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OPENSEQ.org
2wdq_B_A
Genes: A B A+B
Length: 238 588 728
Sequences: 2049 2946 696
Seq/Len: 8.61 5.01 0.96
MirrorTree (Pazo et al. 2001) 0.90
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 0.01 0.01 0.75
2 0.01 0.01 0.77
5 0.01 0.01 0.83
10 0.01 0.01 0.84
20 0.01 0.01 0.84
100 0.01 0.03 0.94
∞ 0.08 0.14 1.41
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
141_E 325_S 1.70 0.87 0.16
23_Y 469_H 1.62 0.83 0.13
144_D 362_T 1.40 0.69 0.07
56_R 207_R 1.31 0.61 0.05
51_F 112_G 1.25 0.56 0.04
47_P 384_F 1.24 0.54 0.04
118_K 477_G 1.24 0.54 0.04
59_V 254_T 1.23 0.53 0.04
181_F 151_Q 1.21 0.52 0.04
215_V 527_A 1.15 0.46 0.03
42_L 336_T 1.13 0.45 0.03
47_P 494_L 1.12 0.43 0.03
198_S 376_E 1.09 0.41 0.03
99_V 523_A 1.07 0.39 0.02
59_V 311_A 1.06 0.38 0.02
193_R 45_H 1.06 0.38 0.02
57_E 329_G 1.06 0.38 0.02
47_P 504_S 1.05 0.38 0.02
141_E 195_A 1.05 0.38 0.02
112_A 471_F 1.04 0.37 0.02
151_L 50_Q 1.04 0.36 0.02
57_E 47_V 1.04 0.36 0.02
19_R 380_V 1.04 0.36 0.02
81_A 20_M 1.03 0.36 0.02
7_I 263_Y 1.03 0.36 0.02
194_L 384_F 1.03 0.35 0.02
11_N 349_V 1.03 0.35 0.02
96_G 463_L 1.03 0.35 0.02
91_I 424_A 1.02 0.35 0.02
49_L 292_S 1.02 0.35 0.02
219_G 473_V 1.02 0.34 0.02
89_I 319_G 1.01 0.34 0.02
57_E 50_Q 1.01 0.34 0.02
185_S 256_G 1.01 0.34 0.02
114_Y 390_A 0.99 0.33 0.02
47_P 209_Y 0.99 0.33 0.02
154_C 50_Q 0.99 0.32 0.02
101_R 193_F 0.99 0.32 0.02
71_N 50_Q 0.98 0.31 0.02
224_R 330_I 0.98 0.31 0.02
105_V 212_T 0.98 0.31 0.02
22_D 10_A 0.97 0.31 0.02
148_E 329_G 0.97 0.31 0.02
151_L 135_A 0.97 0.30 0.02
158_S 137_A 0.96 0.30 0.02
125_G 33_C 0.96 0.30 0.02
99_V 413_R 0.95 0.29 0.02
12_P 362_T 0.95 0.29 0.01
91_I 420_Q 0.95 0.29 0.01
121_L 489_V 0.95 0.29 0.01
193_R 163_E 0.94 0.29 0.01
52_R 163_E 0.94 0.28 0.01
89_I 263_Y 0.94 0.28 0.01
197_L 90_K 0.94 0.28 0.01
10_Y 187_T 0.93 0.28 0.01
92_R 524_Y 0.93 0.28 0.01
120_Y 104_L 0.92 0.27 0.01
25_L 491_R 0.92 0.27 0.01
111_Y 46_T 0.92 0.27 0.01
215_V 319_G 0.92 0.27 0.01
162_F 46_T 0.91 0.26 0.01
148_E 140_R 0.91 0.26 0.01
65_L 546_P 0.91 0.26 0.01
50_S 545_F 0.91 0.26 0.01
186_R 266_N 0.91 0.26 0.01
222_P 165_Y 0.90 0.26 0.01
139_Q 36_L 0.90 0.26 0.01
96_G 353_C 0.90 0.26 0.01
