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OPENSEQ.org
1-2
Genes: A B A+B
Length: 388 452 756
Sequences: 4352 6410 550
Seq/Len: 11.22 14.18 0.73
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 0.05 0.06 0.21
2 0.05 0.06 0.26
5 0.06 0.06 0.47
10 0.06 0.06 0.54
20 0.07 0.06 0.65
100 0.08 0.10 0.99
∞ 0.15 0.22 2.47
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
370_K 270_T 1.09 0.34 0.00
189_T 265_A 1.06 0.32 0.00
124_I 238_I 1.04 0.30 0.00
135_F 417_T 1.03 0.30 0.00
373_V 199_L 1.03 0.30 0.00
284_Y 350_G 1.01 0.29 0.00
29_V 68_D 0.99 0.27 0.00
276_F 368_Q 0.99 0.27 0.00
144_V 385_V 0.98 0.26 0.00
52_V 298_C 0.97 0.26 0.00
139_V 251_V 0.96 0.25 0.00
149_L 261_P 0.96 0.25 0.00
160_T 146_V 0.96 0.25 0.00
202_V 437_G 0.95 0.25 0.00
116_I 384_E 0.95 0.24 0.00
97_T 212_I 0.94 0.24 0.00
322_R 425_I 0.94 0.24 0.00
133_A 226_V 0.94 0.24 0.00
175_W 109_V 0.92 0.22 0.00
280_I 217_A 0.91 0.22 0.00
106_L 413_S 0.90 0.21 0.00
203_I 262_L 0.89 0.21 0.00
170_L 383_I 0.89 0.21 0.00
94_S 222_F 0.89 0.21 0.00
296_E 23_P 0.88 0.20 0.00
356_L 69_F 0.88 0.20 0.00
305_E 365_M 0.88 0.20 0.00
53_L 159_V 0.88 0.20 0.00
175_W 412_H 0.86 0.19 0.00
149_L 102_A 0.86 0.19 0.00
375_L 359_C 0.86 0.19 0.00
156_I 251_V 0.86 0.19 0.00
94_S 175_A 0.86 0.19 0.00
67_F 439_W 0.85 0.19 0.00
150_A 382_G 0.85 0.19 0.00
171_I 225_K 0.85 0.19 0.00
33_I 290_V 0.85 0.19 0.00
124_I 217_A 0.85 0.18 0.00
281_G 374_V 0.85 0.18 0.00
131_V 261_P 0.84 0.18 0.00
151_M 257_S 0.84 0.18 0.00
307_E 371_K 0.84 0.18 0.00
260_V 225_K 0.83 0.18 0.00
220_N 94_L 0.83 0.18 0.00
284_Y 170_G 0.83 0.18 0.00
266_R 155_K 0.83 0.17 0.00
202_V 157_L 0.83 0.17 0.00
273_L 432_A 0.82 0.17 0.00
142_V 161_V 0.82 0.17 0.00
356_L 332_F 0.82 0.17 0.00
151_M 137_L 0.82 0.17 0.00
206_A 265_A 0.82 0.17 0.00
170_L 423_V 0.82 0.17 0.00
189_T 123_L 0.82 0.17 0.00
375_L 155_K 0.81 0.17 0.00
188_E 376_C 0.81 0.17 0.00
373_V 324_D 0.81 0.16 0.00
260_V 208_S 0.81 0.16 0.00
108_H 375_Q 0.80 0.16 0.00
375_L 23_P 0.80 0.16 0.00
139_V 271_T 0.80 0.16 0.00
156_I 261_P 0.80 0.16 0.00
213_E 293_L 0.80 0.16 0.00
247_K 419_S 0.80 0.16 0.00
53_L 21_T 0.79 0.16 0.00
365_N 409_A 0.79 0.16 0.00
94_S 340_A 0.79 0.16 0.00
262_S 443_S 0.79 0.16 0.00
359_M 177_T 0.79 0.15 0.00
333_P 440_D 0.78 0.15 0.00
55_T 334_T 0.78 0.15 0.00
262_S 94_L 0.78 0.15 0.00
319_A 272_C 0.78 0.15 0.00
319_A 360_N 0.78 0.15 0.00
29_V 34_V 0.78 0.15 0.00
141_F 317_L 0.78 0.15 0.00
141_F 348_I 0.78 0.15 0.00
147_T 249_Y 0.77 0.15 0.00
161_A 182_Y 0.77 0.15 0.00
215_T 271_T 0.77 0.15 0.00
202_V 367_D 0.77 0.15 0.00
128_I 263_A 0.77 0.15 0.00
171_I 352_A 0.77 0.15 0.00
109_A 294_R 0.77 0.15 0.00
100_E 443_S 0.76 0.15 0.00
33_I 162_D 0.76 0.14 0.00
291_Q 35_L 0.76 0.14 0.00
217_L 37_A 0.76 0.14 0.00
100_E 272_C 0.76 0.14 0.00
254_A 369_L 0.76 0.14 0.00
104_W 415_L 0.76 0.14 0.00
372_I 414_V 0.76 0.14 0.00
162_I 327_P 0.76 0.14 0.00
276_F 371_K 0.76 0.14 0.00
370_K 123_L 0.75 0.14 0.00
191_P 63_Q 0.75 0.14 0.00
53_L 301_E 0.75 0.14 0.00
156_I 97_G 0.75 0.14 0.00
357_Q 422_P 0.75 0.14 0.00
52_V 205_K 0.75 0.14 0.00
101_I 403_Y 0.75 0.14 0.00
189_T 73_D 0.75 0.14 0.00
105_M 52_D 0.75 0.14 0.00
328_A 301_E 0.75 0.14 0.00
195_F 96_L 0.75 0.14 0.00
91_Y 40_E 0.75 0.14 0.00
253_S 425_I 0.74 0.14 0.00
374_L 183_V 0.74 0.14 0.00
373_V 97_G 0.74 0.14 0.00
144_V 301_E 0.74 0.14 0.00
91_Y 391_Q 0.74 0.14 0.00
187_L 369_L 0.74 0.14 0.00
116_I 428_R 0.74 0.14 0.00
300_I 130_K 0.74 0.13 0.00
217_L 69_F 0.73 0.13 0.00
183_D 18_V 0.73 0.13 0.00
207_A 346_T 0.73 0.13 0.00
276_F 20_V 0.73 0.13 0.00
148_L 188_M 0.73 0.13 0.00
151_M 82_G 0.73 0.13 0.00
131_V 414_V 0.73 0.13 0.00
323_L 238_I 0.73 0.13 0.00
273_L 359_C 0.73 0.13 0.00
284_Y 444_Q 0.73 0.13 0.00
107_S 44_R 0.73 0.13 0.00
54_I 414_V 0.73 0.13 0.00
27_I 32_A 0.73 0.13 0.00
29_V 345_T 0.73 0.13 0.00
95_R 270_T 0.73 0.13 0.00
186_F 419_S 0.73 0.13 0.00
374_L 226_V 0.73 0.13 0.00
163_D 101_T 0.73 0.13 0.00
266_R 403_Y 0.73 0.13 0.00
256_V 432_A 0.73 0.13 0.00
117_I 73_D 0.73 0.13 0.00
67_F 432_A 0.72 0.13 0.00
27_I 404_D 0.72 0.13 0.00
184_L 41_G 0.72 0.13 0.00
88_P 107_T 0.72 0.13 0.00
53_L 202_V 0.72 0.13 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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