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OPENSEQ.org
Mce4A-Mce4B
Genes: A B A+B
Length: 400 350 679
Sequences: 539 1133 474
Seq/Len: 1.35 3.24 0.7
MirrorTree (Pazo et al. 2001) 0.85
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 0.01 0.86 0.63
2 0.01 0.86 0.63
5 0.01 0.86 0.63
10 0.02 0.86 0.63
20 0.02 0.86 0.63
100 0.10 0.86 0.64
∞ 0.21 0.87 0.65
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
73_I 228_L 1.48 0.65 0.00
209_V 214_V 1.40 0.59 0.00
234_I 205_T 1.38 0.57 0.00
278_K 51_D 1.38 0.57 0.00
67_V 292_I 1.34 0.54 0.00
56_K 209_A 1.34 0.53 0.00
272_R 172_L 1.33 0.53 0.00
305_I 115_I 1.31 0.52 0.00
132_V 271_L 1.31 0.51 0.00
311_G 310_A 1.30 0.51 0.00
294_I 18_V 1.30 0.51 0.00
128_P 85_A 1.30 0.50 0.00
96_S 225_V 1.29 0.49 0.00
231_N 263_S 1.27 0.48 0.00
168_S 93_T 1.26 0.47 0.00
132_V 150_R 1.26 0.47 0.00
138_Q 98_T 1.25 0.46 0.00
199_L 282_D 1.25 0.46 0.00
116_I 24_L 1.24 0.46 0.00
190_R 88_I 1.22 0.44 0.00
58_A 245_A 1.22 0.43 0.00
221_N 160_K 1.22 0.43 0.00
189_T 102_I 1.22 0.43 0.00
234_I 199_L 1.19 0.41 0.00
181_L 196_R 1.17 0.40 0.00
192_A 221_F 1.17 0.40 0.00
206_A 189_F 1.16 0.39 0.00
216_A 94_L 1.16 0.39 0.00
24_G 25_L 1.14 0.37 0.00
112_S 25_L 1.14 0.37 0.00
155_I 158_A 1.13 0.36 0.00
338_G 344_G 1.13 0.36 0.00
86_I 268_Q 1.12 0.36 0.00
157_P 104_Y 1.12 0.35 0.00
141_V 98_T 1.12 0.35 0.00
227_L 50_T 1.11 0.35 0.00
303_P 159_D 1.11 0.34 0.00
61_K 234_G 1.10 0.34 0.00
72_D 43_T 1.10 0.34 0.00
304_L 237_K 1.10 0.34 0.00
113_V 244_G 1.08 0.33 0.00
72_D 18_V 1.08 0.33 0.00
182_L 225_V 1.08 0.32 0.00
97_N 289_N 1.08 0.32 0.00
64_G 68_V 1.08 0.32 0.00
88_S 178_P 1.08 0.32 0.00
223_V 26_V 1.08 0.32 0.00
57_G 292_I 1.07 0.32 0.00
186_N 98_T 1.07 0.32 0.00
237_Q 225_V 1.07 0.32 0.00
42_T 74_V 1.07 0.32 0.00
47_S 99_R 1.07 0.32 0.00
244_T 52_A 1.07 0.32 0.00
289_C 345_R 1.07 0.32 0.00
120_T 25_L 1.07 0.32 0.00
167_L 91_S 1.06 0.31 0.00
167_L 265_R 1.06 0.31 0.00
41_D 100_A 1.06 0.31 0.00
234_I 278_A 1.06 0.31 0.00
115_F 239_R 1.05 0.30 0.00
58_A 186_T 1.05 0.30 0.00
115_F 33_V 1.05 0.30 0.00
19_A 22_V 1.04 0.30 0.00
72_D 14_I 1.04 0.30 0.00
43_V 102_I 1.04 0.30 0.00
105_N 105_E 1.04 0.30 0.00
223_V 51_D 1.04 0.30 0.00
243_D 104_Y 1.04 0.30 0.00
321_G 278_A 1.04 0.29 0.00
165_S 157_D 1.03 0.29 0.00
130_A 279_T 1.03 0.29 0.00
205_K 214_V 1.03 0.29 0.00
152_L 164_I 1.03 0.29 0.00
98_A 158_A 1.03 0.29 0.00
311_G 318_S 1.03 0.29 0.00
