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OPENSEQ.org
1aon_D_R
Genes: A B A+B
Length: 547 97 625
Sequences: 3952 2553 1601
Seq/Len: 7.22 26.32 2.56
MirrorTree (Pazo et al. 2001) 0.41
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 0.07 0.08 2.45
2 0.08 0.08 2.47
5 0.08 0.08 2.46
10 0.08 0.08 2.48
20 0.09 0.08 2.49
100 0.10 0.08 2.52
∞ 0.15 0.10 2.70
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
233_L 23_G 1.65 0.97 0.85
196_R 71_Y 1.24 0.82 0.54
62_E 93_A 1.13 0.74 0.43
229_I 27_L 1.08 0.68 0.37
303_E 23_G 1.06 0.66 0.35
399_L 10_V 1.02 0.62 0.32
307_E 30_S 1.02 0.62 0.31
505_Y 70_G 1.01 0.61 0.31
382_A 70_G 0.96 0.55 0.26
487_M 91_I 0.94 0.53 0.24
240_A 25_I 0.94 0.53 0.24
245_P 57_L 0.92 0.50 0.22
269_I 26_V 0.91 0.49 0.21
477_Y 66_I 0.90 0.48 0.21
518_C 67_F 0.90 0.48 0.21
229_I 11_I 0.90 0.48 0.21
181_G 10_V 0.90 0.47 0.20
231_E 70_G 0.88 0.45 0.19
221_L 2_N 0.88 0.45 0.19
120_D 38_G 0.88 0.45 0.19
237_E 21_S 0.87 0.44 0.18
226_I 87_S 0.87 0.44 0.18
343_G 91_I 0.87 0.44 0.18
179_G 26_V 0.86 0.43 0.17
254_E 16_E 0.85 0.43 0.17
244_K 68_N 0.85 0.42 0.17
129_E 39_E 0.85 0.42 0.17
128_E 91_I 0.85 0.42 0.17
223_D 71_Y 0.85 0.42 0.17
249_I 94_I 0.84 0.41 0.17
240_A 11_I 0.84 0.41 0.16
425_L 20_K 0.83 0.40 0.16
72_M 21_S 0.83 0.40 0.16
114_D 27_L 0.83 0.40 0.16
166_D 27_L 0.83 0.39 0.15
83_A 11_I 0.83 0.39 0.15
214_L 59_V 0.82 0.39 0.15
105_A 7_H 0.82 0.38 0.15
475_Y 68_N 0.81 0.38 0.15
160_L 11_I 0.81 0.38 0.14
199_L 95_V 0.81 0.38 0.14
484_Y 4_R 0.81 0.38 0.14
487_M 61_V 0.81 0.37 0.14
351_Q 71_Y 0.81 0.37 0.14
176_V 53_E 0.80 0.37 0.14
224_K 25_I 0.80 0.37 0.14
244_K 3_I 0.79 0.36 0.13
478_N 59_V 0.79 0.35 0.13
205_N 75_S 0.78 0.34 0.13
137_C 36_T 0.78 0.34 0.12
160_L 3_I 0.77 0.34 0.12
117_R 9_R 0.77 0.34 0.12
229_I 26_V 0.77 0.33 0.12
161_I 18_E 0.77 0.33 0.12
199_L 34_K 0.76 0.32 0.12
252_D 73_V 0.76 0.32 0.12
196_R 87_S 0.76 0.32 0.12
421_V 96_E 0.76 0.32 0.12
270_V 3_I 0.76 0.32 0.11
132_A 60_K 0.76 0.32 0.11
283_R 69_D 0.76 0.32 0.11
245_P 88_E 0.76 0.32 0.11
351_Q 4_R 0.75 0.32 0.11
299_V 33_A 0.75 0.31 0.11
303_E 37_R 0.75 0.31 0.11
163_E 61_V 0.74 0.31 0.11
348_I 60_K 0.74 0.31 0.11
340_A 80_N 0.74 0.30 0.11
238_A 14_R 0.74 0.30 0.10
77_A 26_V 0.74 0.30 0.10
160_L 70_G 0.74 0.30 0.10
179_G 27_L 0.73 0.29 0.10
355_A 43_V 0.73 0.29 0.10
425_L 30_S 0.73 0.29 0.10
131_K 13_K 0.73 0.29 0.10
509_V 39_E 0.73 0.29 0.10
372_A 96_E 0.72 0.29 0.10
396_E 3_I 0.72 0.28 0.10
237_E 23_G 0.72 0.28 0.10
180_T 26_V 0.72 0.28 0.10
36_N 9_R 0.72 0.28 0.10
477_Y 64_I 0.72 0.28 0.09
223_D 83_V 0.72 0.28 0.09
99_I 55_K 0.72 0.28 0.09
263_V 29_G 0.72 0.28 0.09
445_A 57_L 0.71 0.28 0.09
179_G 49_L 0.71 0.27 0.09
232_M 33_A 0.71 0.27 0.09
307_E 29_G 0.70 0.27 0.09
232_M 86_M 0.70 0.27 0.09
487_M 84_L 0.70 0.27 0.09
246_L 23_G 0.70 0.26 0.09
382_A 47_R 0.70 0.26 0.08
7_F 26_V 0.69 0.26 0.08
388_M 71_Y 0.69 0.26 0.08
427_D 94_I 0.69 0.26 0.08
105_A 67_F 0.69 0.26 0.08
419_I 53_E 0.69 0.26 0.08
332_I 18_E 0.69 0.25 0.08
419_I 51_N 0.69 0.25 0.08
293_T 59_V 0.69 0.25 0.08
149_I 78_I 0.69 0.25 0.08
203_F 34_K 0.69 0.25 0.08
99_I 12_V 0.69 0.25 0.08
266_M 26_V 0.68 0.25 0.08
289_Q 11_I 0.68 0.24 0.08
437_V 7_H 0.68 0.24 0.08
396_E 73_V 0.68 0.24 0.08
24_D 50_E 0.68 0.24 0.08
487_M 27_L 0.67 0.24 0.07
386_V 7_H 0.67 0.24 0.07
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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