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OPENSEQ.org
BcytoA
Genes: A B A+B
Length: 318 211 524
Sequences: 1408 1992 1337
Seq/Len: 4.43 9.44 2.55
MirrorTree (Pazo et al. 2001) 0.74
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 1.82
2 0.00 0.00 2.03
5 0.01 0.01 2.09
10 0.01 0.01 2.36
20 0.02 0.02 2.53
100 0.03 0.03 2.69
∞ 0.07 0.07 2.90
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
40_F 205_L 1.09 0.69 0.01
316_I 104_L 1.09 0.69 0.01
274_C 94_I 1.08 0.68 0.01
279_L 123_L 1.05 0.65 0.01
72_I 145_I 1.04 0.64 0.01
123_L 154_V 1.02 0.62 0.01
314_I 39_I 1.02 0.62 0.01
159_I 42_V 1.01 0.61 0.01
168_I 79_I 1.01 0.60 0.01
273_L 143_E 0.97 0.57 0.01
232_N 34_A 0.97 0.56 0.01
78_A 114_F 0.97 0.56 0.01
286_I 19_D 0.97 0.56 0.01
216_L 126_I 0.96 0.55 0.01
217_D 12_P 0.95 0.54 0.01
312_G 202_I 0.95 0.54 0.01
192_M 125_K 0.95 0.54 0.01
223_S 13_T 0.94 0.53 0.01
316_I 123_L 0.94 0.52 0.01
121_S 33_A 0.94 0.52 0.01
299_F 15_K 0.93 0.52 0.01
129_V 68_G 0.93 0.51 0.01
172_D 16_K 0.92 0.51 0.01
10_M 110_F 0.92 0.50 0.01
154_S 161_V 0.90 0.48 0.01
145_E 201_I 0.90 0.48 0.01
231_E 127_N 0.90 0.48 0.01
308_F 123_L 0.90 0.47 0.01
199_A 93_P 0.89 0.47 0.01
244_L 180_Q 0.89 0.47 0.01
20_F 30_Q 0.89 0.46 0.01
133_L 114_F 0.89 0.46 0.01
151_A 141_I 0.89 0.46 0.01
272_I 14_S 0.88 0.46 0.01
42_L 16_K 0.88 0.46 0.01
179_S 124_G 0.88 0.46 0.01
296_V 169_L 0.88 0.45 0.01
165_K 17_I 0.87 0.45 0.01
228_V 105_G 0.86 0.44 0.01
153_V 31_D 0.86 0.43 0.01
107_V 131_G 0.86 0.43 0.01
12_R 5_D 0.86 0.43 0.01
121_S 43_T 0.85 0.43 0.01
15_A 109_Q 0.85 0.42 0.01
104_P 42_V 0.85 0.42 0.01
69_I 107_I 0.85 0.42 0.01
191_D 173_E 0.84 0.41 0.01
150_V 31_D 0.84 0.41 0.01
195_E 109_Q 0.84 0.41 0.01
168_I 195_V 0.84 0.41 0.01
252_L 67_I 0.83 0.40 0.01
134_D 71_F 0.83 0.40 0.01
42_L 102_G 0.83 0.40 0.01
214_G 49_M 0.83 0.40 0.01
136_V 13_T 0.83 0.40 0.01
123_L 125_K 0.83 0.40 0.01
147_A 134_N 0.83 0.39 0.01
220_I 135_L 0.82 0.39 0.01
48_A 8_K 0.82 0.38 0.01
99_Y 10_E 0.82 0.38 0.01
196_H 19_D 0.82 0.38 0.01
119_H 137_S 0.82 0.38 0.01
106_S 42_V 0.82 0.38 0.01
244_L 174_L 0.81 0.38 0.01
168_I 188_A 0.81 0.37 0.01
244_L 92_A 0.81 0.37 0.01
240_Y 94_I 0.81 0.37 0.01
286_I 126_I 0.80 0.36 0.01
45_V 20_A 0.80 0.36 0.01
256_L 74_R 0.80 0.36 0.01
152_P 58_N 0.80 0.36 0.01
13_S 35_I 0.80 0.36 0.01
229_L 140_K 0.80 0.36 0.01
123_L 87_V 0.80 0.36 0.01
276_E 202_I 0.80 0.36 0.01
145_E 25_N 0.79 0.35 0.01
