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OPENSEQ.org
AtmxI
Genes: A B A+B
Length: 339 461 750
Sequences: 1350 5981 1069
Seq/Len: 3.98 12.97 1.43
MirrorTree (Pazo et al. 2001) 0.66
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.22 0.07
2 0.01 0.48 0.15
5 0.01 0.50 0.20
10 0.01 0.52 0.39
20 0.02 0.53 1.12
100 0.03 0.56 1.34
∞ 0.07 0.58 1.57
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
32_F 22_I 1.36 0.76 0.02
292_L 320_I 1.34 0.75 0.02
107_N 150_D 1.22 0.65 0.02
85_I 237_S 1.16 0.59 0.01
48_I 344_Y 1.15 0.58 0.01
68_I 78_F 1.12 0.55 0.01
309_A 215_V 1.12 0.55 0.01
68_I 252_I 1.12 0.55 0.01
327_L 364_E 1.08 0.51 0.01
194_I 275_T 1.04 0.46 0.01
218_I 226_L 1.03 0.45 0.01
142_N 150_D 1.02 0.45 0.01
301_V 100_L 1.02 0.45 0.01
32_F 312_D 1.02 0.45 0.01
141_I 178_I 1.02 0.44 0.01
310_L 204_Q 1.01 0.44 0.01
202_A 133_M 1.01 0.44 0.01
146_V 130_I 1.01 0.44 0.01
252_I 175_M 1.00 0.43 0.01
157_Q 280_P 1.00 0.43 0.01
241_S 247_K 0.99 0.42 0.01
133_I 175_M 0.98 0.41 0.01
324_L 117_I 0.97 0.40 0.01
112_V 150_D 0.96 0.39 0.01
134_V 342_G 0.96 0.39 0.01
297_T 45_L 0.96 0.39 0.01
239_A 425_Q 0.96 0.39 0.01
191_Q 93_I 0.96 0.39 0.01
211_K 181_N 0.95 0.38 0.01
223_I 285_S 0.95 0.38 0.01
126_G 285_S 0.95 0.38 0.01
324_L 45_L 0.94 0.37 0.01
182_D 214_T 0.94 0.37 0.01
226_I 51_E 0.94 0.37 0.01
153_V 236_M 0.93 0.36 0.01
215_V 211_L 0.93 0.36 0.01
185_T 300_K 0.93 0.36 0.01
272_I 89_A 0.93 0.36 0.01
136_C 285_S 0.93 0.36 0.01
221_T 209_G 0.93 0.36 0.01
305_L 342_G 0.93 0.36 0.01
26_S 256_V 0.93 0.36 0.01
182_D 204_Q 0.93 0.36 0.01
100_M 318_D 0.93 0.35 0.01
305_L 370_R 0.92 0.35 0.01
148_K 356_V 0.92 0.35 0.01
165_M 161_L 0.92 0.35 0.01
278_K 78_F 0.91 0.34 0.01
53_L 220_T 0.90 0.34 0.01
284_A 276_T 0.89 0.33 0.01
177_N 323_Q 0.89 0.33 0.01
292_L 104_V 0.89 0.33 0.01
59_L 351_N 0.89 0.32 0.01
33_L 78_F 0.89 0.32 0.01
207_S 323_Q 0.89 0.32 0.01
307_I 247_K 0.88 0.32 0.01
252_I 374_R 0.88 0.32 0.01
264_I 230_Y 0.88 0.32 0.01
323_A 192_I 0.88 0.31 0.01
283_F 224_S 0.88 0.31 0.01
252_I 218_V 0.87 0.31 0.01
95_I 143_P 0.87 0.30 0.01
267_T 181_N 0.87 0.30 0.01
223_I 398_E 0.86 0.30 0.01
269_T 294_T 0.86 0.30 0.01
217_G 276_T 0.86 0.30 0.01
282_N 144_V 0.86 0.30 0.01
193_V 144_V 0.86 0.30 0.01
221_T 326_S 0.86 0.30 0.01
322_M 342_G 0.86 0.30 0.01
252_I 401_E 0.86 0.29 0.01
171_A 115_G 0.85 0.29 0.01
