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OPENSEQ.org
MjA and MjB
Genes: A B A+B
Length: 188 310 494
Sequences: 16261 1912 51
Seq/Len: 86.49 6.17 0.1
MirrorTree (Pazo et al. 2001) 0.47
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 0.04 0.05
2 0.03 0.04 0.06
5 0.03 0.04 0.06
10 0.04 0.04 0.08
20 0.05 0.04 0.10
100 0.12 0.04 0.18
∞ 0.20 0.05 0.34
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
112_F 67_V 1.62 0.24 0.00
4_I 111_D 1.45 0.19 0.00
147_V 292_V 1.37 0.16 0.00
99_A 213_N 1.33 0.15 0.00
53_P 82_V 1.25 0.13 0.00
148_E 285_I 1.24 0.13 0.00
49_L 123_E 1.22 0.13 0.00
138_I 16_K 1.20 0.12 0.00
111_L 261_K 1.18 0.12 0.00
98_Y 262_S 1.18 0.12 0.00
137_E 273_I 1.16 0.11 0.00
143_D 205_K 1.15 0.11 0.00
20_K 277_L 1.14 0.11 0.00
112_F 235_V 1.13 0.11 0.00
37_E 262_S 1.12 0.11 0.00
7_N 114_E 1.11 0.10 0.00
38_I 143_S 1.11 0.10 0.00
155_K 36_V 1.10 0.10 0.00
101_T 165_Y 1.10 0.10 0.00
2_I 178_L 1.09 0.10 0.00
2_I 45_I 1.08 0.10 0.00
137_E 65_E 1.07 0.10 0.00
4_I 120_I 1.07 0.10 0.00
112_F 62_G 1.06 0.10 0.00
13_H 131_A 1.06 0.10 0.00
15_I 205_K 1.05 0.10 0.00
86_Y 151_H 1.04 0.09 0.00
135_G 27_A 1.03 0.09 0.00
62_I 195_V 1.03 0.09 0.00
11_Y 53_F 1.02 0.09 0.00
81_L 100_E 1.02 0.09 0.00
160_V 38_A 1.02 0.09 0.00
135_G 13_E 1.02 0.09 0.00
58_A 89_L 1.02 0.09 0.00
28_I 197_V 1.01 0.09 0.00
184_G 253_W 1.00 0.09 0.00
88_G 192_G 1.00 0.09 0.00
7_N 62_G 0.99 0.08 0.00
147_V 110_I 0.99 0.08 0.00
6_D 242_T 0.99 0.08 0.00
112_F 220_V 0.98 0.08 0.00
91_G 131_A 0.98 0.08 0.00
32_T 178_L 0.98 0.08 0.00
49_L 36_V 0.97 0.08 0.00
36_E 93_K 0.97 0.08 0.00
161_Q 202_T 0.96 0.08 0.00
9_G 131_A 0.96 0.08 0.00
134_E 234_A 0.95 0.08 0.00
50_S 242_T 0.95 0.08 0.00
4_I 277_L 0.95 0.08 0.00
39_E 206_L 0.95 0.08 0.00
90_V 236_V 0.95 0.08 0.00
2_I 300_T 0.95 0.08 0.00
98_Y 230_W 0.94 0.08 0.00
82_I 111_D 0.94 0.08 0.00
32_T 286_T 0.94 0.08 0.00
66_L 158_V 0.94 0.08 0.00
182_V 72_R 0.94 0.08 0.00
162_F 131_A 0.94 0.08 0.00
82_I 153_M 0.93 0.08 0.00
39_E 197_V 0.93 0.07 0.00
93_A 232_Y 0.92 0.07 0.00
88_G 204_E 0.92 0.07 0.00
148_E 122_A 0.92 0.07 0.00
48_I 104_I 0.92 0.07 0.00
5_L 111_D 0.91 0.07 0.00
135_G 50_T 0.91 0.07 0.00
52_G 210_R 0.91 0.07 0.00
49_L 215_I 0.91 0.07 0.00
19_L 131_A 0.90 0.07 0.00
46_G 78_N 0.90 0.07 0.00
157_I 161_L 0.90 0.07 0.00
157_I 273_I 0.90 0.07 0.00
14_R 23_K 0.90 0.07 0.00
174_E 292_V 0.90 0.07 0.00
73_L 179_P 0.90 0.07 0.00
27_K 173_A 0.89 0.07 0.00
46_G 143_S 0.89 0.07 0.00
52_G 233_F 0.89 0.07 0.00
157_I 93_K 0.88 0.07 0.00
96_E 82_V 0.88 0.07 0.00
121_A 86_D 0.88 0.07 0.00
81_L 47_D 0.87 0.07 0.00
5_L 300_T 0.87 0.07 0.00
4_I 171_L 0.87 0.07 0.00
28_I 155_L 0.87 0.07 0.00
142_S 131_A 0.86 0.07 0.00
138_I 203_E 0.86 0.07 0.00
97_E 38_A 0.86 0.07 0.00
99_A 242_T 0.86 0.07 0.00
92_R 174_K 0.86 0.07 0.00
94_E 207_N 0.86 0.07 0.00
28_I 174_K 0.86 0.07 0.00
1_M 218_E 0.86 0.07 0.00
47_I 216_V 0.86 0.07 0.00
19_L 124_V 0.86 0.07 0.00
175_I 77_L 0.86 0.07 0.00
19_L 209_C 0.86 0.07 0.00
133_P 276_D 0.85 0.07 0.00
184_G 96_T 0.85 0.07 0.00
27_K 56_T 0.85 0.07 0.00
164_P 169_V 0.85 0.07 0.00
180_C 48_K 0.85 0.07 0.00
81_L 288_E 0.85 0.06 0.00
50_S 38_A 0.85 0.06 0.00
110_D 26_I 0.85 0.06 0.00
1_M 262_S 0.84 0.06 0.00
129_V 224_N 0.84 0.06 0.00
6_D 61_K 0.84 0.06 0.00
47_I 53_F 0.84 0.06 0.00
45_K 107_K 0.84 0.06 0.00
3_V 86_D 0.84 0.06 0.00
5_L 252_N 0.84 0.06 0.00
90_V 76_G 0.84 0.06 0.00
109_N 200_E 0.84 0.06 0.00
72_I 178_L 0.84 0.06 0.00
92_R 296_V 0.83 0.06 0.00
86_Y 148_A 0.83 0.06 0.00
40_S 198_L 0.83 0.06 0.00
140_A 307_I 0.83 0.06 0.00
182_V 123_E 0.83 0.06 0.00
5_L 114_E 0.83 0.06 0.00
130_K 62_G 0.83 0.06 0.00
32_T 27_A 0.83 0.06 0.00
177_K 291_N 0.83 0.06 0.00
5_L 45_I 0.82 0.06 0.00
30_P 259_M 0.82 0.06 0.00
58_A 285_I 0.82 0.06 0.00
177_K 297_F 0.82 0.06 0.00
31_N 130_I 0.82 0.06 0.00
96_E 154_V 0.82 0.06 0.00
98_Y 82_V 0.82 0.06 0.00
162_F 77_L 0.82 0.06 0.00
70_L 253_W 0.82 0.06 0.00
171_Y 273_I 0.82 0.06 0.00
93_A 186_Q 0.82 0.06 0.00
23_G 278_L 0.82 0.06 0.00
52_G 87_R 0.82 0.06 0.00
103_V 253_W 0.82 0.06 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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