187_S 99_M 0.79 0.35 0.01
17_S 8_K 0.79 0.35 0.01
219_F 56_I 0.79 0.35 0.01
93_E 56_I 0.79 0.35 0.01
119_H 153_I 0.79 0.35 0.01
209_Y 82_K 0.79 0.35 0.01
216_L 43_T 0.78 0.34 0.01
145_E 170_P 0.78 0.34 0.01
238_G 87_V 0.78 0.34 0.01
275_V 210_V 0.78 0.34 0.01
244_L 177_M 0.78 0.34 0.01
251_T 141_I 0.78 0.34 0.01
281_K 177_M 0.78 0.34 0.01
236_R 195_V 0.78 0.34 0.01
176_I 136_F 0.78 0.34 0.01
201_L 149_L 0.78 0.34 0.01
118_A 101_A 0.78 0.34 0.01
120_A 114_F 0.77 0.33 0.01
168_I 178_V 0.77 0.33 0.01
116_I 108_M 0.77 0.33 0.01
168_I 82_K 0.77 0.33 0.01
225_S 143_E 0.77 0.33 0.01
223_S 94_I 0.77 0.33 0.01
55_D 174_L 0.76 0.32 0.01
173_M 152_G 0.76 0.32 0.01
148_L 73_L 0.76 0.32 0.01
7_I 135_L 0.76 0.32 0.01
89_N 167_Q 0.76 0.32 0.01
114_E 109_Q 0.76 0.32 0.01
283_I 126_I 0.76 0.32 0.01
249_T 158_A 0.76 0.32 0.01
258_A 94_I 0.75 0.31 0.01
42_L 112_F 0.75 0.31 0.01
144_I 200_L 0.75 0.31 0.01
8_R 103_V 0.75 0.31 0.01
302_I 163_L 0.75 0.31 0.01
200_S 159_F 0.75 0.31 0.01
75_K 141_I 0.75 0.31 0.01
54_P 36_V 0.75 0.31 0.01
52_I 41_G 0.75 0.31 0.01
109_S 110_F 0.75 0.31 0.01
151_A 93_P 0.75 0.31 0.01
50_A 124_G 0.75 0.31 0.01
168_I 50_S 0.75 0.31 0.01
176_I 95_V 0.75 0.31 0.01
140_Y 119_I 0.75 0.31 0.01
137_K 19_D 0.75 0.31 0.01
68_E 189_I 0.74 0.30 0.01
124_L 207_V 0.74 0.30 0.01
25_I 152_G 0.74 0.30 0.01
251_T 100_I 0.74 0.30 0.01
70_E 85_F 0.74 0.30 0.01
178_E 109_Q 0.74 0.30 0.01
275_V 170_P 0.74 0.30 0.01
7_I 189_I 0.74 0.30 0.01
25_I 140_K 0.74 0.30 0.01
146_D 111_G 0.73 0.29 0.01
134_D 61_R 0.73 0.29 0.01
273_L 28_K 0.73 0.29 0.01
116_I 152_G 0.73 0.29 0.01
9_S 208_F 0.73 0.29 0.01
87_D 12_P 0.73 0.29 0.01
7_I 88_L 0.73 0.29 0.01
40_F 176_T 0.73 0.29 0.01
170_I 207_V 0.73 0.29 0.01
97_N 100_I 0.73 0.29 0.01
259_E 138_L 0.73 0.29 0.01
86_I 45_T 0.73 0.29 0.01
277_P 131_G 0.73 0.29 0.01
306_T 109_Q 0.73 0.29 0.01
202_A 202_I 0.72 0.28 0.01
298_S 150_K 0.72 0.28 0.01
157_Q 12_P 0.72 0.28 0.01
132_L 131_G 0.72 0.28 0.01
260_V 31_D 0.72 0.28 0.01
275_V 191_L 0.72 0.28 0.01
92_D 84_I 0.72 0.28 0.01
279_L 36_V 0.72 0.28 0.01
153_V 151_V 0.72 0.28 0.01
108_I 102_G 0.72 0.28 0.01
242_L 94_I 0.72 0.28 0.01
119_H 5_D 0.72 0.28 0.01
286_I 5_D 0.71 0.28 0.01
55_D 89_I 0.71 0.28 0.01
193_I 111_G 0.71 0.28 0.01
36_N 35_I 0.71 0.28 0.01
241_H 13_T 0.71 0.28 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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