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OPENSEQ.org
Ec AZ
Genes: A B A+B
Length: 420 383 727
Sequences: 2365 2098 1248
Seq/Len: 5.63 5.48 1.72
MirrorTree (Pazo et al. 2001) 0.58
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 0.02 1.52
2 0.00 0.02 1.53
5 0.00 0.02 1.55
10 0.00 0.02 1.55
20 0.00 0.02 1.55
100 0.01 0.03 1.59
∞ 0.09 0.05 1.73
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
341_I 306_L 1.32 0.79 0.04
52_N 100_I 1.28 0.75 0.04
334_L 323_I 1.10 0.59 0.02
186_I 180_D 1.08 0.57 0.02
219_A 260_V 1.07 0.55 0.02
244_A 150_I 1.06 0.55 0.02
55_E 288_D 1.06 0.55 0.02
235_A 186_N 1.05 0.53 0.02
297_I 92_L 1.04 0.52 0.02
298_E 26_V 1.04 0.52 0.02
139_Y 171_V 1.03 0.51 0.02
202_R 175_G 1.03 0.51 0.02
65_I 305_E 1.02 0.50 0.02
65_I 289_N 1.00 0.48 0.02
178_C 60_I 0.99 0.47 0.02
161_I 302_M 0.98 0.46 0.02
35_I 40_F 0.97 0.45 0.01
43_S 115_V 0.97 0.45 0.01
124_E 187_D 0.97 0.45 0.01
63_R 116_V 0.97 0.45 0.01
142_G 244_I 0.97 0.44 0.01
69_E 274_E 0.97 0.44 0.01
182_V 258_R 0.95 0.43 0.01
339_A 16_I 0.94 0.42 0.01
51_V 113_A 0.94 0.42 0.01
72_A 80_A 0.94 0.41 0.01
286_R 264_I 0.94 0.41 0.01
31_G 140_K 0.94 0.41 0.01
198_T 162_T 0.94 0.41 0.01
80_Y 76_V 0.93 0.41 0.01
209_V 58_I 0.93 0.40 0.01
220_V 150_I 0.92 0.39 0.01
308_V 144_A 0.91 0.39 0.01
379_A 21_G 0.91 0.38 0.01
357_R 21_G 0.90 0.37 0.01
401_V 26_V 0.90 0.37 0.01
199_E 76_V 0.89 0.37 0.01
301_Y 115_V 0.89 0.36 0.01
84_S 267_G 0.88 0.36 0.01
208_V 234_D 0.88 0.35 0.01
394_E 60_I 0.87 0.35 0.01
127_V 125_I 0.87 0.35 0.01
109_V 299_D 0.87 0.34 0.01
298_E 187_D 0.87 0.34 0.01
188_A 23_G 0.86 0.34 0.01
289_Q 206_M 0.86 0.34 0.01
100_S 57_T 0.86 0.34 0.01
302_T 265_T 0.86 0.34 0.01
25_G 194_Q 0.86 0.34 0.01
331_G 246_S 0.86 0.33 0.01
409_I 92_L 0.86 0.33 0.01
211_I 73_N 0.85 0.33 0.01
145_N 26_V 0.85 0.33 0.01
156_A 199_L 0.85 0.33 0.01
61_V 236_A 0.85 0.33 0.01
4_A 224_M 0.85 0.33 0.01
383_L 23_G 0.85 0.33 0.01
234_Y 230_A 0.85 0.32 0.01
76_I 78_R 0.84 0.32 0.01
135_Y 231_S 0.84 0.32 0.01
413_N 234_D 0.84 0.32 0.01
243_I 201_T 0.83 0.31 0.01
128_L 53_A 0.83 0.31 0.01
53_D 55_G 0.83 0.31 0.01
162_T 159_S 0.83 0.31 0.01
326_H 16_I 0.83 0.30 0.01
