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OPENSEQ.org
Nadia
Genes: A B A+B
Length: 350 422 724
Sequences: 7724 2951 944
Seq/Len: 22.07 6.99 1.3
MirrorTree (Pazo et al. 2001) 0.66
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 1.17
2 0.08 0.00 1.19
5 0.09 0.00 1.19
10 0.10 0.01 1.20
20 0.10 0.01 1.22
100 0.11 0.04 1.43
∞ 0.19 0.14 2.12
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
253_A 365_L 1.35 0.73 0.01
12_A 358_V 1.33 0.72 0.01
129_P 197_A 1.24 0.63 0.01
52_V 41_G 1.18 0.58 0.01
92_L 360_I 1.18 0.58 0.01
267_P 292_A 1.17 0.57 0.01
33_R 340_I 1.09 0.49 0.01
156_R 127_N 1.02 0.42 0.01
31_T 150_W 1.00 0.40 0.01
95_Y 310_F 0.98 0.39 0.01
46_P 181_A 0.98 0.38 0.01
123_A 370_S 0.96 0.37 0.01
313_E 91_M 0.96 0.36 0.01
24_Y 370_S 0.95 0.35 0.00
322_R 225_A 0.94 0.35 0.00
327_Q 382_L 0.94 0.34 0.00
253_A 104_L 0.93 0.34 0.00
77_A 300_L 0.93 0.34 0.00
264_A 336_I 0.93 0.34 0.00
95_Y 129_L 0.93 0.33 0.00
50_I 189_L 0.92 0.33 0.00
286_E 73_R 0.91 0.32 0.00
113_I 371_A 0.91 0.32 0.00
158_E 277_Q 0.91 0.32 0.00
63_L 262_L 0.90 0.31 0.00
101_G 279_W 0.90 0.31 0.00
346_E 105_L 0.89 0.30 0.00
301_S 96_F 0.89 0.30 0.00
79_R 320_I 0.89 0.30 0.00
176_L 98_M 0.88 0.30 0.00
259_S 382_L 0.88 0.29 0.00
176_L 61_K 0.88 0.29 0.00
301_S 340_I 0.87 0.29 0.00
299_Q 295_G 0.87 0.29 0.00
276_A 279_W 0.87 0.29 0.00
34_G 310_F 0.87 0.28 0.00
175_N 358_V 0.86 0.28 0.00
45_L 171_P 0.85 0.27 0.00
82_R 342_A 0.85 0.27 0.00
250_I 198_V 0.85 0.27 0.00
26_V 372_L 0.85 0.27 0.00
175_N 357_I 0.84 0.27 0.00
176_L 104_L 0.84 0.26 0.00
303_G 45_V 0.84 0.26 0.00
113_I 52_L 0.84 0.26 0.00
88_C 135_L 0.83 0.26 0.00
108_G 40_T 0.83 0.26 0.00
210_Q 358_V 0.83 0.26 0.00
125_R 205_V 0.83 0.26 0.00
79_R 87_V 0.83 0.26 0.00
250_I 214_V 0.83 0.26 0.00
177_L 155_Y 0.83 0.25 0.00
52_V 300_L 0.82 0.25 0.00
267_P 347_N 0.82 0.25 0.00
269_F 45_V 0.82 0.25 0.00
10_F 361_P 0.82 0.25 0.00
338_R 86_Y 0.82 0.25 0.00
42_K 361_P 0.81 0.24 0.00
51_Q 195_L 0.81 0.24 0.00
52_V 361_P 0.81 0.24 0.00
249_V 140_S 0.81 0.24 0.00
344_C 184_V 0.81 0.24 0.00
187_P 188_D 0.81 0.24 0.00
262_T 381_M 0.81 0.24 0.00
299_Q 358_V 0.81 0.24 0.00
290_R 200_I 0.81 0.24 0.00
192_L 305_T 0.81 0.24 0.00
19_F 116_T 0.81 0.24 0.00
188_L 42_L 0.81 0.24 0.00
162_D 129_L 0.81 0.24 0.00
12_A 233_H 0.80 0.24 0.00
130_I 184_V 0.80 0.23 0.00
278_D 357_I 0.80 0.23 0.00
92_L 292_A 0.80 0.23 0.00
230_A 192_A 0.80 0.23 0.00
259_S 307_L 0.80 0.23 0.00
192_L 373_L 0.79 0.23 0.00
