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OPENSEQ.org
BxE
Genes: A B A+B
Length: 362 98 449
Sequences: 1858 888 617
Seq/Len: 5.13 9.06 1.37
MirrorTree (Pazo et al. 2001) 0.69
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 0.00
2 0.00 0.00 0.00
5 0.01 0.00 0.02
10 0.01 0.00 0.06
20 0.02 0.00 1.01
100 0.03 0.01 1.34
∞ 0.07 0.01 1.63
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
262_D 71_K 1.59 0.89 0.27
16_K 72_A 1.50 0.84 0.22
123_L 37_I 1.38 0.76 0.15
269_T 66_A 1.27 0.68 0.11
134_N 97_Q 1.23 0.64 0.10
262_D 94_T 1.23 0.64 0.10
219_R 40_L 1.21 0.62 0.09
344_F 40_L 1.20 0.61 0.09
137_S 77_K 1.20 0.61 0.09
114_F 96_T 1.15 0.57 0.08
208_F 76_M 1.13 0.55 0.07
243_R 55_A 1.07 0.48 0.06
49_M 81_E 1.06 0.47 0.06
248_E 60_K 1.05 0.47 0.05
102_G 73_E 1.05 0.46 0.05
344_F 68_A 1.04 0.46 0.05
341_V 47_G 1.04 0.46 0.05
134_N 73_E 1.04 0.46 0.05
349_N 91_K 1.03 0.45 0.05
9_T 41_N 1.02 0.44 0.05
208_F 78_F 1.02 0.44 0.05
21_R 72_A 1.01 0.43 0.05
266_T 65_A 1.01 0.43 0.05
237_Q 50_A 1.00 0.41 0.04
64_Q 65_A 0.99 0.41 0.04
101_A 98_I 0.99 0.41 0.04
265_I 28_E 0.99 0.41 0.04
316_L 71_K 0.98 0.40 0.04
142_V 67_I 0.97 0.39 0.04
328_D 68_A 0.95 0.37 0.04
344_F 94_T 0.95 0.37 0.04
311_Y 54_I 0.94 0.36 0.04
31_D 81_E 0.94 0.35 0.04
229_Y 98_I 0.94 0.35 0.04
63_Y 74_S 0.94 0.35 0.04
312_E 92_E 0.92 0.34 0.03
94_I 39_D 0.92 0.34 0.03
235_D 63_H 0.91 0.34 0.03
95_V 47_G 0.91 0.33 0.03
219_R 31_K 0.91 0.33 0.03
293_D 69_I 0.90 0.33 0.03
200_L 17_N 0.90 0.32 0.03
221_S 48_E 0.90 0.32 0.03
41_G 27_D 0.89 0.32 0.03
119_I 17_N 0.89 0.31 0.03
139_K 81_E 0.89 0.31 0.03
344_F 79_M 0.89 0.31 0.03
126_I 48_E 0.89 0.31 0.03
343_G 93_I 0.88 0.31 0.03
117_K 61_D 0.88 0.31 0.03
15_K 93_I 0.88 0.30 0.03
101_A 34_K 0.87 0.30 0.03
110_F 76_M 0.87 0.29 0.03
333_E 27_D 0.87 0.29 0.03
194_I 70_T 0.87 0.29 0.03
327_N 93_I 0.87 0.29 0.03
137_S 79_M 0.86 0.29 0.03
319_E 50_A 0.86 0.29 0.03
17_I 95_R 0.85 0.28 0.03
164_K 37_I 0.84 0.28 0.02
47_F 30_A 0.84 0.27 0.02
342_L 33_L 0.84 0.27 0.02
341_V 30_A 0.84 0.27 0.02
330_I 66_A 0.83 0.27 0.02
210_V 36_E 0.83 0.27 0.02
50_S 42_K 0.83 0.27 0.02
238_V 76_M 0.83 0.27 0.02
245_L 68_A 0.83 0.27 0.02
134_N 44_Q 0.83 0.27 0.02
201_I 62_L 0.83 0.27 0.02
46_L 93_I 0.83 0.27 0.02
333_E 53_D 0.83 0.27 0.02
167_Q 38_N 0.83 0.26 0.02
207_V 76_M 0.83 0.26 0.02
12_P 48_E 0.83 0.26 0.02
334_M 43_A 0.82 0.26 0.02
265_I 63_H 0.82 0.26 0.02
54_E 72_A 0.82 0.26 0.02
151_V 61_D 0.82 0.26 0.02
44_I 56_T 0.82 0.26 0.02
15_K 28_E 0.82 0.25 0.02
44_I 67_I 0.82 0.25 0.02
31_D 68_A 0.82 0.25 0.02
104_L 49_A 0.81 0.25 0.02
300_K 92_E 0.81 0.25 0.02
6_Q 30_A 0.81 0.25 0.02
19_D 74_S 0.81 0.25 0.02
264_V 45_E 0.81 0.25 0.02
298_R 73_E 0.81 0.25 0.02
104_L 52_T 0.81 0.25 0.02
150_K 94_T 0.81 0.24 0.02
219_R 79_M 0.80 0.24 0.02
93_P 69_I 0.80 0.24 0.02
144_S 30_A 0.80 0.24 0.02
145_I 50_A 0.80 0.24 0.02
129_L 47_G 0.80 0.24 0.02
7_E 54_I 0.80 0.24 0.02
248_E 65_A 0.80 0.24 0.02
3_G 91_K 0.79 0.24 0.02
105_G 35_N 0.79 0.23 0.02
60_Y 74_S 0.79 0.23 0.02
94_I 47_G 0.79 0.23 0.02
163_L 70_T 0.79 0.23 0.02
123_L 41_N 0.78 0.23 0.02
203_A 42_K 0.78 0.23 0.02
123_L 54_I 0.78 0.23 0.02
283_Q 82_V 0.78 0.23 0.02
103_V 75_S 0.78 0.23 0.02
344_F 50_A 0.78 0.23 0.02
134_N 82_V 0.78 0.23 0.02
134_N 53_D 0.77 0.22 0.02
241_R 75_S 0.77 0.22 0.02
335_F 77_K 0.77 0.22 0.02
193_A 53_D 0.77 0.22 0.02
244_R 59_V 0.77 0.22 0.02
111_G 71_K 0.77 0.22 0.02
169_L 92_E 0.77 0.22 0.02
76_I 54_I 0.77 0.22 0.02
244_R 91_K 0.76 0.22 0.02
298_R 96_T 0.76 0.21 0.02
273_V 54_I 0.76 0.21 0.02
107_I 98_I 0.76 0.21 0.02
197_V 45_E 0.76 0.21 0.02
90_I 79_M 0.76 0.21 0.02
153_I 39_D 0.75 0.21 0.02
162_L 38_N 0.75 0.21 0.02
110_F 55_A 0.75 0.21 0.02
134_N 96_T 0.75 0.21 0.02
28_K 61_D 0.75 0.21 0.02
218_L 70_T 0.75 0.20 0.02
332_R 54_I 0.75 0.20 0.02
88_L 20_Q 0.75 0.20 0.02
302_V 74_S 0.74 0.20 0.02
30_Q 66_A 0.74 0.20 0.02
27_P 27_D 0.74 0.20 0.02
340_E 63_H 0.74 0.20 0.02
102_G 36_E 0.74 0.20 0.01
229_Y 67_I 0.74 0.20 0.01
200_L 38_N 0.74 0.20 0.01
244_R 61_D 0.74 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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