170_I 15_A 0.90 0.26 0.01
101_R 190_V 0.90 0.25 0.01
120_Y 437_V 0.90 0.25 0.01
234_L 323_L 0.89 0.25 0.01
94_L 53_I 0.89 0.25 0.01
177_A 151_Q 0.89 0.25 0.01
202_S 145_L 0.89 0.25 0.01
135_Q 105_P 0.89 0.25 0.01
53_R 50_Q 0.89 0.25 0.01
179_Y 182_A 0.88 0.24 0.01
139_Q 90_K 0.88 0.24 0.01
100_I 426_Q 0.88 0.24 0.01
68_N 23_A 0.88 0.24 0.01
202_S 520_M 0.88 0.24 0.01
58_G 140_R 0.88 0.24 0.01
1_M 545_F 0.87 0.24 0.01
79_I 285_G 0.87 0.24 0.01
108_G 476_E 0.87 0.23 0.01
160_P 137_A 0.87 0.23 0.01
125_G 12_V 0.87 0.23 0.01
209_I 98_E 0.87 0.23 0.01
73_L 179_G 0.86 0.23 0.01
23_Y 151_Q 0.86 0.23 0.01
80_S 488_K 0.86 0.23 0.01
59_V 367_Q 0.86 0.23 0.01
7_I 363_K 0.86 0.23 0.01
25_L 212_T 0.86 0.23 0.01
222_P 134_T 0.86 0.23 0.01
56_R 213_T 0.86 0.23 0.01
167_D 340_V 0.86 0.23 0.01
35_L 459_I 0.86 0.23 0.01
105_V 214_N 0.86 0.23 0.01
38_A 90_K 0.85 0.23 0.01
22_D 199_V 0.85 0.23 0.01
94_L 326_R 0.85 0.22 0.01
30_G 545_F 0.85 0.22 0.01
139_Q 534_T 0.85 0.22 0.01
218_K 337_F 0.85 0.22 0.01
101_R 510_R 0.85 0.22 0.01
222_P 213_T 0.84 0.22 0.01
172_P 38_K 0.84 0.22 0.01
31_R 11_V 0.84 0.22 0.01
10_Y 386_V 0.84 0.22 0.01
47_P 508_T 0.84 0.22 0.01
202_S 251_V 0.84 0.21 0.01
207_H 253_V 0.84 0.21 0.01
59_V 471_F 0.84 0.21 0.01
101_R 197_A 0.83 0.21 0.01
219_G 527_A 0.83 0.21 0.01
169_F 545_F 0.83 0.21 0.01
44_E 345_E 0.83 0.21 0.01
181_F 164_W 0.83 0.21 0.01
172_P 515_E 0.83 0.21 0.01
22_D 226_A 0.83 0.21 0.01
21_Q 529_S 0.83 0.21 0.01
22_D 170_V 0.83 0.21 0.01
58_G 11_V 0.83 0.21 0.01
108_G 409_V 0.83 0.21 0.01
139_Q 11_V 0.83 0.21 0.01
135_Q 250_G 0.83 0.21 0.01
23_Y 70_Y 0.83 0.21 0.01
169_F 27_S 0.83 0.21 0.01
63_D 239_W 0.83 0.21 0.01
35_L 24_L 0.82 0.21 0.01
44_E 190_V 0.82 0.20 0.01
1_M 4_P 0.82 0.20 0.01
230_K 405_L 0.82 0.20 0.01
23_Y 492_E 0.82 0.20 0.01
59_V 534_T 0.82 0.20 0.01
141_E 539_A 0.82 0.20 0.01
153_A 284_A 0.82 0.20 0.01
35_L 167_L 0.81 0.20 0.01
35_L 193_F 0.81 0.20 0.01
98_P 39_V 0.81 0.20 0.01
153_A 209_Y 0.81 0.20 0.01
50_S 225_M 0.81 0.20 0.01
4_E 462_A 0.81 0.20 0.01
209_I 144_A 0.81 0.20 0.01
56_R 145_L 0.81 0.20 0.01
99_V 529_S 0.81 0.20 0.01
231_S 56_A 0.81 0.20 0.01
218_K 80_G 0.81 0.20 0.01
66_N 114_I 0.81 0.20 0.01
146_L 56_A 0.81 0.20 0.01