18_A 205_L 0.82 0.30 0.01
106_Q 88_L 0.82 0.30 0.01
200_D 64_I 0.82 0.30 0.01
243_I 259_G 0.82 0.30 0.01
202_R 233_E 0.82 0.30 0.01
76_I 41_A 0.82 0.30 0.01
131_I 116_V 0.82 0.30 0.01
104_V 282_I 0.82 0.29 0.01
257_I 130_V 0.82 0.29 0.01
151_G 141_K 0.81 0.29 0.01
239_V 300_P 0.81 0.29 0.01
25_G 58_I 0.81 0.29 0.01
172_V 21_G 0.81 0.29 0.01
17_T 21_G 0.81 0.29 0.01
339_A 56_Q 0.81 0.29 0.01
185_L 302_M 0.81 0.29 0.01
218_I 303_N 0.81 0.29 0.01
157_K 100_I 0.81 0.29 0.01
216_M 97_M 0.81 0.29 0.01
274_S 116_V 0.81 0.29 0.01
202_R 78_R 0.81 0.28 0.01
321_Q 308_V 0.80 0.28 0.01
232_I 72_A 0.80 0.28 0.01
89_S 316_G 0.80 0.28 0.01
377_S 318_D 0.79 0.27 0.01
220_V 289_N 0.79 0.27 0.01
255_E 128_V 0.79 0.27 0.01
114_H 219_E 0.79 0.27 0.01
143_I 272_L 0.79 0.27 0.01
158_V 96_D 0.79 0.27 0.01
54_L 21_G 0.79 0.27 0.01
156_A 279_G 0.79 0.27 0.01
53_D 282_I 0.79 0.27 0.01
33_V 30_V 0.79 0.27 0.01
305_L 307_R 0.79 0.27 0.01
55_E 121_K 0.79 0.27 0.01
25_G 73_N 0.79 0.27 0.01
63_R 141_K 0.78 0.27 0.01
338_A 198_E 0.78 0.26 0.01
235_A 27_E 0.78 0.26 0.01
50_G 21_G 0.78 0.26 0.01
202_R 214_R 0.78 0.26 0.01
340_Q 34_I 0.78 0.26 0.01
209_V 300_P 0.77 0.26 0.01
83_L 217_M 0.77 0.26 0.01
104_V 128_V 0.77 0.26 0.01
178_C 171_V 0.77 0.26 0.01
31_G 26_V 0.77 0.26 0.01
169_K 177_S 0.77 0.26 0.01
47_D 129_A 0.77 0.26 0.01
301_Y 52_T 0.77 0.26 0.01
275_V 159_S 0.77 0.26 0.01
330_A 21_G 0.77 0.26 0.01
104_V 130_V 0.77 0.26 0.01
233_P 160_L 0.77 0.26 0.01
36_I 21_G 0.77 0.26 0.01
321_Q 280_N 0.77 0.25 0.01
115_T 199_L 0.77 0.25 0.01
148_G 246_S 0.77 0.25 0.01
276_E 192_A 0.77 0.25 0.01
33_V 299_D 0.77 0.25 0.01
15_I 199_L 0.77 0.25 0.01
25_G 16_I 0.77 0.25 0.01
14_E 40_F 0.76 0.25 0.01
223_G 261_L 0.76 0.25 0.01
163_C 262_V 0.76 0.25 0.01
344_L 156_H 0.76 0.25 0.01
160_L 155_K 0.76 0.25 0.01
160_L 245_S 0.76 0.25 0.01
60_C 118_E 0.76 0.25 0.01
48_K 72_A 0.76 0.25 0.01
329_A 262_V 0.76 0.24 0.01
22_A 128_V 0.76 0.24 0.01
236_G 34_I 0.76 0.24 0.01
104_V 234_D 0.76 0.24 0.01
109_V 88_L 0.76 0.24 0.01
341_I 27_E 0.76 0.24 0.01
309_N 26_V 0.75 0.24 0.01
62_Q 57_T 0.75 0.24 0.01
311_E 299_D 0.75 0.24 0.01
20_V 62_S 0.75 0.24 0.01
