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OPENSEQ.org
MATs
Genes: A B A+B
Length: 362 334 612
Sequences: 2354 3160 131
Seq/Len: 6.5 9.46 0.21
MirrorTree (Pazo et al. 2001) 0.26
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 0.07 0.00 0.00
2 0.07 0.01 0.00
5 0.07 0.01 0.01
10 0.07 0.01 0.02
20 0.07 0.01 0.03
100 0.08 0.02 0.19
∞ 0.09 0.07 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
165_A 200_M 1.41 0.28 0.00
108_V 157_N 1.39 0.28 0.00
341_S 183_P 1.36 0.26 0.00
41_V 120_L 1.26 0.22 0.00
305_L 259_Y 1.24 0.21 0.00
244_L 30_R 1.23 0.20 0.00
141_Y 40_L 1.15 0.17 0.00
316_V 114_V 1.10 0.16 0.00
318_V 133_Y 1.10 0.16 0.00
259_A 79_H 1.07 0.15 0.00
157_A 203_K 1.07 0.15 0.00
87_V 114_V 1.06 0.14 0.00
294_A 276_L 1.04 0.14 0.00
319_S 91_V 1.04 0.14 0.00
82_V 90_I 1.03 0.14 0.00
33_I 80_H 1.03 0.14 0.00
147_E 214_D 1.02 0.13 0.00
85_E 120_L 1.02 0.13 0.00
275_G 186_Y 1.01 0.13 0.00
40_A 292_N 1.01 0.13 0.00
56_C 247_T 1.00 0.13 0.00
157_A 54_H 1.00 0.13 0.00
349_V 111_Q 1.00 0.13 0.00
301_V 91_V 0.98 0.12 0.00
326_H 134_I 0.97 0.12 0.00
106_V 37_T 0.97 0.12 0.00
110_L 202_D 0.96 0.12 0.00
319_S 161_K 0.96 0.12 0.00
189_M 279_I 0.96 0.12 0.00
157_A 77_A 0.95 0.11 0.00
110_L 214_D 0.95 0.11 0.00
101_Y 186_Y 0.95 0.11 0.00
298_A 288_Q 0.94 0.11 0.00
17_T 276_L 0.94 0.11 0.00
108_V 89_V 0.94 0.11 0.00
244_L 168_K 0.94 0.11 0.00
62_T 246_G 0.93 0.11 0.00
243_H 42_R 0.93 0.11 0.00
202_T 204_V 0.93 0.11 0.00
305_L 288_Q 0.92 0.11 0.00
107_L 36_A 0.92 0.11 0.00
167_L 251_S 0.92 0.11 0.00
342_E 134_I 0.92 0.11 0.00
33_I 315_I 0.90 0.10 0.00
78_D 257_T 0.89 0.10 0.00
115_P 88_H 0.88 0.10 0.00
316_V 287_A 0.88 0.10 0.00
87_V 251_S 0.88 0.10 0.00
152_L 200_M 0.88 0.10 0.00
343_R 117_S 0.88 0.10 0.00
101_Y 150_E 0.87 0.10 0.00
200_V 282_S 0.86 0.09 0.00
110_L 157_N 0.86 0.09 0.00
329_S 140_F 0.86 0.09 0.00
213_V 56_V 0.86 0.09 0.00
242_Y 111_Q 0.86 0.09 0.00
349_V 31_V 0.86 0.09 0.00
115_P 165_D 0.85 0.09 0.00
87_V 215_H 0.85 0.09 0.00
37_I 40_L 0.85 0.09 0.00
202_T 288_Q 0.85 0.09 0.00
330_I 191_K 0.85 0.09 0.00
157_A 202_D 0.84 0.09 0.00
144_D 132_I 0.84 0.09 0.00
349_V 44_V 0.84 0.09 0.00
347_E 126_A 0.84 0.09 0.00
214_C 76_N 0.84 0.09 0.00
180_S 232_R 0.83 0.09 0.00
355_L 39_L 0.83 0.09 0.00
83_V 82_I 0.83 0.09 0.00
122_H 313_I 0.83 0.09 0.00
223_K 320_W 0.83 0.09 0.00
166_E 218_Q 0.83 0.09 0.00
71_I 187_G 0.83 0.09 0.00
46_L 55_A 0.82 0.09 0.00
270_T 187_G 0.82 0.09 0.00
107_L 183_P 0.82 0.09 0.00
362_R 40_L 0.82 0.09 0.00
319_S 272_P 0.82 0.09 0.00
236_L 235_A 0.82 0.09 0.00
227_I 74_D 0.82 0.09 0.00
301_V 281_D 0.82 0.09 0.00
203_I 33_V 0.82 0.09 0.00
275_G 185_L 0.82 0.09 0.00
328_L 272_P 0.82 0.09 0.00
166_E 296_D 0.82 0.09 0.00
86_A 187_G 0.81 0.09 0.00
242_Y 283_P 0.81 0.08 0.00
244_L 288_Q 0.81 0.08 0.00
74_R 260_E 0.81 0.08 0.00
67_L 177_A 0.81 0.08 0.00
201_H 220_F 0.81 0.08 0.00
34_C 101_V 0.81 0.08 0.00
123_L 30_R 0.80 0.08 0.00
319_S 220_F 0.80 0.08 0.00
180_S 102_V 0.80 0.08 0.00
228_K 319_L 0.80 0.08 0.00
157_A 148_R 0.80 0.08 0.00
46_L 250_W 0.80 0.08 0.00
319_S 296_D 0.80 0.08 0.00
71_I 73_L 0.80 0.08 0.00
86_A 124_A 0.80 0.08 0.00
222_L 58_C 0.80 0.08 0.00
330_I 164_L 0.79 0.08 0.00
165_A 36_A 0.79 0.08 0.00
318_V 224_V 0.79 0.08 0.00
312_R 165_D 0.79 0.08 0.00
313_R 172_E 0.79 0.08 0.00
240_T 186_Y 0.79 0.08 0.00
227_I 206_F 0.79 0.08 0.00
312_R 248_F 0.79 0.08 0.00
62_T 87_P 0.79 0.08 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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