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OPENSEQ.org
1I2M_AB
Genes: A B A+B
Length: 216 402 563
Sequences: 5399 3675 112
Seq/Len: 25 9.14 0.2
MirrorTree (Pazo et al. 2001) 0.30
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 0.03 0.05 0.01
2 0.04 0.05 0.03
5 0.04 0.06 0.05
10 0.06 0.06 0.09
20 0.07 0.06 0.18
100 0.14 0.08 0.60
∞ 0.20 0.14 1.31
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
117_I 243_Y 1.51 0.33 0.00
106_R 331_V 1.31 0.23 0.00
20_G 252_Q 1.29 0.22 0.00
18_D 70_Y 1.22 0.19 0.00
151_A 388_G 1.20 0.18 0.00
18_D 176_T 1.15 0.17 0.00
18_D 21_L 1.13 0.16 0.00
156_N 66_S 1.13 0.16 0.00
115_I 333_C 1.09 0.15 0.00
108_L 274_T 1.07 0.14 0.00
151_A 186_G 1.05 0.14 0.00
134_K 392_T 1.05 0.14 0.00
111_V 69_V 1.03 0.13 0.00
16_V 322_I 1.02 0.13 0.00
147_Y 231_Y 1.01 0.13 0.00
120_C 341_V 1.01 0.13 0.00
65_D 73_G 0.99 0.12 0.00
14_V 53_A 0.98 0.12 0.00
135_S 342_T 0.97 0.12 0.00
101_V 40_K 0.97 0.12 0.00
141_K 277_W 0.97 0.12 0.00
43_L 292_S 0.97 0.12 0.00
151_A 246_G 0.96 0.11 0.00
46_E 333_C 0.96 0.11 0.00
153_S 277_W 0.95 0.11 0.00
83_A 116_T 0.95 0.11 0.00
13_L 344_D 0.95 0.11 0.00
29_R 266_N 0.94 0.11 0.00
124_V 114_A 0.94 0.11 0.00
30_H 155_V 0.93 0.11 0.00
121_G 22_G 0.93 0.11 0.00
123_K 186_G 0.93 0.11 0.00
18_D 314_E 0.92 0.10 0.00
24_T 98_L 0.92 0.10 0.00
114_N 290_M 0.92 0.10 0.00
98_Y 168_L 0.91 0.10 0.00
117_I 330_S 0.91 0.10 0.00
139_H 319_P 0.91 0.10 0.00
80_Y 161_G 0.91 0.10 0.00
100_N 176_T 0.91 0.10 0.00
19_G 46_I 0.91 0.10 0.00
24_T 302_A 0.91 0.10 0.00
100_N 96_V 0.91 0.10 0.00
156_N 151_L 0.90 0.10 0.00
97_T 273_S 0.90 0.10 0.00
17_G 246_G 0.90 0.10 0.00
125_D 246_G 0.90 0.10 0.00
159_K 19_L 0.90 0.10 0.00
90_F 89_S 0.89 0.10 0.00
88_I 84_T 0.88 0.10 0.00
43_L 357_Q 0.88 0.10 0.00
87_I 333_C 0.88 0.09 0.00
143_N 226_A 0.87 0.09 0.00
58_P 328_V 0.87 0.09 0.00
59_I 143_S 0.87 0.09 0.00
10_Q 236_I 0.86 0.09 0.00
83_A 363_D 0.86 0.09 0.00
20_G 228_C 0.86 0.09 0.00
66_T 73_G 0.86 0.09 0.00
133_A 277_W 0.86 0.09 0.00
22_G 334_G 0.85 0.09 0.00
23_K 334_G 0.85 0.09 0.00
120_C 121_V 0.85 0.09 0.00
138_F 233_T 0.85 0.09 0.00
83_A 117_D 0.84 0.09 0.00
121_G 280_F 0.84 0.09 0.00
5_G 166_V 0.84 0.09 0.00
92_V 170_A 0.83 0.09 0.00
90_F 19_L 0.83 0.09 0.00
50_L 154_P 0.83 0.09 0.00
135_S 134_I 0.83 0.09 0.00
14_V 116_T 0.83 0.09 0.00
97_T 19_L 0.83 0.09 0.00
151_A 178_G 0.82 0.08 0.00
17_G 22_G 0.82 0.08 0.00
125_D 22_G 0.82 0.08 0.00
155_Y 290_M 0.82 0.08 0.00
87_I 53_A 0.82 0.08 0.00
86_A 72_F 0.82 0.08 0.00
152_K 299_L 0.82 0.08 0.00
65_D 246_G 0.82 0.08 0.00
152_K 73_G 0.82 0.08 0.00
113_E 159_A 0.82 0.08 0.00
24_T 190_E 0.82 0.08 0.00
90_F 275_K 0.82 0.08 0.00
145_Q 50_V 0.81 0.08 0.00
139_H 174_L 0.81 0.08 0.00
13_L 19_L 0.81 0.08 0.00
31_L 155_V 0.81 0.08 0.00
109_V 385_V 0.81 0.08 0.00
13_L 365_D 0.81 0.08 0.00
146_Y 294_G 0.81 0.08 0.00
38_K 333_C 0.81 0.08 0.00
159_K 69_V 0.81 0.08 0.00
141_K 176_T 0.80 0.08 0.00
65_D 264_P 0.80 0.08 0.00
120_C 101_K 0.80 0.08 0.00
20_G 231_Y 0.80 0.08 0.00
98_Y 235_A 0.80 0.08 0.00
17_G 73_G 0.79 0.08 0.00
125_D 73_G 0.79 0.08 0.00
90_F 87_E 0.79 0.08 0.00
114_N 306_R 0.79 0.08 0.00
54_T 166_V 0.79 0.08 0.00
88_I 93_P 0.79 0.08 0.00
122_N 236_I 0.79 0.08 0.00
58_P 117_D 0.79 0.08 0.00
13_L 172_G 0.79 0.08 0.00
165_A 301_R 0.78 0.08 0.00
150_S 73_G 0.78 0.08 0.00
115_I 253_L 0.78 0.08 0.00
81_I 345_G 0.78 0.08 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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