383_L 206_M 0.75 0.24 0.01
24_V 206_M 0.75 0.24 0.01
365_T 260_V 0.75 0.24 0.01
173_K 121_K 0.75 0.24 0.01
351_V 216_V 0.75 0.24 0.01
343_G 30_V 0.74 0.23 0.01
419_E 57_T 0.74 0.23 0.01
11_V 309_T 0.74 0.23 0.01
208_V 231_S 0.74 0.23 0.01
233_P 81_A 0.74 0.23 0.01
300_R 197_A 0.74 0.23 0.01
371_A 231_S 0.74 0.23 0.01
24_V 187_D 0.74 0.23 0.01
67_Q 215_T 0.74 0.23 0.01
70_L 162_T 0.74 0.23 0.01
329_A 211_A 0.74 0.23 0.01
390_H 88_L 0.74 0.23 0.01
137_I 238_E 0.74 0.23 0.01
41_C 60_I 0.74 0.23 0.01
282_G 151_T 0.74 0.23 0.01
359_G 277_T 0.74 0.23 0.01
60_C 27_E 0.73 0.23 0.01
346_A 52_T 0.73 0.23 0.01
103_E 175_G 0.73 0.23 0.01
352_F 116_V 0.73 0.23 0.01
383_L 89_R 0.73 0.23 0.01
224_G 275_F 0.73 0.23 0.01
246_A 159_S 0.73 0.23 0.01
99_I 285_F 0.73 0.23 0.01
52_N 101_A 0.73 0.23 0.01
131_I 98_V 0.73 0.23 0.01
160_L 291_T 0.73 0.23 0.01
235_A 191_G 0.73 0.23 0.01
341_I 282_I 0.73 0.23 0.01
386_G 191_G 0.73 0.22 0.01
20_V 284_A 0.73 0.22 0.01
10_V 208_V 0.73 0.22 0.01
84_S 168_L 0.73 0.22 0.01
386_G 194_Q 0.72 0.22 0.01
226_L 238_E 0.72 0.22 0.01
56_S 82_D 0.72 0.22 0.01
259_V 60_I 0.72 0.22 0.01
312_I 42_V 0.72 0.22 0.01
284_P 214_R 0.72 0.22 0.01
71_M 259_G 0.72 0.22 0.01
147_V 125_I 0.72 0.22 0.01
128_L 23_G 0.72 0.22 0.01
374_P 306_L 0.72 0.21 0.01
339_A 161_I 0.72 0.21 0.01
298_E 310_V 0.72 0.21 0.01
32_M 264_I 0.72 0.21 0.01
350_R 197_A 0.72 0.21 0.01
275_V 283_R 0.72 0.21 0.01
125_H 176_I 0.72 0.21 0.01
338_A 267_G 0.71 0.21 0.01
73_D 83_E 0.71 0.21 0.01
166_D 119_V 0.71 0.21 0.01
330_A 308_V 0.71 0.21 0.01
289_Q 129_A 0.71 0.21 0.01
176_E 33_R 0.71 0.21 0.01
158_V 95_A 0.71 0.21 0.01
285_P 100_I 0.71 0.21 0.01
113_V 75_E 0.71 0.21 0.01
227_R 192_A 0.71 0.21 0.01
62_Q 188_V 0.71 0.21 0.01
277_V 258_R 0.71 0.21 0.01
239_V 84_D 0.71 0.21 0.01
137_I 59_Q 0.71 0.21 0.01
412_L 180_D 0.71 0.21 0.01
200_D 164_P 0.71 0.21 0.01
72_A 41_A 0.71 0.21 0.01
297_I 57_T 0.70 0.21 0.01
387_K 180_D 0.70 0.21 0.01
33_V 73_N 0.70 0.20 0.01
53_D 59_Q 0.70 0.20 0.01
61_V 319_K 0.70 0.20 0.01
339_A 257_A 0.70 0.20 0.01
235_A 81_A 0.70 0.20 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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