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OPENSEQ.org
TS_both
Genes: A B A+B
Length: 269 393 611
Sequences: 2757 6180 1900
Seq/Len: 10.25 15.73 3.11
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 0.08 0.03 2.61
2 0.08 0.03 2.71
5 0.08 0.03 2.76
10 0.08 0.04 2.84
20 0.08 0.04 2.87
100 0.08 0.06 2.90
∞ 0.09 0.18 3.16
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
109_N 273_T 2.79 1.00 1.00
60_V 172_F 2.61 1.00 1.00
104_Y 276_I 1.97 1.00 0.98
108_Y 281_L 1.60 0.97 0.93
81_K 289_D 1.47 0.95 0.89
80_I 289_D 1.37 0.93 0.84
79_N 289_D 1.34 0.91 0.82
67_Q 170_E 1.29 0.89 0.79
108_Y 276_I 1.20 0.84 0.71
81_K 288_E 1.18 0.82 0.70
181_M 180_D 1.08 0.74 0.60
60_V 195_Y 0.86 0.49 0.34
35_S 58_Y 0.81 0.42 0.27
56_F 292_I 0.81 0.42 0.27
96_K 181_T 0.79 0.40 0.25
158_A 179_L 0.76 0.36 0.22
108_Y 280_S 0.73 0.33 0.20
124_V 51_A 0.72 0.32 0.19
199_K 328_K 0.72 0.32 0.18
117_K 366_K 0.69 0.29 0.16
139_D 281_L 0.68 0.28 0.16
79_N 321_K 0.68 0.28 0.15
216_S 338_C 0.68 0.27 0.15
61_A 83_A 0.68 0.27 0.15
64_K 241_G 0.68 0.27 0.15
45_N 312_A 0.68 0.27 0.15
67_Q 173_R 0.66 0.26 0.14
175_I 98_Y 0.66 0.26 0.14
181_M 177_S 0.66 0.26 0.14
60_V 168_I 0.66 0.26 0.14
224_V 256_A 0.66 0.25 0.14
256_I 124_L 0.65 0.25 0.14
108_Y 274_E 0.65 0.25 0.13
39_A 325_I 0.65 0.25 0.13
222_K 205_V 0.65 0.24 0.13
109_N 130_I 0.64 0.24 0.12
180_V 278_H 0.63 0.23 0.12
232_A 241_G 0.63 0.23 0.12
239_I 172_F 0.63 0.23 0.12
181_M 179_L 0.62 0.22 0.11
14_K 211_R 0.62 0.22 0.11
132_L 57_L 0.61 0.21 0.10
259_Y 256_A 0.61 0.21 0.10
148_N 125_G 0.60 0.21 0.10
156_S 179_L 0.60 0.21 0.10
21_F 195_Y 0.60 0.21 0.10
101_L 173_R 0.60 0.20 0.10
81_K 198_M 0.60 0.20 0.10
157_Q 195_Y 0.60 0.20 0.10
60_V 277_L 0.59 0.20 0.10
181_M 121_G 0.59 0.20 0.10
130_A 280_S 0.59 0.20 0.10
45_N 373_N 0.59 0.20 0.10
159_T 262_T 0.59 0.20 0.10
219_E 387_K 0.59 0.19 0.09
163_R 88_N 0.59 0.19 0.09
152_I 72_Y 0.59 0.19 0.09
206_D 240_S 0.59 0.19 0.09
159_T 89_A 0.58 0.19 0.09
35_S 148_E 0.58 0.19 0.09
263_M 124_L 0.58 0.19 0.09
109_N 286_Q 0.58 0.19 0.09
83_C 86_I 0.58 0.19 0.09
25_L 179_L 0.58 0.18 0.09
6_Y 172_F 0.58 0.18 0.09
109_N 211_R 0.57 0.18 0.09
44_D 358_K 0.57 0.18 0.08
60_V 186_I 0.56 0.18 0.08
22_I 178_N 0.56 0.18 0.08
153_F 86_I 0.56 0.17 0.08
69_A 315_Q 0.56 0.17 0.08
155_V 338_C 0.56 0.17 0.08
129_I 250_L 0.56 0.17 0.08
179_S 282_S 0.56 0.17 0.08
186_A 177_S 0.56 0.17 0.08
179_S 105_I 0.56 0.17 0.08
244_D 212_E 0.55 0.17 0.08
178_A 123_K 0.55 0.17 0.08
268_K 350_S 0.55 0.17 0.07
244_D 251_I 0.55 0.17 0.07
127_V 350_S 0.55 0.16 0.07
82_K 289_D 0.55 0.16 0.07
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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