183_E 312_D 0.85 0.29 0.01
27_L 342_G 0.85 0.29 0.01
56_S 43_V 0.85 0.29 0.01
330_G 215_V 0.85 0.29 0.01
178_A 294_T 0.85 0.29 0.01
306_F 347_I 0.85 0.29 0.01
291_L 25_I 0.85 0.29 0.01
238_M 237_S 0.85 0.29 0.01
76_L 131_D 0.84 0.28 0.01
315_P 77_G 0.84 0.28 0.01
230_L 368_W 0.84 0.28 0.01
114_E 161_L 0.84 0.28 0.01
207_S 390_A 0.84 0.28 0.01
157_Q 320_I 0.84 0.28 0.01
64_I 213_D 0.84 0.28 0.01
60_S 164_F 0.84 0.28 0.01
270_A 261_M 0.84 0.28 0.01
202_A 414_G 0.83 0.27 0.01
60_S 388_I 0.83 0.27 0.01
96_A 102_R 0.83 0.27 0.01
324_L 142_F 0.82 0.27 0.01
65_L 338_L 0.82 0.27 0.01
133_I 307_F 0.82 0.26 0.01
303_F 74_F 0.82 0.26 0.01
96_A 115_G 0.82 0.26 0.01
249_I 144_V 0.82 0.26 0.01
27_L 98_E 0.81 0.26 0.01
161_T 166_G 0.81 0.26 0.01
59_L 125_I 0.81 0.26 0.01
319_L 77_G 0.81 0.26 0.01
229_F 312_D 0.81 0.26 0.01
199_F 167_S 0.81 0.26 0.01
199_F 169_V 0.81 0.26 0.01
129_V 111_K 0.81 0.26 0.01
304_V 213_D 0.81 0.25 0.01
70_I 231_G 0.81 0.25 0.01
178_A 83_R 0.81 0.25 0.01
284_A 27_A 0.81 0.25 0.01
150_S 67_S 0.81 0.25 0.01
147_T 322_D 0.81 0.25 0.01
138_L 335_S 0.81 0.25 0.01
330_G 429_L 0.81 0.25 0.01
86_I 259_F 0.80 0.25 0.01
65_L 138_I 0.80 0.25 0.01
235_Q 277_K 0.80 0.25 0.01
154_S 359_D 0.80 0.25 0.01
178_A 312_D 0.80 0.25 0.01
35_C 211_L 0.80 0.25 0.01
310_L 66_F 0.80 0.25 0.01
302_G 217_I 0.80 0.25 0.01
323_A 362_S 0.80 0.25 0.01
37_L 299_G 0.80 0.24 0.01
165_M 186_I 0.79 0.24 0.01
130_I 153_L 0.79 0.24 0.00
303_F 146_V 0.79 0.24 0.00
251_T 70_S 0.79 0.24 0.00
25_K 305_A 0.79 0.24 0.00
96_A 318_D 0.79 0.24 0.00
223_I 348_N 0.78 0.24 0.00
32_F 305_A 0.78 0.24 0.00
177_N 261_M 0.78 0.24 0.00
324_L 93_I 0.78 0.24 0.00
275_R 156_G 0.78 0.24 0.00
287_T 68_Y 0.78 0.23 0.00
218_I 407_E 0.78 0.23 0.00
279_D 422_E 0.78 0.23 0.00
100_M 220_T 0.78 0.23 0.00
122_F 35_L 0.78 0.23 0.00
94_N 34_G 0.78 0.23 0.00
34_V 51_E 0.78 0.23 0.00
221_T 148_T 0.78 0.23 0.00
318_S 39_V 0.78 0.23 0.00
33_L 67_S 0.78 0.23 0.00
194_I 300_K 0.77 0.23 0.00
177_N 390_A 0.77 0.23 0.00
217_G 224_S 0.77 0.23 0.00
142_N 143_P 0.77 0.23 0.00
302_G 388_I 0.77 0.23 0.00
124_V 233_F 0.77 0.23 0.00
46_S 245_Q 0.77 0.23 0.00
123_V 283_V 0.77 0.22 0.00
266_S 412_F 0.77 0.22 0.00
103_S 126_M 0.77 0.22 0.00
202_A 351_N 0.77 0.22 0.00
223_I 31_E 0.76 0.22 0.00
335_Q 376_N 0.76 0.22 0.00
86_I 351_N 0.76 0.22 0.00
123_V 234_C 0.76 0.22 0.00
199_F 390_A 0.76 0.22 0.00
