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OPENSEQ.org
1AON-2
Genes: A B A+B
Length: 524 97 618
Sequences: 4143 2553 1564
Seq/Len: 7.91 26.32 2.53
MirrorTree (Pazo et al. 2001) 0.40
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 2.49
2 0.07 0.08 2.50
5 0.08 0.08 2.50
10 0.08 0.08 2.50
20 0.09 0.08 2.52
100 0.10 0.08 2.57
∞ 0.15 0.10 2.76
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 1.54 0.95 0.70
196_R 71_Y 1.31 0.87 0.51
62_E 93_A 1.31 0.86 0.50
399_L 10_V 1.18 0.78 0.38
229_I 27_L 1.06 0.66 0.27
505_Y 70_G 1.04 0.64 0.26
307_E 30_S 1.01 0.61 0.24
477_Y 66_I 0.98 0.58 0.21
425_L 20_K 0.96 0.55 0.20
518_C 67_F 0.94 0.52 0.18
245_P 57_L 0.94 0.52 0.18
221_L 2_N 0.94 0.52 0.18
382_A 70_G 0.93 0.51 0.17
114_D 27_L 0.92 0.50 0.17
269_I 26_V 0.91 0.49 0.16
254_E 16_E 0.90 0.48 0.16
231_E 70_G 0.90 0.47 0.15
223_D 71_Y 0.89 0.47 0.15
303_E 23_G 0.89 0.47 0.15
240_A 11_I 0.89 0.46 0.15
237_E 21_S 0.89 0.46 0.15
249_I 94_I 0.88 0.45 0.14
166_D 27_L 0.87 0.45 0.14
270_V 3_I 0.87 0.44 0.14
355_A 43_V 0.87 0.44 0.14
351_Q 4_R 0.86 0.43 0.14
72_M 21_S 0.86 0.43 0.13
270_V 23_G 0.85 0.42 0.13
229_I 11_I 0.85 0.42 0.13
160_L 11_I 0.85 0.41 0.13
224_K 25_I 0.84 0.41 0.12
487_M 91_I 0.84 0.41 0.12
372_A 96_E 0.84 0.41 0.12
128_E 91_I 0.84 0.41 0.12
117_R 9_R 0.83 0.40 0.12
252_D 73_V 0.83 0.40 0.12
343_G 91_I 0.83 0.39 0.12
179_G 26_V 0.82 0.39 0.11
120_D 38_G 0.82 0.38 0.11
105_A 7_H 0.81 0.38 0.11
427_D 94_I 0.81 0.38 0.11
223_D 83_V 0.80 0.36 0.10
137_C 36_T 0.80 0.36 0.10
321_R 3_I 0.80 0.36 0.10
117_R 23_G 0.80 0.36 0.10
240_A 25_I 0.80 0.36 0.10
478_N 59_V 0.80 0.36 0.10
229_I 26_V 0.79 0.35 0.10
237_E 23_G 0.79 0.35 0.10
445_A 57_L 0.79 0.35 0.10
475_Y 68_N 0.79 0.35 0.10
396_E 73_V 0.78 0.34 0.10
419_I 51_N 0.78 0.34 0.10
487_M 84_L 0.78 0.34 0.09
245_P 88_E 0.78 0.34 0.09
205_N 75_S 0.78 0.34 0.09
176_V 53_E 0.78 0.34 0.09
98_I 3_I 0.78 0.33 0.09
80_A 29_G 0.78 0.33 0.09
348_I 60_K 0.77 0.33 0.09
83_A 11_I 0.77 0.33 0.09
238_A 14_R 0.77 0.33 0.09
196_R 87_S 0.77 0.33 0.09
199_L 95_V 0.77 0.33 0.09
163_E 61_V 0.77 0.32 0.09
493_L 94_I 0.76 0.32 0.09
105_A 67_F 0.76 0.32 0.09
441_V 76_E 0.76 0.32 0.09
160_L 89_S 0.75 0.31 0.08
484_Y 4_R 0.75 0.31 0.08
199_L 34_K 0.75 0.31 0.08
161_I 18_E 0.75 0.31 0.08
253_V 30_S 0.75 0.31 0.08
372_A 82_E 0.74 0.30 0.08
331_I 80_N 0.74 0.30 0.08
382_A 47_R 0.74 0.30 0.08
183_Q 41_L 0.74 0.30 0.08
129_E 39_E 0.74 0.30 0.08
477_Y 64_I 0.74 0.29 0.08
147_G 68_N 0.73 0.29 0.08
103_L 86_M 0.73 0.29 0.08
482_E 45_N 0.73 0.29 0.07
206_K 92_L 0.73 0.29 0.07
327_D 76_E 0.73 0.29 0.07
160_L 3_I 0.73 0.28 0.07
7_F 26_V 0.73 0.28 0.07
208_E 13_K 0.73 0.28 0.07
226_I 87_S 0.73 0.28 0.07
244_K 3_I 0.72 0.28 0.07
181_G 10_V 0.72 0.28 0.07
289_Q 11_I 0.72 0.28 0.07
340_A 80_N 0.72 0.28 0.07
117_R 67_F 0.72 0.28 0.07
245_P 28_T 0.71 0.27 0.07
421_V 96_E 0.71 0.27 0.07
99_I 55_K 0.71 0.27 0.07
307_E 29_G 0.71 0.27 0.07
283_R 69_D 0.71 0.27 0.07
396_E 3_I 0.71 0.27 0.07
232_M 86_M 0.71 0.27 0.07
299_V 33_A 0.71 0.27 0.07
487_M 61_V 0.71 0.27 0.07
131_K 13_K 0.71 0.27 0.07
246_L 23_G 0.71 0.27 0.07
77_A 26_V 0.70 0.26 0.07
244_K 68_N 0.70 0.26 0.07
203_F 34_K 0.70 0.26 0.07
270_V 26_V 0.70 0.26 0.07
127_V 61_V 0.70 0.26 0.06
81_N 87_S 0.70 0.26 0.06
327_D 77_K 0.70 0.26 0.06
332_I 18_E 0.69 0.26 0.06
36_N 9_R 0.69 0.26 0.06
340_A 53_E 0.69 0.26 0.06
263_V 29_G 0.69 0.25 0.06
128_E 30_S 0.69 0.25 0.06
214_L 59_V 0.69 0.25 0.06
179_G 27_L 0.69 0.25 0.06
293_T 59_V 0.69 0.25 0.06
160_L 92_L 0.69 0.25 0.06
514_I 21_S 0.69 0.25 0.06
231_E 20_K 0.69 0.25 0.06
416_V 23_G 0.69 0.25 0.06
93_V 9_R 0.68 0.24 0.06
232_M 33_A 0.68 0.24 0.06
452_Q 87_S 0.68 0.24 0.06
157_V 93_A 0.68 0.24 0.06
521_T 32_A 0.68 0.24 0.06
241_K 36_T 0.68 0.24 0.06
179_G 49_L 0.68 0.24 0.06
224_K 94_I 0.68 0.24 0.06
229_I 71_Y 0.68 0.24 0.06
180_T 26_V 0.68 0.24 0.06
489_D 81_E 0.67 0.23 0.06
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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