0.22 0.01
112_V 16_W 0.64 0.22 0.01
12_T 11_S 0.64 0.21 0.01
67_R 90_E 0.64 0.21 0.01
124_W 34_Q 0.64 0.21 0.01
343_R 41_V 0.63 0.21 0.01
6_P 96_P 0.63 0.21 0.01
115_S 92_V 0.63 0.21 0.01
326_A 47_E 0.63 0.21 0.01
184_I 103_F 0.63 0.21 0.01
222_G 66_A 0.63 0.20 0.01
268_E 79_V 0.63 0.20 0.01
316_T 34_Q 0.63 0.20 0.01
314_S 39_D 0.62 0.20 0.01
57_L 81_V 0.62 0.20 0.01
125_I 107_A 0.62 0.20 0.01
82_K 68_S 0.62 0.20 0.01
322_G 109_D 0.62 0.20 0.01
58_R 17_L 0.62 0.20 0.01
285_V 75_S 0.62 0.20 0.01
22_H 77_E 0.61 0.19 0.01
319_P 45_L 0.61 0.19 0.01
312_I 69_D 0.61 0.19 0.01
92_S 79_V 0.61 0.19 0.01
43_D 27_V 0.61 0.19 0.01
318_S 100_G 0.60 0.19 0.01
175_F 71_Y 0.60 0.18 0.01
40_V 54_A 0.60 0.18 0.01
314_S 5_P 0.60 0.18 0.01
49_V 68_S 0.60 0.18 0.01
309_E 88_S 0.60 0.18 0.01
111_L 64_V 0.60 0.18 0.01
4_Q 29_I 0.60 0.18 0.01
136_I 97_Y 0.60 0.18 0.01
297_P 78_I 0.59 0.18 0.01
342_I 41_V 0.59 0.18 0.01
156_A 52_V 0.59 0.18 0.01
316_T 39_D 0.59 0.18 0.01
239_E 66_A 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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