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OPENSEQ.org
BxP
Genes: A B A+B
Length: 362 244 583
Sequences: 1858 1471 1474
Seq/Len: 5.13 6.03 2.53
MirrorTree (Pazo et al. 2001) 0.82
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.00
2 0.00 0.00 0.15
5 0.01 0.01 1.79
10 0.01 0.01 1.98
20 0.02 0.02 2.18
100 0.03 0.03 2.43
∞ 0.07 0.07 2.63
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
343_G 86_T 1.14 0.74 0.03
131_G 186_F 1.14 0.74 0.03
217_G 71_S 1.06 0.67 0.02
93_P 216_I 1.03 0.63 0.02
199_F 51_A 1.00 0.59 0.02
71_F 52_L 0.99 0.58 0.02
135_L 68_V 0.98 0.57 0.02
184_L 197_M 0.96 0.55 0.02
327_N 224_I 0.95 0.53 0.01
181_L 79_T 0.92 0.49 0.01
88_L 116_L 0.91 0.49 0.01
28_K 129_G 0.90 0.48 0.01
116_T 190_L 0.90 0.47 0.01
321_Y 124_E 0.90 0.47 0.01
342_L 224_I 0.88 0.46 0.01
343_G 224_I 0.88 0.45 0.01
254_M 206_M 0.88 0.45 0.01
218_L 234_L 0.87 0.45 0.01
178_V 92_A 0.86 0.43 0.01
221_S 136_F 0.86 0.43 0.01
9_T 216_I 0.86 0.43 0.01
219_R 88_L 0.86 0.43 0.01
221_S 206_M 0.85 0.42 0.01
209_L 99_I 0.85 0.42 0.01
6_Q 187_L 0.84 0.41 0.01
253_R 212_P 0.84 0.41 0.01
180_Q 188_I 0.84 0.40 0.01
121_P 226_V 0.83 0.40 0.01
212_F 67_I 0.83 0.40 0.01
312_E 206_M 0.83 0.40 0.01
16_K 166_L 0.82 0.38 0.01
138_L 139_K 0.82 0.38 0.01
41_G 147_A 0.82 0.38 0.01
147_I 216_I 0.81 0.38 0.01
288_V 147_A 0.81 0.38 0.01
229_Y 71_S 0.81 0.38 0.01
26_V 124_E 0.81 0.38 0.01
227_D 65_R 0.81 0.37 0.01
248_E 98_F 0.80 0.37 0.01
226_K 188_I 0.80 0.36 0.01
127_N 144_K 0.80 0.36 0.01
91_L 67_I 0.79 0.35 0.01
99_M 139_K 0.79 0.35 0.01
3_G 194_V 0.79 0.35 0.01
244_R 241_S 0.79 0.35 0.01
109_Q 175_I 0.79 0.35 0.01
347_N 206_M 0.78 0.34 0.01
109_Q 212_P 0.78 0.34 0.01
11_E 81_S 0.78 0.34 0.01
235_D 212_P 0.78 0.34 0.01
216_K 222_L 0.78 0.34 0.01
326_V 106_K 0.78 0.34 0.01
16_K 160_T 0.78 0.34 0.01
320_L 79_T 0.78 0.34 0.01
231_Q 189_Y 0.78 0.34 0.01
289_A 177_E 0.78 0.34 0.01
307_N 127_I 0.78 0.34 0.01
45_T 160_T 0.77 0.33 0.01
15_K 149_F 0.77 0.33 0.01
18_E 41_L 0.77 0.33 0.01
112_F 58_F 0.77 0.33 0.01
173_E 134_K 0.77 0.33 0.01
139_K 197_M 0.76 0.32 0.01
115_T 56_I 0.76 0.32 0.01
210_V 165_P 0.76 0.32 0.01
123_L 200_S 0.76 0.32 0.01
100_I 87_I 0.76 0.32 0.01
208_F 212_P 0.76 0.32 0.01
233_E 92_A 0.76 0.32 0.01
139_K 38_V 0.76 0.32 0.01
243_R 161_I 0.76 0.32 0.01
30_Q 158_P 0.76 0.32 0.01
299_I 200_S 0.76 0.32 0.01
312_E 148_L 0.76 0.31 0.01
36_V 58_F 0.75 0.31 0.01
154_V 44_V 0.75 0.31 0.01
203_A 228_V 0.75 0.31 0.01
16_K 204_M 0.75 0.31 0.01
