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OPENSEQ.org
AtmxR
Genes: A B A+B
Length: 339 255 564
Sequences: 1350 1848 1292
Seq/Len: 3.98 7.25 2.29
MirrorTree (Pazo et al. 2001) 0.78
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 0.00 0.32
2 0.01 0.00 1.47
5 0.01 0.01 1.56
10 0.01 0.01 1.79
20 0.02 0.02 1.96
100 0.03 0.03 2.18
∞ 0.07 0.07 2.41
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
211_K 101_A 1.44 0.91 0.41
138_L 34_H 1.27 0.82 0.27
274_T 87_Q 1.26 0.81 0.27
237_D 194_L 1.25 0.80 0.26
274_T 113_D 1.24 0.79 0.25
95_I 216_Y 1.22 0.78 0.24
153_V 101_A 1.20 0.76 0.23
127_N 135_F 1.18 0.75 0.21
113_S 219_K 1.16 0.73 0.20
211_K 219_K 1.14 0.71 0.19
267_T 104_M 1.13 0.70 0.18
134_V 160_F 1.13 0.70 0.18
113_S 196_D 1.12 0.69 0.18
59_L 197_V 1.11 0.68 0.17
142_N 87_Q 1.11 0.68 0.17
89_F 185_S 1.10 0.67 0.17
53_L 142_H 1.09 0.67 0.17
270_A 101_A 1.07 0.64 0.15
202_A 126_I 1.06 0.63 0.15
178_A 123_T 1.05 0.62 0.14
327_L 201_L 1.05 0.62 0.14
69_Y 25_L 1.04 0.61 0.14
67_S 152_L 1.04 0.60 0.14
107_N 219_K 1.03 0.60 0.14
33_L 52_Y 1.02 0.59 0.13
142_N 219_K 1.01 0.57 0.12
104_E 229_A 1.00 0.57 0.12
54_A 139_D 1.00 0.56 0.12
333_T 33_S 0.99 0.56 0.12
142_N 101_A 0.99 0.56 0.12
309_A 222_L 0.99 0.55 0.12
82_L 166_L 0.98 0.55 0.11
266_S 130_L 0.98 0.54 0.11
279_D 134_F 0.98 0.54 0.11
273_I 212_L 0.97 0.53 0.11
305_L 211_L 0.97 0.53 0.11
211_K 104_M 0.96 0.52 0.10
272_I 115_S 0.96 0.52 0.10
92_S 34_H 0.96 0.52 0.10
57_I 221_A 0.95 0.51 0.10
290_Q 42_K 0.95 0.51 0.10
154_S 191_I 0.95 0.50 0.10
222_I 85_M 0.94 0.50 0.10
211_K 196_D 0.94 0.49 0.10
311_V 218_I 0.94 0.49 0.09
101_I 180_I 0.93 0.49 0.09
95_I 29_F 0.93 0.48 0.09
177_N 106_F 0.93 0.48 0.09
240_L 155_I 0.93 0.48 0.09
154_S 67_F 0.92 0.47 0.09
264_I 200_G 0.92 0.47 0.09
202_A 47_L 0.92 0.47 0.09
314_L 223_G 0.92 0.47 0.09
296_R 12_V 0.91 0.46 0.09
68_I 35_N 0.91 0.46 0.09
138_L 40_V 0.91 0.46 0.09
75_D 43_S 0.91 0.46 0.09
193_V 52_Y 0.91 0.46 0.09
272_I 126_I 0.91 0.46 0.09
115_I 141_H 0.91 0.45 0.08
81_T 8_G 0.90 0.45 0.08
154_S 186_F 0.90 0.45 0.08
268_A 232_L 0.90 0.45 0.08
151_T 212_L 0.90 0.45 0.08
46_S 178_F 0.90 0.45 0.08
251_T 103_T 0.90 0.44 0.08
258_S 108_M 0.90 0.44 0.08
30_V 180_I 0.89 0.44 0.08
86_I 121_P 0.89 0.44 0.08
262_G 206_M 0.89 0.44 0.08
113_S 101_A 0.89 0.43 0.08
88_L 204_K 0.89 0.43 0.08
284_A 103_T 0.88 0.43 0.08
234_F 218_I 0.88 0.43 0.08
38_A 70_L 0.88 0.43 0.08
60_S 132_L 0.88 0.43 0.08
53_L 109_A 0.88 0.43 0.08
199_F 106_F 0.88 0.42 0.07
177_N 215_G 0.88 0.42 0.07
240_L 77_I 0.88 0.42 0.07
39_I 186_F 0.88 0.42 0.07
330_G 197_V 0.87 0.41 0.07
53_L 186_F 0.87 0.41 0.07
265_T 208_Q 0.87 0.41 0.07
305_L 221_A 0.86 0.41 0.07
323_A 45_I 0.86 0.40 0.07
215_V 234_M 0.86 0.40 0.07
120_G 114_P 0.86 0.40 0.07
223_I 32_F 0.85 0.40 0.07
103_S 232_L 0.85 0.39 0.07
241_S 229_A 0.85 0.39 0.07
202_A 110_S 0.85 0.39 0.07
95_I 84_L 0.85 0.39 0.07
199_F 141_H 0.85 0.39 0.07
61_V 178_F 0.84 0.39 0.07
157_Q 103_T 0.84 0.38 0.07
139_V 214_I 0.84 0.38 0.07
154_S 149_S 0.84 0.38 0.07