44_L 413_L 0.76 0.22 0.00
223_I 178_I 0.76 0.22 0.00
120_G 154_T 0.76 0.22 0.00
219_I 133_M 0.76 0.22 0.00
233_S 377_S 0.76 0.22 0.00
307_I 153_L 0.76 0.22 0.00
199_F 323_Q 0.76 0.22 0.00
72_K 230_Y 0.76 0.22 0.00
271_I 192_I 0.76 0.22 0.00
144_M 224_S 0.76 0.22 0.00
170_M 291_M 0.76 0.22 0.00
96_A 112_D 0.76 0.22 0.00
211_K 369_A 0.76 0.22 0.00
266_S 390_A 0.76 0.22 0.00
252_I 296_K 0.75 0.21 0.00
61_V 356_V 0.75 0.21 0.00
148_K 280_P 0.75 0.21 0.00
147_T 81_G 0.75 0.21 0.00
207_S 261_M 0.75 0.21 0.00
219_I 427_L 0.75 0.21 0.00
58_A 107_F 0.75 0.21 0.00
128_M 280_P 0.74 0.21 0.00
264_I 29_S 0.74 0.21 0.00
239_A 30_I 0.74 0.21 0.00
101_I 383_E 0.74 0.21 0.00
219_I 320_I 0.74 0.21 0.00
78_T 142_F 0.74 0.21 0.00
24_A 201_E 0.74 0.21 0.00
200_Y 181_N 0.74 0.21 0.00
92_S 235_A 0.74 0.20 0.00
296_R 106_P 0.74 0.20 0.00
34_V 39_V 0.74 0.20 0.00
265_T 318_D 0.74 0.20 0.00
39_I 144_V 0.74 0.20 0.00
92_S 151_A 0.74 0.20 0.00
197_A 261_M 0.74 0.20 0.00
93_L 42_I 0.74 0.20 0.00
308_F 403_I 0.74 0.20 0.00
200_Y 133_M 0.74 0.20 0.00
302_G 10_L 0.74 0.20 0.00
275_R 229_K 0.73 0.20 0.00
318_S 306_F 0.73 0.20 0.00
266_S 395_S 0.73 0.20 0.00
74_T 279_Y 0.73 0.20 0.00
118_A 411_K 0.73 0.20 0.00
113_S 150_D 0.73 0.20 0.00
238_M 386_L 0.73 0.20 0.00
75_D 123_M 0.73 0.20 0.00
101_I 229_K 0.73 0.20 0.00
231_I 403_I 0.73 0.20 0.00
207_S 166_G 0.73 0.20 0.00
269_T 224_S 0.73 0.20 0.00
241_S 349_I 0.73 0.20 0.00
164_A 265_E 0.73 0.20 0.00
61_V 344_Y 0.73 0.20 0.00
217_G 306_F 0.73 0.20 0.00
306_F 241_Y 0.73 0.20 0.00
302_G 21_E 0.73 0.20 0.00
203_M 314_D 0.73 0.20 0.00
46_S 121_K 0.73 0.20 0.00
310_L 157_V 0.73 0.20 0.00
97_T 35_L 0.73 0.20 0.00
252_I 259_F 0.72 0.20 0.00
273_I 144_V 0.72 0.20 0.00
217_G 190_A 0.72 0.20 0.00
96_A 317_S 0.72 0.20 0.00
255_G 318_D 0.72 0.20 0.00
51_F 367_L 0.72 0.19 0.00
178_A 94_G 0.72 0.19 0.00
227_G 186_I 0.72 0.19 0.00
296_R 45_L 0.72 0.19 0.00
132_V 218_V 0.72 0.19 0.00
132_V 93_I 0.72 0.19 0.00
56_S 335_S 0.72 0.19 0.00
153_V 369_A 0.72 0.19 0.00
307_I 306_F 0.72 0.19 0.00
207_S 276_T 0.72 0.19 0.00
51_F 116_A 0.72 0.19 0.00
20_P 192_I 0.72 0.19 0.00
123_V 233_F 0.72 0.19 0.00
176_L 189_V 0.72 0.19 0.00
27_L 372_F 0.72 0.19 0.00
187_R 373_K 0.72 0.19 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 (0.56 > 0.4) of paralogs.
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