293_D 206_M 0.75 0.30 0.01
8_K 55_S 0.74 0.30 0.01
197_V 160_T 0.74 0.30 0.01
233_E 41_L 0.74 0.30 0.01
144_S 66_L 0.74 0.30 0.01
172_V 241_S 0.74 0.29 0.01
21_R 84_P 0.74 0.29 0.01
235_D 84_P 0.74 0.29 0.01
312_E 242_F 0.73 0.29 0.01
55_R 205_A 0.73 0.29 0.01
140_K 53_A 0.73 0.29 0.01
238_V 216_I 0.73 0.29 0.01
31_D 137_M 0.73 0.29 0.01
8_K 170_V 0.73 0.29 0.01
201_I 26_L 0.73 0.29 0.01
334_M 223_L 0.73 0.29 0.01
262_D 199_V 0.73 0.29 0.01
287_V 224_I 0.73 0.29 0.01
15_K 186_F 0.72 0.28 0.01
320_L 158_P 0.72 0.28 0.01
11_E 200_S 0.72 0.28 0.01
170_P 235_V 0.72 0.28 0.01
191_L 41_L 0.72 0.28 0.01
314_P 65_R 0.72 0.28 0.01
343_G 98_F 0.72 0.28 0.01
107_I 117_A 0.72 0.28 0.01
104_L 117_A 0.72 0.28 0.01
204_V 146_L 0.72 0.28 0.01
307_N 67_I 0.71 0.27 0.01
168_E 202_V 0.71 0.27 0.01
140_K 87_I 0.71 0.27 0.01
346_Y 65_R 0.71 0.27 0.01
194_I 223_L 0.71 0.27 0.01
106_N 175_I 0.71 0.27 0.01
310_V 134_K 0.71 0.27 0.01
84_I 45_I 0.71 0.27 0.01
105_G 241_S 0.71 0.27 0.01
314_P 72_F 0.71 0.27 0.01
344_F 234_L 0.71 0.27 0.01
177_M 117_A 0.70 0.26 0.01
266_T 180_T 0.70 0.26 0.01
148_I 197_M 0.70 0.26 0.01
70_E 200_S 0.70 0.26 0.01
153_I 164_V 0.70 0.26 0.01
237_Q 53_A 0.70 0.26 0.01
238_V 97_F 0.70 0.26 0.01
242_I 86_T 0.70 0.26 0.01
95_V 205_A 0.70 0.26 0.01
160_I 103_V 0.69 0.25 0.01
330_I 226_V 0.69 0.25 0.01
305_E 172_A 0.69 0.25 0.01
186_D 117_A 0.69 0.25 0.01
126_I 187_L 0.69 0.25 0.01
319_E 222_L 0.69 0.25 0.01
294_F 205_A 0.69 0.25 0.01
245_L 228_V 0.69 0.25 0.01
194_I 72_F 0.69 0.25 0.01
295_L 137_M 0.68 0.24 0.01
219_R 143_E 0.68 0.24 0.01
163_L 168_V 0.68 0.24 0.01
131_G 64_L 0.68 0.24 0.01
199_F 179_K 0.68 0.24 0.01
239_K 78_G 0.68 0.24 0.01
16_K 80_Q 0.68 0.24 0.01
122_N 198_V 0.68 0.24 0.01
331_P 132_P 0.68 0.24 0.01
113_I 216_I 0.68 0.24 0.01
31_D 142_R 0.68 0.24 0.01
73_L 152_I 0.68 0.24 0.01
162_L 202_V 0.68 0.24 0.01
51_F 162_D 0.68 0.24 0.01
178_V 51_A 0.68 0.24 0.01
319_E 200_S 0.68 0.24 0.01
284_A 212_P 0.68 0.24 0.01
353_R 58_F 0.68 0.24 0.01
100_I 150_Y 0.68 0.24 0.01
93_P 103_V 0.68 0.24 0.01
50_S 109_N 0.67 0.24 0.01
152_G 232_N 0.67 0.24 0.01
31_D 227_L 0.67 0.23 0.01
23_E 229_D 0.67 0.23 0.01
350_N 234_L 0.67 0.23 0.01
330_I 87_I 0.67 0.23 0.01
103_V 85_N 0.67 0.23 0.01
149_L 147_A 0.67 0.23 0.01
247_M 234_L 0.67 0.23 0.01
110_F 204_M 0.67 0.23 0.01
266_T 163_D 0.67 0.23 0.01
308_V 138_L 0.66 0.23 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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