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OPENSEQ.org
Grasx3
Genes: A B A+B
Length: 307 346 614
Sequences: 201 19045 101
Seq/Len: 0.65 55.04 0.16
MirrorTree (Pazo et al. 2001) 0.43
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 0.00 0.00 0.00
2 0.00 0.01 0.03
5 0.00 0.02 0.03
10 0.00 0.04 0.03
20 0.00 0.07 0.04
100 0.00 0.15 0.07
∞ 0.03 0.22 0.15
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
79_A 132_K 1.50 0.27 0.00
69_V 72_F 1.28 0.19 0.00
254_Y 282_F 1.28 0.19 0.00
79_A 277_I 1.24 0.17 0.00
110_I 302_D 1.22 0.17 0.00
146_V 262_I 1.21 0.17 0.00
45_M 224_I 1.20 0.16 0.00
11_T 56_I 1.20 0.16 0.00
244_F 129_H 1.19 0.16 0.00
244_F 134_P 1.19 0.16 0.00
244_F 237_N 1.19 0.16 0.00
244_F 295_G 1.19 0.16 0.00
244_F 297_G 1.19 0.16 0.00
274_A 47_V 1.19 0.16 0.00
144_V 324_V 1.17 0.15 0.00
268_I 235_L 1.17 0.15 0.00
185_K 241_Y 1.14 0.14 0.00
249_E 279_E 1.12 0.14 0.00
5_V 173_R 1.09 0.13 0.00
27_E 118_N 1.09 0.13 0.00
123_E 56_I 1.08 0.13 0.00
5_V 192_V 1.08 0.13 0.00
122_I 22_L 1.08 0.13 0.00
69_V 299_Y 1.07 0.12 0.00
286_V 32_S 1.06 0.12 0.00
4_K 210_F 1.06 0.12 0.00
98_G 164_M 1.06 0.12 0.00
19_S 238_A 1.05 0.12 0.00
28_L 208_I 1.04 0.12 0.00
244_F 266_G 1.04 0.12 0.00
136_N 19_F 1.04 0.12 0.00
18_L 254_I 1.04 0.12 0.00
278_K 23_F 1.04 0.12 0.00
274_A 12_K 1.03 0.12 0.00
244_F 298_L 1.02 0.12 0.00
280_M 25_N 1.02 0.11 0.00
24_N 168_Q 1.02 0.11 0.00
69_V 300_L 1.01 0.11 0.00
129_G 230_I 1.01 0.11 0.00
23_E 304_V 1.00 0.11 0.00
76_K 199_T 1.00 0.11 0.00
9_G 129_H 1.00 0.11 0.00
9_G 134_P 1.00 0.11 0.00
9_G 237_N 1.00 0.11 0.00
9_G 295_G 1.00 0.11 0.00
9_G 297_G 1.00 0.11 0.00
70_F 9_Y 1.00 0.11 0.00
129_G 281_G 1.00 0.11 0.00
10_G 239_L 0.99 0.11 0.00
91_L 175_E 0.99 0.11 0.00
180_W 113_Q 0.98 0.11 0.00
130_T 171_I 0.98 0.11 0.00
110_I 187_S 0.98 0.10 0.00
62_M 140_L 0.98 0.10 0.00
11_T 260_L 0.98 0.10 0.00
264_L 274_M 0.97 0.10 0.00
45_M 251_T 0.97 0.10 0.00
12_G 129_H 0.97 0.10 0.00
12_G 134_P 0.97 0.10 0.00
12_G 237_N 0.97 0.10 0.00
12_G 295_G 0.97 0.10 0.00
12_G 297_G 0.97 0.10 0.00
131_P 55_L 0.97 0.10 0.00
107_K 67_K 0.97 0.10 0.00
79_A 122_Q 0.97 0.10 0.00
68_A 58_L 0.97 0.10 0.00
195_H 59_I 0.97 0.10 0.00
191_T 148_Q 0.97 0.10 0.00
38_K 40_I 0.97 0.10 0.00
209_L 72_F 0.96 0.10 0.00
56_E 249_I 0.96 0.10 0.00
274_A 280_R 0.96 0.10 0.00
171_K 241_Y 0.96 0.10 0.00
96_N 241_Y 0.95 0.10 0.00
10_G 167_T 0.95 0.10 0.00
14_I 88_E 0.94 0.10 0.00
272_I 22_L 0.94 0.10 0.00
10_G 319_G 0.94 0.10 0.00
7_L 256_Q 0.94 0.10 0.00
244_F 264_D 0.94 0.10 0.00
271_F 44_F 0.93 0.10 0.00
94_A 309_G 0.93 0.10 0.00
70_F 198_L 0.93 0.10 0.00
278_K 27_L 0.93 0.09 0.00
117_Y 274_M 0.93 0.09 0.00
14_I 62_F 0.92 0.09 0.00
202_I 279_E 0.92 0.09 0.00
68_A 84_K 0.92 0.09 0.00
7_L 204_Q 0.92 0.09 0.00
127_A 152_Q 0.92 0.09 0.00
110_I 239_L 0.92 0.09 0.00
45_M 149_E 0.92 0.09 0.00
245_R 217_D 0.91 0.09 0.00
