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OPENSEQ.org
3n3a_D_A
Genes: A B A+B
Length: 153 319 444
Sequences: 661 1954 423
Seq/Len: 4.32 6.13 0.95
MirrorTree (Pazo et al. 2001) 0.84
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 0.05 0.02 0.18
2 0.05 0.02 0.73
5 0.05 0.02 0.85
10 0.05 0.02 0.87
20 0.05 0.02 0.90
100 0.05 0.02 0.92
∞ 0.07 0.07 1.00
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
111_G 194_V 1.67 0.85 0.11
104_R 152_I 1.49 0.74 0.07
104_R 222_A 1.35 0.64 0.05
106_F 87_E 1.26 0.56 0.03
130_E 266_G 1.19 0.50 0.03
145_V 136_Q 1.11 0.43 0.02
145_V 220_S 1.11 0.42 0.02
38_I 242_A 1.10 0.41 0.02
126_L 189_I 1.07 0.39 0.02
106_F 201_Y 1.07 0.39 0.02
145_V 152_I 1.06 0.38 0.02
67_P 202_K 1.06 0.38 0.02
31_S 207_M 1.06 0.38 0.02
138_I 44_A 1.04 0.37 0.02
25_V 279_N 1.02 0.35 0.02
31_S 55_L 1.01 0.33 0.01
110_Y 209_K 1.01 0.33 0.01
67_P 151_K 1.01 0.33 0.01
107_G 176_G 0.99 0.32 0.01
26_Y 183_D 0.99 0.32 0.01
97_G 38_L 0.98 0.31 0.01
27_F 232_N 0.97 0.31 0.01
119_R 145_D 0.97 0.31 0.01
97_G 190_R 0.97 0.31 0.01
110_Y 136_Q 0.97 0.30 0.01
97_G 187_L 0.96 0.30 0.01
29_S 279_N 0.96 0.30 0.01
106_F 180_N 0.96 0.30 0.01
34_T 96_F 0.96 0.30 0.01
110_Y 215_R 0.93 0.27 0.01
97_G 9_I 0.92 0.27 0.01
70_G 232_N 0.92 0.27 0.01
41_L 272_P 0.91 0.26 0.01
100_A 194_V 0.91 0.26 0.01
40_R 118_V 0.90 0.26 0.01
97_G 37_P 0.90 0.25 0.01
101_S 211_S 0.90 0.25 0.01
32_E 203_Y 0.90 0.25 0.01
95_L 107_S 0.90 0.25 0.01
148_F 282_I 0.89 0.25 0.01
114_G 103_R 0.89 0.24 0.01
31_S 184_L 0.89 0.24 0.01
129_F 30_F 0.88 0.24 0.01
34_T 202_K 0.88 0.24 0.01
86_L 314_D 0.88 0.24 0.01
132_M 263_M 0.87 0.23 0.01
126_L 268_E 0.87 0.23 0.01
111_G 107_S 0.87 0.23 0.01
106_F 202_K 0.86 0.23 0.01
113_A 271_F 0.86 0.23 0.01
74_T 246_W 0.86 0.23 0.01
129_F 65_L 0.86 0.23 0.01
62_Y 315_E 0.86 0.23 0.01
131_L 294_H 0.86 0.23 0.01
68_S 255_C 0.86 0.23 0.01
65_I 206_N 0.85 0.22 0.01
31_S 244_T 0.85 0.22 0.01
35_Q 310_V 0.85 0.22 0.01
114_G 156_F 0.85 0.22 0.01
67_P 96_F 0.85 0.22 0.01
106_F 312_T 0.85 0.22 0.01
125_W 138_I 0.84 0.22 0.01
32_E 122_Y 0.84 0.21 0.01
101_S 172_F 0.84 0.21 0.01
147_E 216_E 0.84 0.21 0.01
79_P 176_G 0.83 0.21 0.01
111_G 76_P 0.83 0.21 0.01
143_K 211_S 0.83 0.21 0.01
114_G 33_P 0.83 0.21 0.01
110_Y 273_A 0.83 0.21 0.01
141_V 198_Y 0.83 0.21 0.01
41_L 314_D 0.83 0.21 0.01
40_R 225_L 0.83 0.21 0.01
96_R 207_M 0.83 0.21 0.01
100_A 20_L 0.82 0.20 0.01
136_S 273_A 0.82 0.20 0.01
136_S 216_E 0.82 0.20 0.01
114_G 275_M 0.82 0.20 0.01
143_K 209_K 0.82 0.20 0.01
50_L 315_E 0.82 0.20 0.01
63_I 54_Q 0.82 0.20 0.01
106_F 93_N 0.82 0.20 0.01
99_I 303_S 0.81 0.20 0.01
36_R 85_P 0.81 0.20 0.01
82_V 180_N 0.81 0.20 0.01
139_E 215_R 0.81 0.20 0.01
71_G 26_L 0.81 0.20 0.01
58_V 129_A 0.81 0.20 0.01
150_Q 246_W 0.81 0.20 0.01
73_G 246_W 0.81 0.20 0.01
106_F 205_K 0.81 0.20 0.01
69_Y 202_K 0.81 0.19 0.01
62_Y 52_E 0.80 0.19 0.01
54_E 273_A 0.80 0.19 0.01
38_I 306_M 0.80 0.19 0.01
111_G 227_L 0.80 0.19 0.01
149_W 99_A 0.80 0.19 0.01
108_E 116_K 0.79 0.19 0.01
120_K 286_L 0.79 0.19 0.01
132_M 122_Y 0.79 0.19 0.01
77_A 119_D 0.79 0.19 0.01
38_I 129_A 0.79 0.19 0.01
71_G 203_Y 0.79 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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