161_N 183_L 1.03 0.29 0.00
113_V 278_A 1.03 0.29 0.00
91_M 187_G 1.02 0.29 0.00
83_K 134_A 1.02 0.28 0.00
149_I 273_N 1.02 0.28 0.00
91_M 108_V 1.02 0.28 0.00
39_S 25_L 1.02 0.28 0.00
52_L 110_D 1.02 0.28 0.00
89_G 160_K 1.01 0.28 0.00
27_V 252_T 1.01 0.28 0.00
25_S 113_L 1.01 0.28 0.00
142_N 299_Y 1.01 0.28 0.00
257_E 12_M 1.01 0.28 0.00
182_L 126_P 1.01 0.28 0.00
47_S 75_K 1.01 0.28 0.00
243_D 18_V 1.01 0.27 0.00
104_G 60_K 1.00 0.27 0.00
340_P 323_I 1.00 0.27 0.00
176_D 257_T 1.00 0.27 0.00
101_R 33_V 1.00 0.27 0.00
177_D 17_S 1.00 0.27 0.00
73_I 210_V 1.00 0.27 0.00
273_L 311_F 1.00 0.27 0.00
39_S 212_A 0.99 0.27 0.00
269_A 299_Y 0.99 0.27 0.00
234_I 90_R 0.99 0.27 0.00
168_S 177_G 0.99 0.26 0.00
203_F 101_V 0.99 0.26 0.00
48_P 190_S 0.99 0.26 0.00
127_S 29_G 0.99 0.26 0.00
320_L 165_T 0.99 0.26 0.00
29_T 32_V 0.99 0.26 0.00
309_K 298_D 0.98 0.26 0.00
57_G 54_R 0.98 0.26 0.00
32_S 273_N 0.98 0.26 0.00
113_V 181_N 0.98 0.26 0.00
86_I 251_S 0.98 0.26 0.00
167_L 246_I 0.98 0.26 0.00
331_L 34_F 0.98 0.26 0.00
149_I 51_D 0.98 0.25 0.00
69_K 113_L 0.97 0.25 0.00
66_Q 221_F 0.97 0.25 0.00
294_I 291_D 0.97 0.25 0.00
20_G 21_V 0.97 0.25 0.00
151_L 91_S 0.97 0.25 0.00
167_L 166_S 0.97 0.25 0.00
130_A 183_L 0.97 0.25 0.00
110_A 105_E 0.97 0.25 0.00
146_Q 82_I 0.97 0.25 0.00
178_L 261_R 0.97 0.25 0.00
112_S 167_A 0.97 0.25 0.00
82_L 299_Y 0.96 0.25 0.00
13_V 287_E 0.96 0.24 0.00
79_Q 160_K 0.96 0.24 0.00
91_M 209_A 0.96 0.24 0.00
192_A 28_A 0.96 0.24 0.00
165_S 146_L 0.96 0.24 0.00
275_A 168_V 0.95 0.24 0.00
80_A 281_L 0.95 0.24 0.00
119_K 101_V 0.95 0.24 0.00
214_A 114_E 0.95 0.24 0.00
331_L 38_R 0.95 0.24 0.00
329_E 64_A 0.95 0.24 0.00
219_D 40_G 0.95 0.23 0.00
176_D 177_G 0.94 0.23 0.00
54_M 127_P 0.94 0.23 0.00
321_G 143_D 0.94 0.23 0.00
210_A 257_T 0.94 0.23 0.00
110_A 23_M 0.94 0.23 0.00
214_A 76_L 0.94 0.23 0.00
168_S 233_S 0.94 0.23 0.00
13_V 270_I 0.94 0.23 0.00
229_T 187_G 0.93 0.23 0.00
297_G 319_V 0.93 0.23 0.00
245_L 302_L 0.93 0.23 0.00
172_R 343_K 0.93 0.23 0.00
9_T 10_R 0.93 0.23 0.00
189_T 17_S 0.93 0.22 0.00
227_L 16_V 0.93 0.22 0.00
25_S 141_D 0.93 0.22 0.00
107_I 114_E 0.93 0.22 0.00
174_H 238_N 0.93 0.22 0.00
118_P 113_L 0.92 0.22 0.00
287_F 227_Q 0.92 0.22 0.00
104_G 224_S 0.92 0.22 0.00
31_L 250_A 0.92 0.22 0.00
140_E 264_R 0.92 0.22 0.00
285_P 66_V 0.92 0.22 0.00
233_T 197_D 0.92 0.22 0.00
17_L 212_A 0.92 0.22 0.00
168_S 74_V 0.92 0.22 0.00
137_V 38_R 0.92 0.22 0.00
