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OPENSEQ.org
3pnl_B_A
Genes: A B A+B
Length: 211 357 529
Sequences: 2044 1718 847
Seq/Len: 9.69 4.81 1.6
MirrorTree (Pazo et al. 2001) 0.71
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 0.01 1.43
2 0.05 0.07 1.46
5 0.05 0.09 1.49
10 0.05 0.10 1.49
20 0.05 0.10 1.49
100 0.06 0.11 1.50
∞ 0.09 0.14 1.51
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
90_I 120_L 1.39 0.81 0.07
90_I 123_D 1.26 0.72 0.05
91_R 119_E 1.12 0.58 0.03
121_R 115_E 1.12 0.58 0.03
80_A 80_T 1.08 0.54 0.03
43_M 212_M 1.01 0.47 0.02
182_Y 108_T 0.98 0.44 0.02
29_G 202_K 0.98 0.44 0.02
39_H 84_P 0.98 0.44 0.02
34_I 80_T 0.94 0.39 0.02
73_L 80_T 0.93 0.38 0.02
37_A 152_A 0.92 0.38 0.02
121_R 119_E 0.92 0.38 0.02
32_R 204_S 0.91 0.37 0.02
140_E 11_D 0.90 0.36 0.02
73_L 77_E 0.90 0.35 0.01
123_K 115_E 0.89 0.35 0.01
94_Q 123_D 0.88 0.34 0.01
13_L 35_Y 0.85 0.31 0.01
118_V 98_E 0.85 0.31 0.01
197_S 84_P 0.83 0.29 0.01
193_P 138_A 0.83 0.29 0.01
75_S 85_D 0.82 0.29 0.01
200_F 297_V 0.82 0.28 0.01
81_S 73_A 0.81 0.28 0.01
135_W 204_S 0.81 0.28 0.01
79_G 58_E 0.81 0.28 0.01
131_M 84_P 0.80 0.27 0.01
165_S 127_K 0.80 0.27 0.01
182_Y 61_H 0.80 0.26 0.01
33_E 187_S 0.79 0.26 0.01
77_V 80_T 0.78 0.25 0.01
45_R 80_T 0.78 0.25 0.01
42_N 80_T 0.76 0.24 0.01
125_E 89_E 0.75 0.23 0.01
182_Y 105_K 0.75 0.23 0.01
61_D 112_L 0.74 0.22 0.01
81_S 61_H 0.74 0.22 0.01
80_A 115_E 0.74 0.22 0.01
81_S 105_K 0.74 0.22 0.01
39_H 58_E 0.73 0.22 0.01
78_G 58_E 0.73 0.22 0.01
92_A 72_G 0.73 0.22 0.01
182_Y 147_G 0.73 0.21 0.01
71_M 321_C 0.73 0.21 0.01
45_R 77_E 0.72 0.21 0.01
42_N 105_K 0.72 0.20 0.01
39_H 292_S 0.71 0.20 0.01
75_S 120_L 0.71 0.20 0.01
79_G 352_A 0.71 0.20 0.01
142_L 112_L 0.71 0.20 0.01
13_L 155_V 0.71 0.20 0.01
42_N 158_E 0.71 0.20 0.01
37_A 74_C 0.70 0.20 0.01
107_L 351_P 0.70 0.20 0.01
94_Q 125_G 0.70 0.20 0.01
163_A 71_S 0.70 0.20 0.01
207_L 236_V 0.70 0.19 0.01
182_Y 154_T 0.70 0.19 0.01
9_I 101_L 0.70 0.19 0.01
51_V 132_V 0.69 0.19 0.01
83_P 58_E 0.69 0.19 0.01
81_S 64_Y 0.69 0.19 0.01
83_P 292_S 0.69 0.19 0.01
177_K 105_K 0.69 0.19 0.01
122_G 114_F 0.69 0.19 0.01
198_V 80_T 0.69 0.19 0.01
147_E 349_H 0.69 0.18 0.01
181_S 147_G 0.69 0.18 0.01
109_Q 8_D 0.68 0.18 0.01
87_T 222_P 0.68 0.18 0.01
18_D 22_K 0.68 0.18 0.01
92_A 236_V 0.68 0.18 0.01
202_M 327_T 0.68 0.18 0.01
79_G 154_T 0.68 0.18 0.01
13_L 156_L 0.67 0.18 0.01
29_G 240_F 0.67 0.17 0.01
41_L 200_A 0.66 0.17 0.01
197_S 80_T 0.66 0.17 0.01
103_T 240_F 0.66 0.17 0.01
9_I 229_F 0.66 0.17 0.01
81_S 154_T 0.66 0.17 0.01
171_I 283_V 0.66 0.17 0.01
72_T 50_L 0.66 0.17 0.01
187_S 231_S 0.65 0.17 0.01
180_A 51_S 0.65 0.17 0.01
202_M 133_I 0.65 0.16 0.01
81_S 58_E 0.65 0.16 0.01
28_T 146_A 0.65 0.16 0.01
42_N 81_S 0.65 0.16 0.01
49_K 331_I 0.65 0.16 0.01
180_A 197_V 0.65 0.16 0.01
56_A 233_D 0.64 0.16 0.01
32_R 112_L 0.64 0.16 0.01
37_A 153_N 0.64 0.16 0.01
105_E 307_Q 0.64 0.16 0.01
182_Y 70_L 0.64 0.16 0.01
181_S 324_L 0.64 0.16 0.01
81_S 218_I 0.64 0.15 0.01
43_M 49_L 0.64 0.15 0.01
173_M 298_Y 0.64 0.15 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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