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OPENSEQ.org
2y69
Genes: A B A+B
Length: 307 179 438
Sequences: 552 4418 380
Seq/Len: 1.8 24.68 0.87
MirrorTree (Pazo et al. 2001) 0.85
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 0.00 0.04 0.08
2 0.00 0.04 0.63
5 0.00 0.04 0.77
10 0.01 0.04 0.77
20 0.01 0.04 0.78
100 0.01 0.05 0.79
∞ 0.04 0.09 0.87
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
37_L 168_L 1.56 0.77 0.02
219_F 79_Q 1.35 0.61 0.01
104_W 119_T 1.26 0.54 0.01
99_T 11_F 1.26 0.53 0.01
60_E 50_L 1.25 0.52 0.01
152_M 83_I 1.23 0.50 0.01
50_L 165_V 1.18 0.46 0.01
46_L 148_N 1.17 0.45 0.01
50_L 118_A 1.17 0.45 0.01
172_T 23_S 1.15 0.43 0.01
97_V 13_T 1.14 0.42 0.01
222_W 162_F 1.13 0.42 0.01
238_P 179_S 1.12 0.41 0.01
171_K 58_S 1.09 0.39 0.01
69_P 84_T 1.09 0.39 0.01
10_Q 110_V 1.09 0.38 0.01
238_P 153_F 1.09 0.38 0.01
7_L 113_S 1.06 0.36 0.01
46_L 92_T 1.06 0.36 0.01
89_E 109_G 1.06 0.35 0.01
228_H 96_A 1.03 0.33 0.00
184_L 165_V 1.03 0.33 0.00
69_P 61_S 1.02 0.33 0.00
37_L 90_Y 1.02 0.33 0.00
71_I 147_S 1.02 0.33 0.00
197_S 93_L 1.02 0.32 0.00
160_L 85_I 1.01 0.32 0.00
192_Y 28_P 1.00 0.31 0.00
76_I 116_F 1.00 0.31 0.00
77_A 84_T 1.00 0.31 0.00
18_E 86_T 1.00 0.31 0.00
226_M 113_S 0.99 0.30 0.00
75_L 79_Q 0.99 0.30 0.00
71_I 53_S 0.99 0.30 0.00
283_W 28_P 0.98 0.30 0.00
246_A 85_I 0.98 0.29 0.00
197_S 92_T 0.98 0.29 0.00
110_Y 98_E 0.98 0.29 0.00
216_L 157_A 0.97 0.29 0.00
229_Q 32_G 0.97 0.29 0.00
74_I 15_F 0.97 0.29 0.00
65_W 69_L 0.97 0.28 0.00
36_S 131_T 0.96 0.28 0.00
225_S 71_E 0.95 0.28 0.00
213_L 13_T 0.95 0.27 0.00
268_L 51_N 0.95 0.27 0.00
40_Y 90_Y 0.95 0.27 0.00
224_A 93_L 0.94 0.27 0.00
238_P 143_F 0.94 0.27 0.00
36_S 70_M 0.94 0.27 0.00
71_I 79_Q 0.93 0.26 0.00
156_S 81_L 0.92 0.25 0.00
33_L 79_Q 0.91 0.25 0.00
63_T 83_I 0.91 0.24 0.00
44_L 134_I 0.90 0.24 0.00
269_M 18_A 0.90 0.24 0.00
62_E 123_G 0.90 0.24 0.00
169_G 83_I 0.90 0.24 0.00
77_A 112_G 0.89 0.23 0.00
17_M 110_V 0.89 0.23 0.00
137_E 170_L 0.89 0.23 0.00
34_I 136_C 0.89 0.23 0.00
173_D 58_S 0.89 0.23 0.00
235_M 10_L 0.89 0.23 0.00
66_T 65_A 0.89 0.23 0.00
45_M 51_N 0.89 0.23 0.00
154_V 136_C 0.88 0.23 0.00
48_T 8_E 0.88 0.23 0.00
183_T 91_F 0.88 0.22 0.00
220_E 81_L 0.87 0.22 0.00
207_M 167_W 0.87 0.22 0.00
229_Q 177_W 0.87 0.22 0.00
7_L 168_L 0.87 0.22 0.00
192_Y 73_D 0.87 0.22 0.00
269_M 169_F 0.87 0.22 0.00
236_V 89_V 0.86 0.22 0.00
228_H 82_F 0.86 0.22 0.00
246_A 56_L 0.86 0.22 0.00
33_L 131_T 0.86 0.21 0.00
43_S 16_F 0.86 0.21 0.00
110_Y 58_S 0.86 0.21 0.00
283_W 43_N 0.86 0.21 0.00