168_S 102_I 0.92 0.22 0.00
110_A 143_D 0.92 0.22 0.00
19_A 17_S 0.92 0.22 0.00
266_F 236_A 0.92 0.22 0.00
72_D 73_A 0.92 0.22 0.00
285_P 201_G 0.92 0.22 0.00
36_A 257_T 0.92 0.22 0.00
21_L 257_T 0.92 0.22 0.00
21_L 43_T 0.92 0.22 0.00
7_R 261_R 0.91 0.21 0.00
314_T 137_Q 0.91 0.21 0.00
154_K 123_R 0.91 0.21 0.00
270_I 33_V 0.91 0.21 0.00
113_V 18_V 0.91 0.21 0.00
168_S 169_I 0.91 0.21 0.00
47_S 143_D 0.91 0.21 0.00
262_A 173_Q 0.91 0.21 0.00
167_L 244_G 0.91 0.21 0.00
185_L 16_V 0.91 0.21 0.00
138_Q 95_Y 0.90 0.21 0.00
189_T 345_R 0.90 0.21 0.00
126_L 267_L 0.90 0.21 0.00
20_G 278_A 0.90 0.21 0.00
269_A 20_A 0.90 0.21 0.00
263_E 153_L 0.90 0.21 0.00
169_E 52_A 0.90 0.21 0.00
73_I 156_F 0.90 0.21 0.00
141_V 63_I 0.90 0.21 0.00
295_A 63_I 0.90 0.21 0.00
338_G 328_G 0.90 0.21 0.00
96_S 45_Y 0.90 0.21 0.00
227_L 18_V 0.90 0.20 0.00
206_A 134_A 0.90 0.20 0.00
221_N 256_L 0.89 0.20 0.00
278_K 263_S 0.89 0.20 0.00
28_L 116_T 0.89 0.20 0.00
259_L 214_V 0.89 0.20 0.00
236_D 301_R 0.89 0.20 0.00
230_I 189_F 0.89 0.20 0.00
176_D 127_P 0.89 0.20 0.00
171_L 206_N 0.89 0.20 0.00
22_M 21_V 0.89 0.20 0.00
258_T 171_L 0.89 0.20 0.00
119_K 278_A 0.89 0.20 0.00
16_A 220_Q 0.89 0.20 0.00
17_L 21_V 0.89 0.20 0.00
52_L 38_R 0.89 0.20 0.00
236_D 182_V 0.89 0.20 0.00
123_P 123_R 0.88 0.20 0.00
284_S 249_L 0.88 0.20 0.00
214_A 271_L 0.88 0.20 0.00
309_K 79_D 0.88 0.20 0.00
96_S 316_F 0.88 0.20 0.00
335_N 265_R 0.88 0.20 0.00
344_G 96_S 0.88 0.20 0.00
231_N 239_R 0.88 0.20 0.00
148_L 182_V 0.88 0.20 0.00
148_L 246_I 0.88 0.20 0.00
51_G 106_N 0.88 0.20 0.00
241_L 55_L 0.88 0.20 0.00
299_K 281_L 0.88 0.20 0.00
126_L 228_L 0.88 0.20 0.00
41_D 21_V 0.88 0.20 0.00
310_A 291_D 0.88 0.20 0.00
125_P 246_I 0.88 0.20 0.00
244_T 32_V 0.88 0.20 0.00
128_P 93_T 0.88 0.20 0.00
234_I 43_T 0.88 0.20 0.00
286_V 323_I 0.88 0.20 0.00
38_T 126_P 0.88 0.19 0.00
253_N 83_D 0.88 0.19 0.00
227_L 286_A 0.87 0.19 0.00
178_L 277_L 0.87 0.19 0.00
223_V 82_I 0.87 0.19 0.00
123_P 272_E 0.87 0.19 0.00
217_A 55_L 0.87 0.19 0.00
19_A 211_L 0.87 0.19 0.00
125_P 102_I 0.87 0.19 0.00
238_K 134_A 0.87 0.19 0.00
280_T 247_S 0.87 0.19 0.00
308_R 250_A 0.87 0.19 0.00
180_A 70_S 0.87 0.19 0.00
47_S 200_I 0.87 0.19 0.00
104_G 347_A 0.87 0.19 0.00
99_T 91_S 0.87 0.19 0.00
139_L 145_L 0.87 0.19 0.00
312_L 225_V 0.87 0.19 0.00
59_K 245_A 0.87 0.19 0.00
86_I 132_N 0.87 0.19 0.00
91_M 106_N 0.87 0.19 0.00
41_D 226_D 0.87 0.19 0.00