52_I 199_T 0.91 0.09 0.00
257_L 233_Q 0.91 0.09 0.00
279_M 33_L 0.91 0.09 0.00
24_N 77_E 0.91 0.09 0.00
143_L 54_T 0.91 0.09 0.00
190_K 274_M 0.91 0.09 0.00
245_R 269_I 0.90 0.09 0.00
271_F 34_I 0.90 0.09 0.00
247_I 19_F 0.90 0.09 0.00
137_L 28_M 0.90 0.09 0.00
113_P 43_L 0.90 0.09 0.00
136_N 34_I 0.90 0.09 0.00
280_M 13_S 0.89 0.09 0.00
183_Y 15_K 0.89 0.09 0.00
15_G 129_H 0.89 0.09 0.00
15_G 134_P 0.89 0.09 0.00
15_G 237_N 0.89 0.09 0.00
15_G 295_G 0.89 0.09 0.00
15_G 297_G 0.89 0.09 0.00
19_S 34_I 0.89 0.09 0.00
5_V 88_E 0.88 0.09 0.00
5_V 280_R 0.88 0.09 0.00
228_S 20_W 0.88 0.09 0.00
272_I 15_K 0.88 0.09 0.00
265_F 32_S 0.88 0.09 0.00
5_V 121_E 0.88 0.09 0.00
85_S 138_M 0.88 0.09 0.00
22_I 289_N 0.88 0.09 0.00
108_K 231_I 0.87 0.08 0.00
276_M 12_K 0.87 0.08 0.00
7_L 247_V 0.87 0.08 0.00
280_M 31_I 0.87 0.08 0.00
151_S 190_R 0.87 0.08 0.00
223_T 279_E 0.86 0.08 0.00
69_V 132_K 0.86 0.08 0.00
63_N 330_L 0.86 0.08 0.00
274_A 122_Q 0.86 0.08 0.00
60_A 313_Q 0.86 0.08 0.00
45_M 312_L 0.86 0.08 0.00
34_Y 299_Y 0.86 0.08 0.00
134_T 313_Q 0.86 0.08 0.00
279_M 40_I 0.86 0.08 0.00
171_K 312_L 0.86 0.08 0.00
111_Y 322_T 0.86 0.08 0.00
14_I 271_K 0.85 0.08 0.00
67_I 242_S 0.85 0.08 0.00
6_L 301_V 0.85 0.08 0.00
138_V 112_D 0.85 0.08 0.00
282_H 247_V 0.85 0.08 0.00
260_Y 51_L 0.85 0.08 0.00
110_I 311_Q 0.85 0.08 0.00
276_M 8_V 0.85 0.08 0.00
171_K 308_L 0.85 0.08 0.00
163_V 32_S 0.85 0.08 0.00
162_V 284_S 0.84 0.08 0.00
265_F 15_K 0.84 0.08 0.00
102_A 190_R 0.84 0.08 0.00
18_L 259_A 0.84 0.08 0.00
99_R 127_F 0.84 0.08 0.00
86_A 132_K 0.84 0.08 0.00
242_L 132_K 0.84 0.08 0.00
127_A 285_T 0.83 0.08 0.00
25_D 224_I 0.83 0.08 0.00
149_Q 275_P 0.83 0.08 0.00
69_V 160_R 0.83 0.08 0.00
183_Y 326_L 0.83 0.08 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)
ID Seq/Len Name Options I_Prob Status
10137 0.09 grasx10 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10135 0.09 Grasx9 Δgene:(1, ∞) A:(1E-60, 8) B:(1E-06, 4) msa: HHblits (2015_06) 0.01 Done - Shared
10134 0 Grasx8 Δgene:(1, 1) A:(1E-60, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed - Shared
10133 0 Grasx7 Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 4) msa: HHblits (2015_06) Killed - Shared
10131 1.18 Grasx6 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 2) msa: HHblits (2015_06) 0.00 Done - Shared
10130 1.2 Grasx5 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 4) msa: HHblits (2015_06) 0.00 Done - Shared
10129 0.68 Grasx4 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10128 0.16 Grasx3 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10127 0.09 grasx2 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10126 0.72 grasx1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10124 1.16 Grasx Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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