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OPENSEQ.org
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Genes: A B A+B
Length: 223 439 607
Sequences: 517 5051 402
Seq/Len: 2.32 11.51 0.66
MirrorTree (Pazo et al. 2001) 0.66
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 0.00 0.14 0.59
2 0.00 0.43 0.59
5 0.00 0.44 0.59
10 0.00 0.45 0.60
20 0.00 0.45 0.61
100 0.00 0.47 0.62
∞ 0.03 0.50 0.65
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
198_S 190_V 1.85 0.85 0.14
106_M 220_V 1.51 0.66 0.06
80_A 430_T 1.45 0.61 0.05
126_V 282_R 1.32 0.50 0.03
175_V 382_K 1.29 0.48 0.03
178_D 27_V 1.28 0.47 0.03
196_D 156_L 1.20 0.40 0.02
201_G 151_R 1.19 0.40 0.02
195_I 229_P 1.17 0.38 0.02
79_E 115_F 1.17 0.38 0.02
202_Q 185_S 1.15 0.36 0.02
149_N 336_I 1.14 0.35 0.02
48_S 417_L 1.12 0.34 0.02
144_V 180_A 1.12 0.34 0.02
153_A 243_I 1.11 0.33 0.02
206_L 119_H 1.09 0.32 0.01
104_Q 238_F 1.09 0.32 0.01
114_V 265_A 1.07 0.30 0.01
102_V 205_E 1.06 0.30 0.01
135_L 71_A 1.06 0.30 0.01
49_A 353_V 1.05 0.29 0.01
146_V 144_T 1.05 0.29 0.01
153_A 353_V 1.04 0.29 0.01
197_A 216_L 1.04 0.28 0.01
134_A 41_G 1.04 0.28 0.01
204_E 380_L 1.04 0.28 0.01
211_S 348_Y 1.03 0.28 0.01
80_A 414_R 1.03 0.28 0.01
172_Y 309_A 1.01 0.27 0.01
57_I 114_P 1.00 0.26 0.01
153_A 316_E 1.00 0.26 0.01
149_N 155_G 1.00 0.26 0.01
126_V 179_L 0.99 0.26 0.01
181_L 222_V 0.99 0.25 0.01
194_I 400_D 0.99 0.25 0.01
156_I 107_V 0.99 0.25 0.01
69_K 72_L 0.98 0.25 0.01
186_C 178_L 0.98 0.24 0.01
149_N 117_G 0.98 0.24 0.01
43_T 177_T 0.97 0.24 0.01
103_E 316_E 0.97 0.24 0.01
43_T 72_L 0.96 0.23 0.01
156_I 205_E 0.96 0.23 0.01
156_I 380_L 0.95 0.23 0.01
80_A 390_L 0.95 0.23 0.01
189_E 322_E 0.95 0.23 0.01
157_R 271_I 0.95 0.23 0.01
64_V 194_A 0.95 0.23 0.01
203_I 94_M 0.94 0.23 0.01
213_T 205_E 0.94 0.22 0.01
144_V 109_D 0.94 0.22 0.01
198_S 280_T 0.94 0.22 0.01
156_I 222_V 0.94 0.22 0.01
142_K 72_L 0.93 0.22 0.01
208_R 403_A 0.93 0.22 0.01
118_L 216_L 0.93 0.21 0.01
118_L 320_M 0.93 0.21 0.01
55_E 397_K 0.93 0.21 0.01
139_S 182_L 0.92 0.21 0.01
95_C 239_V 0.92 0.21 0.01
95_C 115_F 0.92 0.21 0.01
202_Q 50_L 0.92 0.21 0.01
131_V 144_T 0.91 0.21 0.01
144_V 261_V 0.91 0.21 0.01
45_E 101_E 0.91 0.21 0.01
158_E 220_V 0.91 0.20 0.01
118_L 24_R 0.91 0.20 0.01
153_A 133_A 0.91 0.20 0.01
53_D 46_E 0.90 0.20 0.01
131_V 437_L 0.90 0.20 0.01
186_C 396_Q 0.90 0.20 0.01
138_V 194_A 0.90 0.20 0.01
189_E 167_I 0.90 0.20 0.01
173_L 380_L 0.90 0.20 0.01
81_R 429_E 0.90 0.20 0.01
39_S 343_A 0.90 0.20 0.01
48_S 218_K 0.89 0.20 0.01
160_I 360_V 0.89 0.20 0.01
195_I 222_V 0.89 0.20 0.01
56_K 431_L 0.89 0.20 0.01
197_A 223_V 0.89 0.20 0.01
106_M 137_M 0.89 0.20 0.01
207_S 230_S 0.89 0.19 0.01
62_Q 190_V 0.89 0.19 0.01
122_D 406_A 0.89 0.19 0.01