33_L 38_P 0.84 0.38 0.07
26_S 75_E 0.84 0.38 0.06
111_A 101_A 0.83 0.38 0.06
154_S 182_F 0.83 0.37 0.06
219_I 221_A 0.83 0.37 0.06
112_V 101_A 0.83 0.37 0.06
211_K 124_S 0.83 0.37 0.06
194_I 216_Y 0.83 0.37 0.06
177_N 16_M 0.83 0.37 0.06
94_N 106_F 0.83 0.37 0.06
268_A 130_L 0.82 0.36 0.06
30_V 75_E 0.82 0.36 0.06
313_G 55_P 0.82 0.36 0.06
62_L 177_I 0.82 0.36 0.06
335_Q 154_Y 0.82 0.36 0.06
197_A 43_S 0.82 0.36 0.06
264_I 227_L 0.82 0.36 0.06
67_S 182_F 0.82 0.36 0.06
239_A 76_V 0.82 0.36 0.06
171_A 216_Y 0.82 0.36 0.06
323_A 120_M 0.82 0.36 0.06
262_G 202_L 0.82 0.35 0.06
55_L 78_F 0.82 0.35 0.06
330_G 148_L 0.81 0.35 0.06
202_A 124_S 0.81 0.35 0.06
295_Y 19_L 0.81 0.35 0.06
130_I 121_P 0.81 0.35 0.06
202_A 26_I 0.81 0.34 0.06
67_S 22_M 0.80 0.34 0.06
309_A 217_P 0.80 0.34 0.06
121_E 198_I 0.80 0.34 0.06
154_S 190_G 0.80 0.34 0.06
271_I 202_L 0.80 0.34 0.06
265_T 242_I 0.80 0.34 0.06
83_I 73_I 0.80 0.34 0.05
112_V 219_K 0.80 0.34 0.05
222_I 123_T 0.80 0.34 0.05
151_T 81_I 0.80 0.34 0.05
37_L 152_L 0.80 0.34 0.05
178_A 185_S 0.80 0.33 0.05
101_I 18_L 0.80 0.33 0.05
107_N 196_D 0.79 0.33 0.05
165_M 82_A 0.79 0.33 0.05
85_I 233_V 0.79 0.33 0.05
164_A 105_G 0.79 0.33 0.05
218_I 195_A 0.79 0.33 0.05
322_M 22_M 0.79 0.33 0.05
70_I 42_K 0.79 0.32 0.05
238_M 81_I 0.79 0.32 0.05
324_L 143_L 0.79 0.32 0.05
171_A 129_L 0.78 0.32 0.05
81_T 85_M 0.78 0.32 0.05
122_F 119_S 0.78 0.32 0.05
63_I 165_N 0.78 0.32 0.05
239_A 168_H 0.78 0.32 0.05
144_M 145_L 0.78 0.31 0.05
200_Y 192_S 0.77 0.31 0.05
231_I 186_F 0.77 0.31 0.05
299_L 80_M 0.77 0.31 0.05
171_A 196_D 0.77 0.31 0.05
240_L 32_F 0.77 0.31 0.05
34_V 31_F 0.77 0.31 0.05
271_I 137_A 0.77 0.31 0.05
223_I 226_V 0.77 0.31 0.05
231_I 83_G 0.77 0.31 0.05
244_A 197_V 0.77 0.31 0.05
238_M 239_K 0.77 0.31 0.05
273_I 105_G 0.77 0.31 0.05
313_G 42_K 0.77 0.31 0.05
207_S 106_F 0.77 0.31 0.05
217_G 41_I 0.77 0.31 0.05
61_V 193_L 0.77 0.30 0.05
260_I 117_G 0.76 0.30 0.05
287_T 39_M 0.76 0.30 0.05
140_L 50_T 0.76 0.30 0.05
227_G 194_L 0.76 0.30 0.05
302_G 224_F 0.76 0.30 0.05
54_A 227_L 0.76 0.29 0.04
195_A 218_I 0.76 0.29 0.04
314_L 230_I 0.75 0.29 0.04
239_A 194_L 0.75 0.29 0.04
138_L 22_M 0.75 0.29 0.04
223_I 213_V 0.75 0.29 0.04
117_A 56_L 0.75 0.29 0.04
69_Y 119_S 0.75 0.29 0.04
40_I 91_A 0.75 0.29 0.04
231_I 26_I 0.75 0.29 0.04
151_T 101_A 0.75 0.29 0.04
97_T 193_L 0.75 0.29 0.04
71_P 194_L 0.75 0.29 0.04
246_T 228_I 0.75 0.29 0.04
306_F 70_L 0.75 0.28 0.04
272_I 233_V 0.74 0.28 0.04
138_L 94_M 0.74 0.28 0.04
154_S 34_H 0.74 0.28 0.04
29_I 17_L 0.74 0.28 0.04
185_T 70_L 0.74 0.28 0.04
310_L 221_A 0.74 0.28 0.04
242_D 53_L 0.74 0.28 0.04
247_Y 60_E 0.74 0.28 0.04
153_V 196_D 0.74 0.28 0.04
45_P 194_L 0.74 0.28 0.04
226_I 109_A 0.74 0.28 0.04
317_L 247_T 0.74 0.28 0.04
116_I 134_F 0.74 0.28 0.04
188_A 199_F 0.74 0.28 0.04
311_V 47_L 0.73 0.28 0.04
272_I 193_L 0.73 0.28 0.04
116_I 68_F 0.73 0.27 0.04
83_I 223_G 0.73 0.27 0.04
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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