180_N 87_L 0.86 0.21 0.00
224_A 75_K 0.86 0.21 0.00
70_A 168_L 0.85 0.21 0.00
165_V 75_K 0.85 0.21 0.00
33_L 113_S 0.85 0.21 0.00
206_F 95_Q 0.85 0.21 0.00
190_G 30_L 0.85 0.21 0.00
199_I 115_F 0.85 0.21 0.00
167_S 78_L 0.85 0.21 0.00
170_L 22_S 0.85 0.21 0.00
110_Y 175_Y 0.85 0.21 0.00
108_Y 127_I 0.84 0.20 0.00
101_G 48_P 0.84 0.20 0.00
84_L 95_Q 0.84 0.20 0.00
184_L 36_P 0.84 0.20 0.00
33_L 89_V 0.84 0.20 0.00
150_I 143_F 0.84 0.20 0.00
66_T 91_F 0.84 0.20 0.00
208_P 95_Q 0.84 0.20 0.00
47_T 86_T 0.84 0.20 0.00
282_W 22_S 0.83 0.20 0.00
175_I 148_N 0.83 0.20 0.00
79_P 115_F 0.83 0.20 0.00
81_L 174_I 0.83 0.20 0.00
101_G 78_L 0.83 0.20 0.00
64_I 131_T 0.83 0.20 0.00
280_Y 116_F 0.83 0.20 0.00
34_I 96_A 0.83 0.20 0.00
36_S 142_K 0.83 0.20 0.00
52_H 174_I 0.83 0.20 0.00
261_H 139_R 0.83 0.20 0.00
156_S 73_D 0.83 0.20 0.00
222_W 171_Y 0.83 0.20 0.00
225_S 96_A 0.83 0.20 0.00
184_L 66_H 0.82 0.19 0.00
264_S 112_G 0.82 0.19 0.00
219_F 130_S 0.82 0.19 0.00
48_T 112_G 0.82 0.19 0.00
262_F 52_T 0.82 0.19 0.00
226_M 162_F 0.82 0.19 0.00
147_E 24_L 0.82 0.19 0.00
57_D 164_D 0.81 0.19 0.00
229_Q 50_L 0.81 0.19 0.00
208_P 102_A 0.81 0.19 0.00
205_S 81_L 0.81 0.19 0.00
165_V 17_W 0.81 0.19 0.00
141_R 26_P 0.81 0.19 0.00
253_T 89_V 0.81 0.19 0.00
103_Q 115_F 0.81 0.18 0.00
95_L 24_L 0.81 0.18 0.00
30_I 162_F 0.81 0.18 0.00
195_Q 102_A 0.81 0.18 0.00
23_F 175_Y 0.81 0.18 0.00
144_L 36_P 0.81 0.18 0.00
68_L 4_F 0.80 0.18 0.00
192_Y 26_P 0.80 0.18 0.00
104_W 179_S 0.80 0.18 0.00
170_L 99_Y 0.80 0.18 0.00
191_L 41_P 0.80 0.18 0.00
86_M 64_W 0.80 0.18 0.00
169_G 156_A 0.80 0.18 0.00
88_D 50_L 0.80 0.18 0.00
69_P 164_D 0.80 0.18 0.00
112_D 132_F 0.80 0.18 0.00
156_S 86_T 0.79 0.18 0.00
61_V 144_H 0.79 0.18 0.00
63_T 84_T 0.79 0.18 0.00
77_A 121_F 0.79 0.18 0.00
192_Y 57_A 0.79 0.17 0.00
165_V 93_L 0.79 0.17 0.00
35_S 155_A 0.79 0.17 0.00
57_D 170_L 0.79 0.17 0.00
146_M 146_T 0.79 0.17 0.00
225_S 135_V 0.79 0.17 0.00
57_D 176_W 0.79 0.17 0.00
148_M 138_F 0.79 0.17 0.00
64_I 78_L 0.79 0.17 0.00
141_R 19_F 0.78 0.17 0.00
213_L 81_L 0.78 0.17 0.00
100_M 94_L 0.78 0.17 0.00
30_I 127_I 0.78 0.17 0.00
35_S 169_F 0.78 0.17 0.00
71_I 50_L 0.78 0.17 0.00
279_M 131_T 0.78 0.17 0.00
205_S 77_M 0.78 0.17 0.00
23_F 121_F 0.78 0.17 0.00
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)
ID Seq/Len Name Options I_Prob Status
12327 0.87 2y69 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.02 Done
10438 3.03 2Y69_BC Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.46 Done - Shared
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