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OPENSEQ.org
a1d
Genes: A B A+B
Length: 360 388 697
Sequences: 17236 819 75
Seq/Len: 47.88 2.11 0.11
MirrorTree (Pazo et al. 2001) 0.24
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 0.02 0.02 0.02
2 0.03 0.02 0.02
5 0.04 0.03 0.05
10 0.05 0.03 0.06
20 0.07 0.03 0.10
100 0.13 0.05 0.31
∞ 0.21 0.10 0.67
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
93_K 168_D 1.53 0.23 0.00
80_E 243_N 1.40 0.18 0.00
273_K 323_I 1.36 0.17 0.00
336_A 95_L 1.28 0.15 0.00
187_V 265_P 1.24 0.14 0.00
189_V 339_A 1.18 0.13 0.00
67_P 95_L 1.17 0.12 0.00
228_G 118_N 1.17 0.12 0.00
42_F 214_N 1.17 0.12 0.00
152_W 274_C 1.14 0.12 0.00
81_V 296_E 1.11 0.11 0.00
314_D 121_M 1.10 0.11 0.00
197_H 78_V 1.09 0.11 0.00
340_L 225_I 1.08 0.10 0.00
67_P 105_F 1.07 0.10 0.00
48_G 103_H 1.06 0.10 0.00
164_L 40_I 1.06 0.10 0.00
245_A 137_Q 1.05 0.10 0.00
40_V 34_V 1.03 0.10 0.00
258_I 289_L 1.03 0.09 0.00
42_F 33_L 1.02 0.09 0.00
232_F 269_N 1.01 0.09 0.00
135_Y 104_I 1.01 0.09 0.00
204_K 225_I 1.01 0.09 0.00
189_V 121_M 1.00 0.09 0.00
250_G 34_V 0.99 0.09 0.00
50_C 166_T 0.99 0.09 0.00
153_P 236_P 0.99 0.09 0.00
286_L 81_I 0.99 0.09 0.00
321_V 386_F 0.98 0.09 0.00
43_K 361_E 0.98 0.09 0.00
140_D 327_N 0.98 0.09 0.00
331_D 212_M 0.98 0.09 0.00
145_D 110_I 0.97 0.09 0.00
194_G 113_E 0.96 0.08 0.00
275_I 30_S 0.96 0.08 0.00
343_A 104_I 0.96 0.08 0.00
230_D 243_N 0.96 0.08 0.00
82_G 183_D 0.95 0.08 0.00
343_A 50_K 0.95 0.08 0.00
206_F 318_Q 0.95 0.08 0.00
211_T 139_V 0.95 0.08 0.00
80_E 116_Q 0.94 0.08 0.00
233_L 378_I 0.94 0.08 0.00
276_L 267_A 0.94 0.08 0.00
335_T 50_K 0.94 0.08 0.00
91_G 36_G 0.93 0.08 0.00
91_G 39_G 0.93 0.08 0.00
91_G 42_G 0.93 0.08 0.00
91_G 148_Y 0.93 0.08 0.00
91_G 164_P 0.93 0.08 0.00
91_G 273_N 0.93 0.08 0.00
42_F 269_N 0.93 0.08 0.00
76_G 36_G 0.92 0.08 0.00
76_G 39_G 0.92 0.08 0.00
76_G 42_G 0.92 0.08 0.00
76_G 148_Y 0.92 0.08 0.00
76_G 164_P 0.92 0.08 0.00
76_G 273_N 0.92 0.08 0.00
161_G 113_E 0.92 0.08 0.00
184_G 177_F 0.92 0.08 0.00
94_V 185_L 0.91 0.08 0.00
160_I 28_Y 0.91 0.08 0.00
189_V 102_T 0.91 0.07 0.00
82_G 167_E 0.91 0.07 0.00
90_V 187_E 0.91 0.07 0.00
319_H 230_N 0.90 0.07 0.00
71_G 167_E 0.90 0.07 0.00
347_Y 364_F 0.90 0.07 0.00
73_E 236_P 0.90 0.07 0.00
272_G 196_W 0.90 0.07 0.00
15_G 287_K 0.90 0.07 0.00
293_A 383_D 0.90 0.07 0.00
224_L 327_N 0.88 0.07 0.00
35_T 129_V 0.88 0.07 0.00
143_V 106_Y 0.88 0.07 0.00
272_G 220_C 0.88 0.07 0.00
211_T 328_N 0.88 0.07 0.00
211_T 230_N 0.88 0.07 0.00
96_V 61_V 0.88 0.07 0.00
73_E 326_K 0.88 0.07 0.00
286_L 324_V 0.88 0.07 0.00
249_D 185_L 0.87 0.07 0.00
204_K 104_I 0.87 0.07 0.00
248_L 277_G 0.87 0.07 0.00
352_D 198_V 0.87 0.07 0.00
335_T 362_L 0.87 0.07 0.00
278_G 214_N 0.87 0.07 0.00
193_G 33_L 0.87 0.07 0.00
336_A 197_S 0.87 0.07 0.00
85_V 33_L 0.87 0.07 0.00
40_V 286_W 0.87 0.07 0.00
258_I 326_K 0.86 0.07 0.00
332_Y 362_L 0.86 0.07 0.00
152_W 323_I 0.86 0.07 0.00
271_H 370_S 0.86 0.07 0.00
298_I 125_I 0.86 0.07 0.00
330_M 76_K 0.86 0.07 0.00
82_G 143_T 0.86 0.07 0.00
221_Q 216_V 0.86 0.07 0.00
218_S 295_I 0.86 0.07 0.00
255_V 205_F 0.86 0.07 0.00
43_K 296_E 0.85 0.07 0.00
140_D 304_K 0.85 0.07 0.00
40_V 387_I 0.85 0.07 0.00
56_M 126_L 0.85 0.07 0.00
27_P 293_F 0.85 0.07 0.00
42_F 244_C 0.85 0.07 0.00
82_G 206_G 0.85 0.07 0.00
318_K 204_V 0.85 0.07 0.00
274_L 295_I 0.85 0.07 0.00
194_G 387_I 0.84 0.07 0.00
340_L 193_N 0.84 0.07 0.00
224_L 293_F 0.84 0.07 0.00
37_E 86_S 0.84 0.07 0.00
218_S 93_S 0.84 0.07 0.00
59_N 181_L 0.84 0.07 0.00
321_V 122_F 0.84 0.07 0.00
161_G 272_L 0.84 0.07 0.00
42_F 360_K 0.83 0.07 0.00
336_A 266_K 0.83 0.07 0.00
92_D 201_P 0.83 0.07 0.00
193_G 320_W 0.83 0.07 0.00
69_V 362_L 0.83 0.07 0.00
336_A 364_F 0.83 0.07 0.00
243_A 224_T 0.83 0.07 0.00
140_D 65_A 0.83 0.06 0.00
138_Y 276_N 0.83 0.06 0.00
319_H 287_K 0.82 0.06 0.00
84_K 88_N 0.82 0.06 0.00
233_L 251_A 0.82 0.06 0.00
137_G 127_N 0.82 0.06 0.00
317_A 383_D 0.82 0.06 0.00
196_G 33_L 0.82 0.06 0.00
274_L 45_L 0.82 0.06 0.00
208_A 315_D 0.82 0.06 0.00
294_G 275_N 0.82 0.06 0.00
210_V 224_T 0.82 0.06 0.00
321_V 104_I 0.82 0.06 0.00
212_V 97_P 0.82 0.06 0.00
74_I 102_T 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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