71_L 137_M 0.88 0.19 0.01
208_R 407_I 0.88 0.19 0.01
118_L 165_M 0.88 0.19 0.01
62_Q 348_Y 0.87 0.19 0.01
61_A 353_V 0.87 0.19 0.01
129_Q 109_D 0.87 0.18 0.01
130_V 218_K 0.87 0.18 0.01
202_Q 154_D 0.86 0.18 0.01
193_G 237_G 0.86 0.18 0.01
198_S 327_E 0.86 0.18 0.01
146_V 90_P 0.86 0.18 0.01
77_M 156_L 0.86 0.18 0.01
206_L 375_D 0.86 0.18 0.01
106_M 231_M 0.86 0.18 0.01
48_S 150_I 0.86 0.18 0.01
55_E 82_I 0.85 0.18 0.01
188_L 214_E 0.85 0.18 0.01
72_G 249_D 0.85 0.18 0.01
126_V 327_E 0.85 0.17 0.01
193_G 134_P 0.85 0.17 0.01
175_V 421_T 0.85 0.17 0.01
135_L 220_V 0.85 0.17 0.01
210_I 375_D 0.85 0.17 0.01
152_Q 385_E 0.85 0.17 0.01
205_A 353_V 0.84 0.17 0.01
125_D 207_I 0.84 0.17 0.01
149_N 151_R 0.84 0.17 0.01
185_G 285_P 0.84 0.17 0.01
178_D 244_A 0.84 0.17 0.01
163_V 69_H 0.84 0.17 0.01
187_I 54_D 0.84 0.17 0.01
146_V 187_E 0.84 0.17 0.01
113_A 70_Q 0.84 0.17 0.01
196_D 253_R 0.84 0.17 0.01
153_A 97_V 0.83 0.17 0.01
125_D 158_T 0.83 0.17 0.01
93_L 103_L 0.83 0.17 0.01
74_Q 110_G 0.83 0.17 0.01
53_D 190_V 0.83 0.16 0.01
152_Q 106_Q 0.82 0.16 0.01
47_I 433_L 0.82 0.16 0.01
207_S 244_A 0.82 0.16 0.01
140_N 290_A 0.82 0.16 0.01
189_E 315_V 0.82 0.16 0.01
68_Q 365_V 0.82 0.16 0.01
90_E 345_A 0.82 0.16 0.01
143_Q 76_L 0.81 0.16 0.01
205_A 22_Q 0.81 0.16 0.01
61_A 436_T 0.81 0.16 0.01
193_G 133_A 0.81 0.16 0.01
142_K 357_A 0.81 0.16 0.01
202_Q 155_G 0.81 0.16 0.01
174_E 285_P 0.81 0.16 0.01
115_R 296_M 0.81 0.16 0.01
127_T 129_V 0.81 0.16 0.01
112_L 113_Q 0.81 0.16 0.01
94_Q 165_M 0.81 0.15 0.01
198_S 24_R 0.81 0.15 0.01
57_I 111_L 0.81 0.15 0.01
192_V 238_F 0.81 0.15 0.01
96_Q 204_R 0.81 0.15 0.01
143_Q 218_K 0.80 0.15 0.01
179_A 380_L 0.80 0.15 0.01
186_C 179_L 0.80 0.15 0.01
138_V 242_S 0.80 0.15 0.01
149_N 280_T 0.80 0.15 0.01
114_V 20_L 0.80 0.15 0.01
193_G 82_I 0.80 0.15 0.01
144_V 99_V 0.80 0.15 0.01
208_R 421_T 0.80 0.15 0.01
127_T 81_G 0.80 0.15 0.01
199_I 422_H 0.80 0.15 0.01
205_A 289_F 0.80 0.15 0.01
47_I 348_Y 0.80 0.15 0.01
207_S 110_G 0.79 0.15 0.01
202_Q 327_E 0.79 0.15 0.01
48_S 59_L 0.79 0.15 0.01
152_Q 220_V 0.79 0.15 0.01
139_S 310_L 0.79 0.15 0.01
126_V 151_R 0.79 0.15 0.01
43_T 282_R 0.79 0.15 0.01
75_A 213_E 0.79 0.15 0.01
37_Y 229_P 0.79 0.15 0.00
203_I 241_T 0.79 0.15 0.00
84_Q 290_A 0.78 0.14 0.00
88_I 30_V 0.78 0.14 0.00
80_A 156_L 0.78 0.14 0.00
68_Q 360_V 0.78 0.14 0.00
62_Q 284_Y 0.78 0.14 0.00
206_L 145_P 0.78 0.14 0.00
178_D 434_L 0.78 0.14 0.00
117_I 184_R 0.78 0.14 0.00
108_E 218_K 0.78 0.14 0.00
106_M 368_E 0.78 0.14 0.00
209_A 352_D 0.78 0.14 0.00
197_A 137_M 0.78 0.14 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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.45 > 0.4) of paralogs.
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