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OPENSEQ.org
2BRU-2
Genes: A B A+B
Length: 400 176 537
Sequences: 3308 808 944
Seq/Len: 8.27 4.59 1.76
MirrorTree (Pazo et al. 2001) 0.80
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 0.00 0.59
2 0.01 0.00 1.56
5 0.01 0.00 1.64
10 0.01 0.01 1.64
20 0.01 0.01 1.64
100 0.02 0.01 1.65
∞ 0.10 0.02 1.68
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
255_V 108_V 1.30 0.78 0.04
222_F 145_Y 1.19 0.68 0.03
215_A 17_L 1.18 0.68 0.03
74_I 148_V 1.10 0.60 0.02
163_I 85_E 1.07 0.56 0.02
155_F 145_Y 1.06 0.56 0.02
175_M 31_M 1.06 0.55 0.02
163_I 140_S 1.05 0.54 0.02
360_V 151_P 1.04 0.53 0.02
193_L 96_T 1.00 0.49 0.02
141_N 85_E 0.98 0.47 0.01
213_M 65_L 0.98 0.47 0.01
57_V 88_E 0.97 0.46 0.01
341_L 88_E 0.97 0.45 0.01
334_G 42_E 0.97 0.45 0.01
168_K 145_Y 0.96 0.45 0.01
246_E 11_E 0.95 0.44 0.01
31_Q 25_I 0.95 0.44 0.01
361_I 146_A 0.95 0.44 0.01
244_E 120_I 0.94 0.43 0.01
133_L 52_I 0.93 0.41 0.01
344_L 162_F 0.93 0.41 0.01
246_E 101_V 0.91 0.39 0.01
269_A 165_A 0.91 0.39 0.01
218_L 146_A 0.90 0.38 0.01
299_E 56_F 0.89 0.37 0.01
324_R 86_M 0.89 0.37 0.01
140_A 81_D 0.88 0.36 0.01
243_A 94_A 0.86 0.34 0.01
268_P 140_S 0.86 0.34 0.01
334_G 170_D 0.85 0.33 0.01
224_E 31_M 0.85 0.33 0.01
355_D 78_V 0.85 0.33 0.01
282_K 156_E 0.84 0.33 0.01
70_W 12_E 0.84 0.32 0.01
323_G 125_V 0.84 0.32 0.01
338_V 102_I 0.83 0.31 0.01
78_V 96_T 0.82 0.30 0.01
199_A 175_A 0.82 0.30 0.01
269_A 115_D 0.82 0.30 0.01
342_K 17_L 0.82 0.30 0.01
65_E 87_D 0.82 0.30 0.01
192_S 65_L 0.81 0.29 0.01
360_V 87_D 0.81 0.29 0.01
332_L 145_Y 0.80 0.28 0.01
188_G 41_A 0.79 0.28 0.01
169_V 91_D 0.79 0.28 0.01
287_I 175_A 0.79 0.28 0.01
256_D 146_A 0.79 0.27 0.01
367_I 88_E 0.79 0.27 0.01
111_L 143_T 0.78 0.27 0.01
243_A 111_A 0.78 0.27 0.01
199_A 8_I 0.78 0.27 0.01
146_R 101_V 0.78 0.26 0.01
75_I 49_A 0.77 0.26 0.01
155_F 83_V 0.77 0.26 0.01
304_G 53_N 0.77 0.26 0.01
204_P 86_M 0.77 0.26 0.01
238_D 175_A 0.77 0.26 0.01
339_N 56_F 0.76 0.25 0.01
264_I 84_L 0.76 0.25 0.01
301_T 176_L 0.76 0.25 0.01
332_L 85_E 0.76 0.25 0.01
363_G 145_Y 0.76 0.25 0.01
293_Q 145_Y 0.76 0.25 0.01
199_A 31_M 0.75 0.24 0.01
360_V 129_W 0.75 0.24 0.01
129_R 93_F 0.75 0.24 0.01
288_V 146_A 0.75 0.24 0.01
141_N 145_Y 0.74 0.23 0.01
253_K 146_A 0.73 0.23 0.01
89_L 167_A 0.73 0.23 0.01
36_G 56_F 0.73 0.23 0.01
137_S 118_S 0.73 0.23 0.01
36_G 31_M 0.73 0.23 0.01
366_V 11_E 0.73 0.23 0.01
209_Q 19_N 0.73 0.23 0.01
294_N 12_E 0.73 0.23 0.01
251_Q 31_M 0.72 0.22 0.01
128_S 146_A 0.72 0.22 0.01
299_E 96_T 0.72 0.22 0.01
213_M 154_F 0.72 0.22 0.01
137_S 153_F 0.72 0.22 0.01
360_V 4_E 0.72 0.22 0.01
149_V 56_F 0.72 0.22 0.01
210_V 13_T 0.72 0.22 0.01
101_P 44_T 0.71 0.21 0.01
355_D 23_V 0.71 0.21 0.01
142_I 50_R 0.71 0.21 0.01
150_E 129_W 0.70 0.21 0.01
165_A 14_A 0.70 0.21 0.01
264_I 136_V 0.70 0.21 0.01
99_I 162_F 0.70 0.21 0.01
193_L 131_A 0.70 0.21 0.01
269_A 121_A 0.70 0.21 0.01
214_G 128_V 0.70 0.21 0.01
137_S 160_M 0.70 0.21 0.01
279_D 20_S 0.70 0.20 0.01
342_K 149_Q 0.69 0.20 0.01
372_I 24_I 0.69 0.20 0.01
140_A 17_L 0.69 0.20 0.01
153_H 99_V 0.69 0.20 0.01
196_I 14_A 0.69 0.20 0.01
118_V 102_I 0.69 0.20 0.01
276_E 167_A 0.69 0.20 0.01
244_E 133_N 0.69 0.20 0.01
244_E 166_K 0.69 0.20 0.01
109_Q 81_D 0.69 0.20 0.01
151_A 47_L 0.69 0.20 0.01
176_V 20_S 0.68 0.19 0.01
329_S 19_N 0.68 0.19 0.01
248_F 22_S 0.68 0.19 0.01
189_A 15_E 0.68 0.19 0.01
227_G 145_Y 0.68 0.19 0.01
76_L 171_A 0.68 0.19 0.01
112_A 44_T 0.68 0.19 0.01
54_K 26_T 0.68 0.19 0.01
214_G 131_A 0.68 0.19 0.01
274_T 40_V 0.68 0.19 0.01
124_V 31_M 0.68 0.19 0.01
227_G 133_N 0.68 0.19 0.01
49_A 53_N 0.68 0.19 0.01
322_P 44_T 0.67 0.19 0.01
198_R 125_V 0.67 0.19 0.01
156_G 145_Y 0.67 0.19 0.01
198_R 108_V 0.67 0.19 0.01
292_A 175_A 0.67 0.18 0.01
138_S 58_I 0.67 0.18 0.01
207_K 49_A 0.67 0.18 0.01
101_P 95_D 0.67 0.18 0.01
332_L 159_H 0.67 0.18 0.01
290_L 174_K 0.67 0.18 0.01
162_Q 157_N 0.67 0.18 0.01
239_A 88_E 0.66 0.18 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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