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OPENSEQ.org
2ONK_A_C
Genes: A B A+B
Length: 240 284 481
Sequences: 83362 22401 370
Seq/Len: 347.34 78.88 0.77
MirrorTree (Pazo et al. 2001) 0.67
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 0.10 0.40 0.39
2 0.11 0.40 0.61
5 0.15 0.41 0.64
10 0.20 0.42 0.66
20 0.25 0.43 0.71
100 0.35 0.46 0.80
∞ 0.38 0.48 0.83
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
93_Y 185_A 2.59 0.99 0.97
93_Y 198_T 2.22 0.96 0.92
76_P 184_V 1.70 0.82 0.65
83_P 203_L 1.67 0.80 0.62
18_V 51_V 1.61 0.77 0.57
68_E 186_R 1.41 0.63 0.38
55_V 70_V 1.36 0.58 0.33
42_E 183_H 1.36 0.58 0.33
137_L 220_I 1.34 0.57 0.32
194_A 96_A 1.32 0.55 0.29
78_D 180_R 1.25 0.48 0.24
55_V 109_V 1.20 0.45 0.20
197_V 199_V 1.20 0.44 0.20
210_K 82_L 1.19 0.44 0.20
106_R 107_K 1.17 0.42 0.18
86_S 41_L 1.16 0.41 0.17
154_L 132_V 1.15 0.41 0.17
224_E 199_V 1.15 0.40 0.17
67_P 145_L 1.13 0.39 0.16
146_R 76_T 1.12 0.38 0.15
60_A 156_V 1.11 0.37 0.15
47_I 187_T 1.10 0.36 0.14
183_V 84_S 1.09 0.36 0.14
112_E 42_F 1.09 0.35 0.14
73_G 116_L 1.08 0.35 0.13
21_E 108_S 1.08 0.35 0.13
20_F 131_V 1.08 0.35 0.13
162_K 97_Y 1.08 0.34 0.13
7_A 109_V 1.07 0.34 0.12
197_V 51_V 1.07 0.34 0.12
75_V 158_M 1.07 0.34 0.12
165_L 43_V 1.06 0.33 0.12
177_D 240_I 1.05 0.32 0.11
38_S 59_D 1.05 0.32 0.11
224_E 90_I 1.03 0.30 0.10
187_L 240_I 1.02 0.30 0.10
218_K 51_V 1.01 0.30 0.10
205_I 65_A 1.01 0.30 0.10
79_Y 153_G 1.00 0.29 0.09
7_A 156_V 0.99 0.28 0.09
7_A 87_I 0.98 0.27 0.08
85_L 127_I 0.97 0.27 0.08
19_D 132_V 0.97 0.27 0.08
87_V 115_D 0.97 0.27 0.08
21_E 86_L 0.97 0.26 0.08
35_A 194_R 0.96 0.26 0.08
75_V 84_S 0.96 0.26 0.08
179_P 187_T 0.96 0.26 0.08
137_L 274_V 0.95 0.26 0.08
174_R 161_V 0.95 0.26 0.07
131_E 174_F 0.95 0.25 0.07
207_E 260_I 0.95 0.25 0.07
55_V 75_L 0.95 0.25 0.07
10_R 48_A 0.95 0.25 0.07
96_R 230_A 0.95 0.25 0.07
147_L 215_S 0.94 0.25 0.07
137_L 81_A 0.94 0.24 0.07
55_V 114_V 0.93 0.24 0.07
33_T 128_A 0.93 0.24 0.07
35_A 191_S 0.92 0.23 0.07
116_I 236_A 0.92 0.23 0.06
233_L 132_V 0.91 0.23 0.06
22_M 155_V 0.91 0.23 0.06
137_L 65_A 0.90 0.22 0.06
132_R 159_L 0.89 0.22 0.06
80_A 125_A 0.89 0.21 0.06
38_S 72_K 0.89 0.21 0.06
23_G 155_V 0.89 0.21 0.06
193_L 187_T 0.88 0.21 0.05
89_R 82_L 0.88 0.21 0.05
58_N 72_K 0.88 0.21 0.05
76_P 244_Y 0.88 0.21 0.05
217_A 179_V 0.87 0.21 0.05
47_I 162_S 0.87 0.20 0.05
