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OPENSEQ.org
has
Genes: A B A+B
Length: 317 263 560
Sequences: 5021 2971 162
Seq/Len: 15.84 11.3 0.29
MirrorTree (Pazo et al. 2001) 0.62
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.06 0.01 0.03
2 0.06 0.01 0.08
5 0.09 0.02 0.16
10 0.12 0.02 0.24
20 0.14 0.04 0.28
100 0.20 0.05 0.57
∞ 0.23 0.12 1.12
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
42_H 200_T 1.20 0.23 0.00
11_Q 67_K 1.19 0.23 0.00
208_V 224_E 1.18 0.23 0.00
141_L 31_V 1.15 0.21 0.00
289_L 60_P 1.14 0.21 0.00
137_S 82_S 1.13 0.21 0.00
295_G 24_V 1.13 0.20 0.00
44_A 85_P 1.11 0.20 0.00
152_L 183_P 1.11 0.20 0.00
303_L 212_L 1.11 0.20 0.00
155_G 205_G 1.11 0.20 0.00
92_A 21_L 1.10 0.19 0.00
118_G 54_V 1.08 0.18 0.00
99_V 197_V 1.07 0.18 0.00
134_D 165_E 1.05 0.17 0.00
138_A 52_V 1.05 0.17 0.00
137_S 84_P 1.04 0.17 0.00
113_Y 27_L 1.04 0.17 0.00
256_L 240_A 1.03 0.16 0.00
59_L 201_L 1.02 0.16 0.00
137_S 201_L 1.02 0.16 0.00
308_L 95_D 1.01 0.16 0.00
89_A 25_L 1.01 0.16 0.00
205_S 195_G 1.00 0.15 0.00
15_W 217_G 0.99 0.15 0.00
35_W 216_A 0.99 0.15 0.00
174_V 120_P 0.99 0.15 0.00
139_I 131_P 0.99 0.15 0.00
147_E 212_L 0.99 0.15 0.00
223_Q 12_G 0.98 0.15 0.00
133_L 62_A 0.98 0.15 0.00
10_Q 184_K 0.98 0.15 0.00
285_G 225_I 0.98 0.15 0.00
121_R 229_V 0.98 0.14 0.00
137_S 256_F 0.98 0.14 0.00
88_A 124_P 0.97 0.14 0.00
150_V 106_K 0.97 0.14 0.00
284_S 66_A 0.97 0.14 0.00
291_K 120_P 0.97 0.14 0.00
29_R 256_F 0.97 0.14 0.00
31_A 47_V 0.97 0.14 0.00
133_L 221_L 0.96 0.14 0.00
289_L 86_E 0.96 0.14 0.00
12_A 186_A 0.96 0.14 0.00
85_W 197_V 0.95 0.14 0.00
42_H 251_T 0.95 0.14 0.00
201_V 254_I 0.95 0.14 0.00
95_V 233_S 0.95 0.14 0.00
126_P 32_A 0.95 0.14 0.00
185_G 225_I 0.94 0.13 0.00
305_A 197_V 0.94 0.13 0.00
15_W 215_S 0.94 0.13 0.00
204_H 171_R 0.94 0.13 0.00
182_Q 25_L 0.94 0.13 0.00
307_Q 242_A 0.94 0.13 0.00
198_D 194_V 0.93 0.13 0.00
98_G 30_L 0.93 0.13 0.00
152_L 186_A 0.93 0.13 0.00
208_V 145_G 0.93 0.13 0.00
255_P 225_I 0.92 0.13 0.00
89_A 197_V 0.92 0.13 0.00
283_V 236_P 0.92 0.13 0.00
194_E 25_L 0.92 0.13 0.00
45_A 216_A 0.91 0.12 0.00
285_G 193_G 0.91 0.12 0.00
45_A 217_G 0.91 0.12 0.00
223_Q 147_A 0.91 0.12 0.00
34_A 52_V 0.91 0.12 0.00
189_S 202_D 0.90 0.12 0.00
207_R 63_P 0.90 0.12 0.00
260_L 43_E 0.90 0.12 0.00
11_Q 187_L 0.90 0.12 0.00
208_V 107_Q 0.89 0.12 0.00
208_V 212_L 0.89 0.12 0.00
218_V 105_P 0.89 0.12 0.00
168_E 209_A 0.89 0.12 0.00
227_Y 48_P 0.88 0.12 0.00
15_W 222_D 0.88 0.12 0.00
121_R 224_E 0.88 0.12 0.00
150_V 88_L 0.88 0.12 0.00
150_V 162_Q 0.87 0.11 0.00
251_I 25_L 0.87 0.11 0.00
227_Y 230_K 0.87 0.11 0.00
66_A 89_P 0.87 0.11 0.00
292_L 207_V 0.87 0.11 0.00
