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OPENSEQ.org
L1-vs-S4
Genes: A B A+B
Length: 234 206 430
Sequences: 3196 1236 629
Seq/Len: 13.66 6 1.46
MirrorTree (Pazo et al. 2001) 0.65
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 0.09 0.09 0.00
2 0.09 0.09 0.01
5 0.09 0.09 0.01
10 0.09 0.09 0.03
20 0.09 0.09 0.06
100 0.09 0.09 0.58
∞ 0.10 0.09 1.43
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
153_V 70_R 1.02 0.46 0.00
43_D 206_K 0.98 0.41 0.00
42_V 46_P 0.95 0.39 0.00
53_R 44_R 0.91 0.35 0.00
167_K 88_E 0.91 0.35 0.00
125_G 54_Q 0.91 0.34 0.00
169_G 155_V 0.90 0.33 0.00
170_I 190_D 0.88 0.32 0.00
89_A 200_I 0.88 0.32 0.00
134_R 90_L 0.88 0.32 0.00
166_D 100_N 0.88 0.31 0.00
41_S 96_G 0.87 0.31 0.00
212_V 131_N 0.86 0.30 0.00
161_V 64_I 0.86 0.30 0.00
115_I 167_K 0.85 0.30 0.00
164_R 206_K 0.85 0.30 0.00
161_V 190_D 0.85 0.29 0.00
204_A 70_R 0.85 0.29 0.00
54_K 56_R 0.84 0.29 0.00
196_L 144_S 0.84 0.28 0.00
41_S 46_P 0.83 0.28 0.00
15_V 128_R 0.83 0.28 0.00
202_T 191_L 0.82 0.27 0.00
78_F 168_P 0.82 0.27 0.00
29_L 125_V 0.82 0.26 0.00
214_I 131_N 0.81 0.26 0.00
58_N 198_H 0.81 0.26 0.00
150_A 189_S 0.81 0.26 0.00
224_V 142_V 0.80 0.25 0.00
76_A 85_N 0.80 0.25 0.00
99_D 145_I 0.80 0.25 0.00
184_K 149_A 0.80 0.25 0.00
129_Q 122_A 0.79 0.24 0.00
80_Q 43_A 0.78 0.24 0.00
15_V 11_L 0.78 0.24 0.00
209_I 107_F 0.78 0.24 0.00
224_V 128_R 0.77 0.23 0.00
123_V 105_M 0.77 0.23 0.00
23_I 155_V 0.76 0.22 0.00
15_V 137_V 0.76 0.22 0.00
114_V 76_Y 0.76 0.22 0.00
161_V 67_V 0.76 0.22 0.00
110_N 78_E 0.76 0.22 0.00
184_K 107_F 0.75 0.22 0.00
40_E 12_S 0.75 0.22 0.00
43_D 131_N 0.75 0.22 0.00
123_V 43_A 0.75 0.22 0.00
169_G 123_I 0.75 0.21 0.00
113_V 7_P 0.75 0.21 0.00
175_I 81_R 0.75 0.21 0.00
124_V 168_P 0.74 0.21 0.00
13_E 174_D 0.74 0.21 0.00
166_D 7_P 0.74 0.21 0.00
194_V 168_P 0.74 0.21 0.00
182_A 146_R 0.74 0.21 0.00
172_H 74_N 0.74 0.21 0.00
223_A 76_Y 0.74 0.20 0.00
42_V 200_I 0.73 0.20 0.00
45_A 151_K 0.73 0.20 0.00
211_K 110_T 0.73 0.20 0.00
8_M 107_F 0.73 0.20 0.00
62_A 92_A 0.73 0.20 0.00
35_T 206_K 0.73 0.20 0.00
120_A 52_G 0.73 0.20 0.00
88_K 144_S 0.73 0.20 0.00
54_K 5_L 0.72 0.20 0.00
103_Q 110_T 0.72 0.20 0.00
229_L 123_I 0.72 0.20 0.00
177_K 45_K 0.72 0.20 0.00
104_I 62_R 0.72 0.20 0.00
214_I 168_P 0.72 0.20 0.00
217_T 172_E 0.72 0.20 0.00
77_V 67_V 0.72 0.19 0.00
97_M 33_K 0.72 0.19 0.00
148_N 81_R 0.72 0.19 0.00
216_T 62_R 0.71 0.19 0.00
99_D 82_L 0.71 0.19 0.00
166_D 111_R 0.71 0.19 0.00
89_A 61_V 0.71 0.19 0.00
46_V 85_N 0.71 0.19 0.00
187_E 138_S 0.71 0.19 0.00
149_V 177_K 0.70 0.18 0.00
45_A 171_L 0.70 0.18 0.00
47_N 206_K 0.70 0.18 0.00
213_S 75_Y 0.70 0.18 0.00
162_R 121_K 0.70 0.18 0.00
219_G 144_S 0.70 0.18 0.00
23_I 62_R 0.70 0.18 0.00
163_Y 37_A 0.69 0.18 0.00
210_K 81_R 0.69 0.18 0.00
114_V 85_N 0.69 0.18 0.00
62_A 57_E 0.69 0.18 0.00
43_D 30_T 0.69 0.18 0.00
187_E 160_E 0.69 0.17 0.00
32_E 159_L 0.69 0.17 0.00
149_V 86_T 0.69 0.17 0.00
165_N 40_Q 0.69 0.17 0.00
221_G 54_Q 0.69 0.17 0.00
139_N 54_Q 0.69 0.17 0.00
172_H 10_K 0.68 0.17 0.00
90_A 135_Y 0.68 0.17 0.00
200_K 172_E 0.68 0.17 0.00
200_K 169_T 0.68 0.17 0.00
163_Y 167_K 0.68 0.17 0.00
24_N 83_K 0.68 0.17 0.00
175_I 199_L 0.68 0.17 0.00
22_D 137_V 0.68 0.17 0.00
199_A 143_V 0.67 0.17 0.00
98_E 107_F 0.67 0.17 0.00
151_E 125_V 0.67 0.17 0.00
191_A 178_M 0.67 0.17 0.00
129_Q 48_L 0.67 0.17 0.00
79_T 52_G 0.67 0.17 0.00
156_A 96_G 0.67 0.17 0.00
8_M 155_V 0.67 0.17 0.00
196_L 19_L 0.67 0.16 0.00
23_I 74_N 0.67 0.16 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)
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