273_L 350_A 0.79 0.23 0.00
160_F 104_L 0.79 0.22 0.00
316_M 217_M 0.79 0.22 0.00
311_L 46_L 0.79 0.22 0.00
113_I 221_G 0.79 0.22 0.00
57_G 358_V 0.79 0.22 0.00
302_T 115_Y 0.78 0.22 0.00
151_T 335_G 0.78 0.22 0.00
243_Y 360_I 0.78 0.22 0.00
267_P 387_K 0.78 0.22 0.00
186_E 309_L 0.78 0.22 0.00
176_L 327_P 0.78 0.22 0.00
336_A 378_A 0.78 0.22 0.00
14_A 48_L 0.78 0.22 0.00
292_G 311_L 0.78 0.22 0.00
19_F 381_M 0.78 0.22 0.00
66_A 187_R 0.77 0.21 0.00
24_Y 306_V 0.77 0.21 0.00
119_V 190_G 0.77 0.21 0.00
113_I 214_V 0.77 0.21 0.00
109_V 66_N 0.77 0.21 0.00
247_D 292_A 0.76 0.21 0.00
71_L 301_I 0.76 0.20 0.00
108_G 313_L 0.76 0.20 0.00
259_S 81_G 0.75 0.20 0.00
149_L 307_L 0.75 0.20 0.00
120_A 352_I 0.75 0.20 0.00
48_H 57_V 0.75 0.20 0.00
134_V 364_L 0.75 0.20 0.00
118_A 158_K 0.75 0.20 0.00
273_L 358_V 0.75 0.20 0.00
210_Q 260_Y 0.74 0.20 0.00
64_V 373_L 0.74 0.20 0.00
6_G 127_N 0.74 0.20 0.00
19_F 139_P 0.74 0.20 0.00
23_G 325_T 0.74 0.19 0.00
210_Q 316_A 0.74 0.19 0.00
190_K 365_L 0.74 0.19 0.00
64_V 377_I 0.74 0.19 0.00
17_R 352_I 0.74 0.19 0.00
74_L 46_L 0.74 0.19 0.00
267_P 100_A 0.74 0.19 0.00
319_E 169_L 0.74 0.19 0.00
109_V 125_N 0.73 0.19 0.00
253_A 229_T 0.73 0.19 0.00
326_D 76_I 0.73 0.19 0.00
183_L 194_V 0.73 0.19 0.00
72_K 294_I 0.73 0.19 0.00
83_Q 112_V 0.73 0.19 0.00
307_L 261_A 0.73 0.19 0.00
124_N 57_V 0.73 0.19 0.00
117_N 289_F 0.73 0.19 0.00
330_S 137_I 0.73 0.19 0.00
251_C 91_M 0.73 0.18 0.00
177_L 320_I 0.73 0.18 0.00
9_V 206_V 0.73 0.18 0.00
315_L 75_L 0.72 0.18 0.00
246_A 54_A 0.72 0.18 0.00
19_F 48_L 0.72 0.18 0.00
298_P 177_G 0.72 0.18 0.00
72_K 83_P 0.72 0.18 0.00
276_A 295_G 0.72 0.18 0.00
14_A 277_Q 0.72 0.18 0.00
208_R 105_L 0.72 0.18 0.00
19_F 287_T 0.72 0.18 0.00
326_D 87_V 0.72 0.18 0.00
186_E 107_S 0.72 0.18 0.00
261_L 185_G 0.72 0.18 0.00
95_Y 277_Q 0.72 0.18 0.00
238_D 113_L 0.72 0.18 0.00
131_A 322_T 0.72 0.18 0.00
253_A 137_I 0.72 0.18 0.00
129_P 305_T 0.72 0.18 0.00
288_L 367_Y 0.72 0.18 0.00
250_I 49_L 0.72 0.18 0.00
303_G 83_P 0.72 0.18 0.00
119_V 287_T 0.71 0.18 0.00
249_V 194_V 0.71 0.18 0.00
155_V 127_N 0.71 0.18 0.00
12_A 127_N 0.71 0.18 0.00
119_V 385_F 0.71 0.17 0.00
296_L 179_V 0.71 0.17 0.00
342_D 308_A 0.71 0.17 0.00
325_A 217_M 0.71 0.17 0.00
188_L 208_A 0.71 0.17 0.00
78_L 97_R 0.70 0.17 0.00
236_I 262_L 0.70 0.17 0.00
110_P 51_V 0.70 0.17 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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