181_T 251_T 0.87 0.11 0.00
119_E 223_R 0.87 0.11 0.00
82_W 212_L 0.86 0.11 0.00
246_R 27_L 0.86 0.11 0.00
168_E 81_P 0.86 0.11 0.00
123_V 26_A 0.86 0.11 0.00
50_R 256_F 0.86 0.11 0.00
158_Y 229_V 0.86 0.11 0.00
44_A 20_C 0.86 0.11 0.00
10_Q 146_R 0.86 0.11 0.00
285_G 221_L 0.85 0.11 0.00
268_G 123_P 0.85 0.11 0.00
221_Q 209_A 0.85 0.11 0.00
138_A 190_K 0.85 0.11 0.00
263_L 170_S 0.85 0.11 0.00
188_F 231_R 0.85 0.11 0.00
35_W 183_P 0.85 0.11 0.00
51_L 214_S 0.85 0.11 0.00
125_L 205_G 0.84 0.11 0.00
263_L 52_V 0.84 0.11 0.00
197_V 211_T 0.84 0.11 0.00
288_A 258_L 0.84 0.11 0.00
116_V 41_K 0.84 0.11 0.00
263_L 91_V 0.84 0.11 0.00
150_V 71_G 0.84 0.11 0.00
265_R 27_L 0.84 0.11 0.00
5_T 26_A 0.84 0.11 0.00
37_A 120_P 0.84 0.11 0.00
299_I 226_Q 0.84 0.10 0.00
289_L 25_L 0.84 0.10 0.00
10_Q 131_P 0.84 0.10 0.00
129_S 90_L 0.84 0.10 0.00
279_R 21_L 0.84 0.10 0.00
225_A 21_L 0.84 0.10 0.00
155_G 182_Y 0.84 0.10 0.00
142_A 203_R 0.83 0.10 0.00
117_R 168_W 0.83 0.10 0.00
204_H 201_L 0.83 0.10 0.00
8_A 180_K 0.83 0.10 0.00
232_L 29_L 0.83 0.10 0.00
95_V 190_K 0.83 0.10 0.00
41_Q 189_L 0.83 0.10 0.00
108_R 224_E 0.83 0.10 0.00
25_P 22_V 0.83 0.10 0.00
129_S 129_I 0.82 0.10 0.00
25_P 23_L 0.82 0.10 0.00
5_T 258_L 0.82 0.10 0.00
38_A 67_K 0.82 0.10 0.00
11_Q 184_K 0.82 0.10 0.00
186_T 190_K 0.82 0.10 0.00
181_T 201_L 0.82 0.10 0.00
111_A 81_P 0.82 0.10 0.00
303_L 23_L 0.82 0.10 0.00
292_L 231_R 0.82 0.10 0.00
151_R 26_A 0.81 0.10 0.00
275_N 67_K 0.81 0.10 0.00
150_V 67_K 0.81 0.10 0.00
182_Q 107_Q 0.81 0.10 0.00
137_S 225_I 0.81 0.10 0.00
284_S 129_I 0.81 0.10 0.00
12_A 215_S 0.81 0.10 0.00
115_T 20_C 0.81 0.10 0.00
6_A 122_T 0.81 0.10 0.00
96_S 226_Q 0.81 0.10 0.00
249_L 51_A 0.81 0.10 0.00
145_A 109_K 0.81 0.10 0.00
129_S 207_V 0.81 0.10 0.00
95_V 158_T 0.81 0.10 0.00
131_V 208_L 0.81 0.10 0.00
138_A 63_P 0.80 0.10 0.00
208_V 230_K 0.80 0.10 0.00
28_R 123_P 0.80 0.10 0.00
127_D 205_G 0.80 0.10 0.00
304_S 93_A 0.80 0.10 0.00
172_F 20_C 0.80 0.10 0.00
131_V 97_T 0.80 0.10 0.00
168_E 258_L 0.80 0.10 0.00
206_V 231_R 0.80 0.10 0.00
63_Q 70_P 0.80 0.10 0.00
133_L 219_P 0.80 0.10 0.00
265_R 89_P 0.79 0.10 0.00
155_G 193_G 0.79 0.09 0.00
208_V 219_P 0.79 0.09 0.00
158_Y 22_V 0.79 0.09 0.00
172_F 122_T 0.79 0.09 0.00
143_Y 254_I 0.79 0.09 0.00
18_S 54_V 0.79 0.09 0.00
126_P 22_V 0.79 0.09 0.00
244_W 205_G 0.79 0.09 0.00
46_L 207_V 0.79 0.09 0.00
286_V 186_A 0.79 0.09 0.00
299_I 97_T 0.79 0.09 0.00
181_T 110_P 0.79 0.09 0.00
100_Y 224_E 0.79 0.09 0.00
150_V 89_P 0.79 0.09 0.00
39_D 103_V 0.79 0.09 0.00
220_A 130_A 0.78 0.09 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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