130_A 13_V 0.87 0.19 0.00
23_V 102_I 0.87 0.19 0.00
54_M 85_A 0.87 0.19 0.00
291_F 87_A 0.87 0.19 0.00
259_L 319_V 0.87 0.19 0.00
153_H 191_A 0.86 0.19 0.00
62_Y 221_F 0.86 0.19 0.00
57_G 145_L 0.86 0.19 0.00
202_D 54_R 0.86 0.19 0.00
157_P 103_R 0.86 0.19 0.00
181_L 228_L 0.86 0.19 0.00
251_L 240_D 0.86 0.19 0.00
40_T 25_L 0.86 0.19 0.00
76_S 157_D 0.86 0.19 0.00
39_S 244_G 0.86 0.18 0.00
293_G 103_R 0.86 0.18 0.00
72_D 240_D 0.86 0.18 0.00
120_T 133_V 0.85 0.18 0.00
115_F 137_Q 0.85 0.18 0.00
197_P 176_G 0.85 0.18 0.00
21_L 180_A 0.85 0.18 0.00
59_K 60_K 0.85 0.18 0.00
148_L 159_D 0.85 0.18 0.00
39_S 226_D 0.85 0.18 0.00
312_L 32_V 0.85 0.18 0.00
222_T 225_V 0.85 0.18 0.00
55_E 322_K 0.85 0.18 0.00
197_P 243_A 0.85 0.18 0.00
79_Q 303_S 0.85 0.18 0.00
86_I 40_G 0.85 0.18 0.00
141_V 25_L 0.85 0.18 0.00
194_P 181_N 0.85 0.18 0.00
220_L 313_N 0.85 0.18 0.00
40_T 11_S 0.85 0.18 0.00
15_A 302_L 0.84 0.18 0.00
128_P 32_V 0.84 0.18 0.00
85_A 248_P 0.84 0.18 0.00
116_I 135_H 0.84 0.18 0.00
103_A 82_I 0.84 0.18 0.00
15_A 182_V 0.84 0.18 0.00
346_P 315_Y 0.84 0.18 0.00
263_E 203_V 0.84 0.18 0.00
189_T 259_L 0.84 0.18 0.00
275_A 304_A 0.84 0.18 0.00
312_L 133_V 0.84 0.18 0.00
252_S 114_E 0.84 0.18 0.00
281_S 224_S 0.84 0.18 0.00
232_K 18_V 0.84 0.18 0.00
134_A 36_D 0.84 0.18 0.00
290_L 303_S 0.84 0.18 0.00
298_V 319_V 0.84 0.18 0.00
82_L 140_L 0.84 0.18 0.00
192_A 302_L 0.84 0.17 0.00
266_F 311_F 0.84 0.17 0.00
294_I 211_L 0.84 0.17 0.00
87_D 133_V 0.84 0.17 0.00
24_G 223_A 0.84 0.17 0.00
262_A 304_A 0.84 0.17 0.00
16_A 121_E 0.83 0.17 0.00
107_I 146_L 0.83 0.17 0.00
132_V 316_F 0.83 0.17 0.00
65_I 45_Y 0.83 0.17 0.00
165_S 10_R 0.83 0.17 0.00
54_M 320_T 0.83 0.17 0.00
120_T 123_R 0.83 0.17 0.00
302_A 295_L 0.83 0.17 0.00
56_K 46_H 0.83 0.17 0.00
155_I 181_N 0.83 0.17 0.00
334_V 343_K 0.83 0.17 0.00
135_S 51_D 0.83 0.17 0.00
99_T 73_A 0.83 0.17 0.00
80_A 313_N 0.83 0.17 0.00
141_V 150_R 0.83 0.17 0.00
268_D 169_I 0.83 0.17 0.00
268_D 290_N 0.83 0.17 0.00
222_T 205_T 0.83 0.17 0.00
206_A 153_L 0.83 0.17 0.00
232_K 134_A 0.83 0.17 0.00
312_L 76_L 0.83 0.17 0.00
93_F 129_G 0.83 0.17 0.00
320_L 77_N 0.83 0.17 0.00
287_F 271_L 0.83 0.17 0.00
70_V 64_A 0.83 0.17 0.00
267_I 42_T 0.83 0.17 0.00
36_A 250_A 0.82 0.17 0.00
29_T 288_V 0.82 0.17 0.00
297_G 277_L 0.82 0.17 0.00
307_V 278_A 0.82 0.17 0.00
157_P 274_A 0.82 0.17 0.00
29_T 169_I 0.82 0.17 0.00
289_C 264_R 0.82 0.17 0.00
9_T 21_V 0.82 0.17 0.00