115_E 527_A 0.80 0.19 0.01
209_I 54_T 0.80 0.19 0.01
11_N 462_A 0.80 0.19 0.01
50_S 482_K 0.80 0.19 0.01
54_S 217_I 0.80 0.19 0.01
116_K 353_C 0.80 0.19 0.01
151_L 17_G 0.80 0.19 0.01
230_K 464_Q 0.80 0.19 0.01
79_I 353_C 0.80 0.19 0.01
156_S 282_D 0.80 0.19 0.01
222_P 47_V 0.80 0.19 0.01
62_S 222_G 0.79 0.19 0.01
179_Y 209_Y 0.79 0.19 0.01
131_R 193_F 0.79 0.19 0.01
218_K 144_A 0.79 0.19 0.01
48_S 521_E 0.79 0.19 0.01
170_I 437_V 0.79 0.19 0.01
166_P 472_S 0.79 0.19 0.01
101_R 12_V 0.79 0.19 0.01
5_F 319_G 0.79 0.18 0.01
50_S 459_I 0.79 0.18 0.01
193_R 119_F 0.79 0.18 0.01
230_K 410_V 0.79 0.18 0.01
81_A 424_A 0.79 0.18 0.01
177_A 246_I 0.78 0.18 0.01
49_L 265_L 0.78 0.18 0.01
62_S 390_A 0.78 0.18 0.01
101_R 367_Q 0.78 0.18 0.01
98_P 349_V 0.78 0.18 0.01
9_R 346_P 0.78 0.18 0.01
101_R 522_T 0.78 0.18 0.01
169_F 476_E 0.78 0.18 0.01
47_P 8_F 0.78 0.18 0.01
57_E 144_A 0.78 0.18 0.01
14_V 459_I 0.78 0.18 0.01
97_L 54_T 0.78 0.18 0.01
63_D 67_W 0.78 0.18 0.01
100_I 459_I 0.78 0.18 0.01
37_D 290_A 0.78 0.18 0.01
63_D 211_S 0.77 0.18 0.01
167_D 473_V 0.77 0.18 0.01
93_P 526_T 0.77 0.18 0.01
186_R 163_E 0.77 0.18 0.01
233_L 159_T 0.77 0.17 0.01
57_E 217_I 0.77 0.17 0.01
56_R 249_A 0.77 0.17 0.01
112_A 523_A 0.77 0.17 0.01
32_D 339_H 0.77 0.17 0.01
181_F 214_N 0.77 0.17 0.01
131_R 97_L 0.77 0.17 0.01
38_A 92_G 0.77 0.17 0.01
58_G 99_L 0.76 0.17 0.01
119_P 235_D 0.76 0.17 0.01
144_D 330_I 0.76 0.17 0.01
35_L 12_V 0.76 0.17 0.01
115_E 35_L 0.76 0.17 0.01
35_L 33_C 0.76 0.17 0.01
154_C 180_C 0.76 0.17 0.01
141_E 11_V 0.76 0.17 0.01
101_R 183_L 0.76 0.17 0.01
51_F 54_T 0.76 0.17 0.01
101_R 37_S 0.76 0.17 0.01
92_R 187_T 0.76 0.17 0.01
70_K 90_K 0.76 0.17 0.01
6_S 480_M 0.76 0.17 0.01
91_I 190_V 0.76 0.17 0.01
116_K 170_V 0.76 0.17 0.01
62_S 45_H 0.75 0.17 0.01
80_S 96_I 0.75 0.17 0.01
170_I 494_L 0.75 0.17 0.01
223_T 325_S 0.75 0.17 0.01
34_M 136_A 0.75 0.17 0.01
38_A 325_S 0.75 0.16 0.01
41_Q 145_L 0.75 0.16 0.01
132_E 100_E 0.75 0.16 0.01
147_Y 402_G 0.75 0.16 0.01
59_V 141_T 0.75 0.16 0.01
57_E 56_A 0.75 0.16 0.01
81_A 66_E 0.75 0.16 0.01
95_P 553_W 0.75 0.16 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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