42_E 180_R 0.87 0.20 0.05
219_N 52_T 0.87 0.20 0.05
136_A 237_P 0.87 0.20 0.05
132_R 123_T 0.86 0.20 0.05
94_G 84_S 0.86 0.20 0.05
226_L 149_D 0.86 0.20 0.05
20_F 194_R 0.86 0.20 0.05
55_V 188_L 0.85 0.20 0.05
116_I 267_F 0.85 0.19 0.05
207_E 116_L 0.85 0.19 0.05
232_L 199_V 0.85 0.19 0.05
71_G 114_V 0.85 0.19 0.04
211_L 260_I 0.85 0.19 0.04
29_L 54_Q 0.84 0.19 0.04
207_E 178_D 0.84 0.19 0.04
112_E 257_A 0.84 0.19 0.04
162_K 267_F 0.84 0.18 0.04
75_V 196_F 0.83 0.18 0.04
216_S 35_L 0.83 0.18 0.04
38_S 54_Q 0.83 0.18 0.04
186_D 236_A 0.83 0.18 0.04
61_D 105_P 0.83 0.18 0.04
193_L 242_E 0.83 0.18 0.04
178_V 115_D 0.83 0.18 0.04
20_F 98_I 0.83 0.18 0.04
147_L 68_P 0.82 0.18 0.04
35_A 220_I 0.82 0.18 0.04
66_P 203_L 0.82 0.18 0.04
69_R 252_A 0.82 0.18 0.04
180_I 221_S 0.82 0.18 0.04
192_M 112_G 0.82 0.18 0.04
143_I 73_V 0.81 0.17 0.04
72_I 259_L 0.81 0.17 0.04
181_L 207_H 0.81 0.17 0.04
116_I 227_V 0.81 0.17 0.04
205_I 144_P 0.81 0.17 0.04
117_A 191_S 0.81 0.17 0.04
7_A 178_D 0.81 0.17 0.04
69_R 51_V 0.81 0.17 0.04
17_N 75_L 0.81 0.17 0.04
160_K 158_M 0.81 0.17 0.04
21_E 114_V 0.80 0.17 0.04
89_R 83_I 0.80 0.17 0.04
20_F 272_I 0.80 0.17 0.04
46_G 188_L 0.80 0.17 0.04
146_R 265_A 0.80 0.17 0.04
67_P 186_R 0.80 0.17 0.04
35_A 113_I 0.80 0.17 0.04
212_K 204_S 0.80 0.17 0.04
106_R 34_L 0.80 0.17 0.04
181_L 103_S 0.80 0.17 0.04
181_L 262_L 0.80 0.17 0.04
116_I 43_V 0.80 0.17 0.04
86_S 250_S 0.79 0.16 0.03
95_L 82_L 0.79 0.16 0.03
136_A 188_L 0.79 0.16 0.03
181_L 50_T 0.79 0.16 0.03
83_P 181_L 0.79 0.16 0.03
52_R 87_I 0.79 0.16 0.03
121_D 77_T 0.79 0.16 0.03
176_F 196_F 0.79 0.16 0.03
85_L 110_V 0.79 0.16 0.03
84_H 198_T 0.79 0.16 0.03
39_V 122_H 0.79 0.16 0.03
28_V 186_R 0.79 0.16 0.03
58_N 71_W 0.79 0.16 0.03
38_S 187_T 0.79 0.16 0.03
181_L 246_S 0.79 0.16 0.03
234_K 220_I 0.79 0.16 0.03
111_A 137_G 0.79 0.16 0.03
211_L 67_D 0.79 0.16 0.03
47_I 183_H 0.79 0.16 0.03
130_G 126_G 0.79 0.16 0.03
130_G 222_E 0.79 0.16 0.03
165_L 142_F 0.78 0.16 0.03
179_P 67_D 0.78 0.16 0.03
224_E 49_A 0.78 0.16 0.03
186_D 252_A 0.78 0.16 0.03
30_L 96_A 0.78 0.16 0.03
49_K 209_V 0.78 0.16 0.03
96_R 207_H 0.78 0.16 0.03
201_L 208_I 0.78 0.16 0.03
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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.43 > 0.4) of paralogs.
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