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OPENSEQ.org
2bru_A_C
Genes: A B A+B
Length: 401 186 536
Sequences: 3273 788 944
Seq/Len: 8.16 4.24 1.76
MirrorTree (Pazo et al. 2001) 0.83
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 0.58
2 0.01 0.00 1.52
5 0.01 0.00 1.60
10 0.01 0.01 1.61
20 0.01 0.01 1.61
100 0.02 0.01 1.61
∞ 0.10 0.02 1.64
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
256_V 118_V 1.31 0.78 0.04
223_F 155_Y 1.26 0.75 0.04
156_F 155_Y 1.13 0.62 0.02
164_I 95_E 1.12 0.61 0.02
75_I 158_V 1.07 0.56 0.02
216_A 27_L 1.06 0.55 0.02
176_M 41_M 1.05 0.54 0.02
142_N 95_E 1.02 0.51 0.02
32_Q 35_I 1.01 0.50 0.02
194_L 106_T 1.01 0.50 0.02
214_M 75_L 0.98 0.46 0.02
247_E 21_E 0.95 0.44 0.01
361_V 161_P 0.94 0.42 0.01
169_K 155_Y 0.94 0.42 0.01
79_V 106_T 0.94 0.42 0.01
335_G 52_E 0.93 0.41 0.01
270_A 175_A 0.92 0.40 0.01
300_E 66_F 0.92 0.40 0.01
164_I 150_S 0.91 0.39 0.01
189_G 51_A 0.89 0.37 0.01
244_A 104_A 0.89 0.37 0.01
325_R 96_M 0.88 0.36 0.01
333_L 155_Y 0.88 0.36 0.01
138_S 128_S 0.88 0.35 0.01
156_F 93_V 0.87 0.35 0.01
193_S 75_L 0.87 0.35 0.01
58_V 98_E 0.87 0.35 0.01
342_L 98_E 0.87 0.35 0.01
362_I 156_A 0.86 0.34 0.01
142_N 155_Y 0.86 0.34 0.01
265_I 94_L 0.86 0.34 0.01
335_G 180_D 0.86 0.34 0.01
150_V 66_F 0.85 0.33 0.01
134_L 62_I 0.84 0.33 0.01
283_K 166_E 0.84 0.32 0.01
339_V 112_I 0.84 0.32 0.01
356_D 88_V 0.84 0.32 0.01
340_N 66_F 0.84 0.32 0.01
324_G 135_V 0.83 0.31 0.01
345_L 172_F 0.82 0.31 0.01
200_A 41_M 0.82 0.30 0.01
361_V 97_D 0.81 0.30 0.01
138_S 163_F 0.81 0.29 0.01
71_W 22_E 0.81 0.29 0.01
257_D 156_A 0.81 0.29 0.01
157_G 155_Y 0.80 0.29 0.01
270_A 125_D 0.80 0.28 0.01
141_A 91_D 0.79 0.27 0.01
66_E 97_D 0.79 0.27 0.01
219_L 156_A 0.78 0.27 0.01
361_V 139_W 0.78 0.27 0.01
113_A 54_T 0.78 0.27 0.01
269_P 52_E 0.77 0.26 0.01
247_E 111_V 0.77 0.26 0.01
245_E 130_I 0.77 0.26 0.01
302_T 186_L 0.77 0.26 0.01
170_V 101_D 0.77 0.26 0.01
225_E 41_M 0.77 0.26 0.01
288_I 185_A 0.77 0.26 0.01
200_A 185_A 0.77 0.26 0.01
147_R 111_V 0.76 0.25 0.01
239_D 185_A 0.76 0.25 0.01
343_K 27_L 0.76 0.25 0.01
55_K 98_E 0.75 0.24 0.01
166_A 24_A 0.75 0.24 0.01
138_S 170_M 0.75 0.24 0.01
280_D 30_S 0.75 0.24 0.01
125_V 41_M 0.75 0.24 0.01
200_A 18_I 0.74 0.24 0.01
294_Q 155_Y 0.74 0.24 0.01
368_I 98_E 0.74 0.24 0.01
37_G 66_F 0.74 0.23 0.01
254_K 156_A 0.74 0.23 0.01
161_T 75_L 0.74 0.23 0.01
305_G 63_N 0.73 0.23 0.01
215_G 138_V 0.73 0.23 0.01
342_L 126_P 0.73 0.23 0.01
143_I 60_R 0.72 0.22 0.01
210_Q 29_N 0.72 0.22 0.01
98_S 59_A 0.72 0.22 0.01
100_I 172_F 0.72 0.22 0.01
205_P 96_M 0.72 0.22 0.01
120_M 158_V 0.72 0.22 0.01
211_V 23_T 0.72 0.22 0.01
130_R 103_F 0.72 0.22 0.01
154_H 109_V 0.71 0.22 0.01
239_D 147_F 0.71 0.22 0.01
215_G 141_A 0.71 0.21 0.01
275_T 50_V 0.71 0.21 0.01
367_V 21_E 0.71 0.21 0.01
102_P 54_T 0.70 0.21 0.01
277_E 177_A 0.70 0.21 0.01
295_N 22_E 0.70 0.20 0.01
199_R 135_V 0.70 0.20 0.01
244_A 121_A 0.70 0.20 0.01
189_G 131_A 0.70 0.20 0.01
194_L 141_A 0.70 0.20 0.01
163_Q 167_N 0.70 0.20 0.01
265_I 146_V 0.70 0.20 0.01
274_I 167_N 0.69 0.20 0.01
25_A 29_N 0.69 0.20 0.01
151_E 139_W 0.69 0.20 0.01
141_A 27_L 0.69 0.20 0.01
252_Q 41_M 0.69 0.20 0.01
62_A 151_M 0.69 0.20 0.01
355_V 105_D 0.68 0.19 0.01
76_I 59_A 0.68 0.19 0.01
50_A 63_N 0.68 0.19 0.01
289_V 156_A 0.68 0.19 0.01
199_R 118_V 0.68 0.19 0.01
245_E 143_N 0.68 0.19 0.01
94_T 104_A 0.68 0.19 0.01
275_T 54_T 0.68 0.19 0.01
323_P 55_E 0.68 0.19 0.01
177_V 30_S 0.68 0.19 0.01
333_L 95_E 0.68 0.19 0.01
259_I 53_I 0.67 0.19 0.01
361_V 14_E 0.67 0.19 0.01
353_I 63_N 0.67 0.19 0.01
129_S 155_Y 0.67 0.19 0.01
90_L 177_A 0.67 0.19 0.01
245_E 176_K 0.67 0.19 0.01
37_G 41_M 0.67 0.19 0.01
325_R 155_Y 0.67 0.19 0.01
265_I 95_E 0.67 0.19 0.01
155_E 138_V 0.67 0.18 0.01
77_L 181_A 0.67 0.18 0.01
208_K 59_A 0.67 0.18 0.01
110_Q 91_D 0.67 0.18 0.01
335_G 164_F 0.67 0.18 0.01
304_P 96_M 0.67 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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