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OPENSEQ.org
2Y69_B_C
Genes: A B A+B
Length: 227 261 485
Sequences: 4332 2491 1473
Seq/Len: 19.08 9.54 3.04
MirrorTree (Pazo et al. 2001) 0.84
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 0.01 0.01 0.28
2 0.01 0.01 0.48
5 0.01 0.01 2.78
10 0.01 0.01 2.97
20 0.01 0.01 3.02
100 0.02 0.01 3.07
∞ 0.07 0.01 3.13
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
4_P 228_T 1.33 0.91 0.37
36_S 150_S 1.02 0.67 0.15
169_G 141_G 0.98 0.63 0.14
155_S 92_L 0.98 0.62 0.13
65_W 148_H 0.95 0.59 0.12
18_E 250_L 0.95 0.59 0.12
202_S 198_F 0.94 0.58 0.12
156_S 37_F 0.93 0.56 0.11
144_L 127_L 0.92 0.56 0.11
206_F 193_Y 0.92 0.55 0.11
27_T 34_W 0.92 0.55 0.11
215_P 165_I 0.90 0.53 0.10
194_G 90_E 0.89 0.51 0.10
155_S 46_G 0.89 0.51 0.10
99_T 217_V 0.88 0.50 0.09
85_Y 11_V 0.87 0.50 0.09
23_F 198_F 0.87 0.49 0.09
74_I 21_A 0.86 0.48 0.09
191_L 191_G 0.86 0.48 0.09
99_T 132_L 0.85 0.47 0.08
98_K 75_V 0.84 0.46 0.08
15_P 250_L 0.84 0.46 0.08
143_V 92_L 0.84 0.46 0.08
99_T 30_G 0.84 0.45 0.08
182_T 26_L 0.83 0.44 0.08
154_V 36_H 0.83 0.44 0.08
118_F 147_A 0.82 0.43 0.07
70_A 79_L 0.82 0.43 0.07
165_V 100_A 0.82 0.43 0.07
55_T 103_H 0.82 0.43 0.07
67_I 216_I 0.81 0.42 0.07
160_L 6_H 0.81 0.41 0.07
25_D 16_W 0.80 0.41 0.07
211_L 56_Q 0.80 0.41 0.07
80_S 99_W 0.80 0.40 0.07
223_S 38_N 0.80 0.40 0.07
65_W 240_W 0.80 0.40 0.07
24_H 226_H 0.80 0.40 0.07
61_V 247_V 0.80 0.40 0.07
182_T 25_L 0.79 0.40 0.07
99_T 122_H 0.79 0.39 0.06
74_I 102_Y 0.79 0.39 0.06
16_I 239_A 0.78 0.38 0.06
211_L 159_M 0.77 0.37 0.06
19_E 129_V 0.77 0.37 0.06
182_T 51_M 0.77 0.37 0.06
184_L 13_P 0.76 0.36 0.06
57_D 92_L 0.76 0.36 0.06
129_K 23_S 0.76 0.36 0.06
211_L 261_S 0.76 0.36 0.06
223_S 210_I 0.76 0.36 0.06
98_K 250_L 0.76 0.35 0.06
74_I 209_I 0.75 0.35 0.06
6_Q 5_T 0.75 0.35 0.06
130_P 165_I 0.75 0.35 0.06
130_P 168_T 0.75 0.35 0.06
170_L 182_Y 0.75 0.35 0.06
182_T 46_G 0.75 0.35 0.05
211_L 223_L 0.75 0.34 0.05
85_Y 59_R 0.75 0.34 0.05
17_M 206_L 0.74 0.34 0.05
140_N 23_S 0.74 0.33 0.05
150_I 26_L 0.73 0.33 0.05
141_R 95_T 0.73 0.33 0.05
38_V 234_G 0.73 0.33 0.05
203_N 63_R 0.73 0.33 0.05
6_Q 150_S 0.73 0.32 0.05
109_E 136_V 0.73 0.32 0.05
76_I 6_H 0.72 0.32 0.05
43_S 43_L 0.72 0.32 0.05
153_L 49_T 0.72 0.32 0.05
43_S 171_V 0.72 0.32 0.05
224_A 216_I 0.72 0.32 0.05
39_L 91_V 0.72 0.32 0.05
1_M 170_G 0.72 0.32 0.05
9_F 193_Y 0.72 0.32 0.05
110_Y 143_S 0.72 0.32 0.05
89_E 103_H 0.72 0.32 0.05
73_L 131_L 0.72 0.31 0.05
71_I 123_P 0.72 0.31 0.05
31_V 21_A 0.72 0.31 0.05
180_N 11_V 0.71 0.31 0.05
16_I 250_L 0.71 0.30 0.05
65_W 117_P 0.71 0.30 0.04
193_Y 91_V 0.70 0.30 0.04
175_I 146_W 0.70 0.30 0.04
210_V 198_F 0.70 0.30 0.04
60_E 206_L 0.70 0.29 0.04
129_K 22_L 0.70 0.29 0.04
152_M 224_K 0.70 0.29 0.04
66_T 148_H 0.70 0.29 0.04
109_E 60_D 0.69 0.28 0.04
9_F 152_M 0.69 0.28 0.04
74_I 146_W 0.69 0.28 0.04
74_I 119_T 0.69 0.28 0.04
219_F 136_V 0.69 0.28 0.04
165_V 132_L 0.69 0.28 0.04
83_I 163_L 0.69 0.28 0.04
132_E 25_L 0.69 0.28 0.04
155_S 199_V 0.69 0.28 0.04
170_L 55_Y 0.69 0.28 0.04
60_E 162_A 0.69 0.28 0.04
157_E 102_Y 0.69 0.28 0.04
160_L 199_V 0.68 0.28 0.04
100_M 109_T 0.68 0.28 0.04
63_T 217_V 0.68 0.28 0.04
84_L 196_T 0.68 0.28 0.04
100_M 28_T 0.68 0.27 0.04
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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