89_G 50_T 0.82 0.17 0.00
159_E 275_R 0.82 0.17 0.00
238_K 14_I 0.82 0.17 0.00
219_D 50_T 0.82 0.17 0.00
73_I 231_L 0.82 0.17 0.00
118_P 253_T 0.82 0.17 0.00
15_A 323_I 0.82 0.17 0.00
157_P 308_Y 0.82 0.17 0.00
106_T 143_D 0.82 0.17 0.00
241_L 150_R 0.82 0.17 0.00
16_A 17_S 0.82 0.17 0.00
189_T 158_A 0.82 0.17 0.00
287_F 325_G 0.82 0.17 0.00
209_V 217_K 0.82 0.17 0.00
21_L 134_A 0.82 0.17 0.00
44_T 127_P 0.82 0.17 0.00
38_T 169_I 0.82 0.17 0.00
116_I 11_S 0.82 0.17 0.00
233_T 190_S 0.82 0.17 0.00
193_N 66_V 0.82 0.17 0.00
155_I 165_T 0.82 0.17 0.00
22_M 134_A 0.82 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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.86 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
11266 0.7 Mce4A-Mce4B Δgene:(1, 1) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11265 0.7 Mce4A-Mce4B Δgene:(1, 2) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11264 0.7 Mce4A-Mce4B Δgene:(1, 5) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11263 0.01 Mce4A-Mce4B Δgene:(1, 20) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
11262 0 Mce4A-Mce4B Δgene:(1, 20) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2015_06) Killed - Shared
11253 0.71 Mce4A-Mce4B Δgene:(1, 20) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11244 1.08 Mce4A-Mce4B-2 Δgene:(0, 2) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 1.00 Done - Shared
11243 1.08 Mce4A-Mce4B-2 Δgene:(0, 1) A:(1E-02, 8) B:(1E-04, 8) msa: HHblits (2015_06) 1.00 Done - Shared
11242 1.08 Mce4A-Mce4B-2 Δgene:(0, 1) A:(1E-02, 2) B:(1E-04, 2) msa: HHblits (2015_06) 1.00 Done - Shared
11241 0.7 Mce4A-Mce4B Δgene:(1, 10) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11233 0.7 Katherine Δgene:(0, 1) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11232 0 Mce4A-Mce4B Δgene:(1, 1) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2015_06) Killed - Shared
11231 1.08 Mce4A-Mce4B-2 Δgene:(0, 1) A:(1E-02, 2) B:(1E-02, 2) msa: HHblits (2015_06) 1.00 Done - Shared
11230 0.01 Mce4A-Mce4Bx3 Δgene:(1, 1) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
11229 0.01 Mce4A-Mce4B-2 Δgene:(1, 100) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
11223 0.02 Katherine Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) Killed - Shared
11214 0.03 Mce4A-Mce4B Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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