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OPENSEQ.org
LexAfun
Genes: A B A+B
Length: 202 353 524
Sequences: 4735 1819 208
Seq/Len: 23.44 5.15 0.4
MirrorTree (Pazo et al. 2001) 0.68
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 0.05 0.07 0.02
2 0.05 0.07 0.03
5 0.05 0.07 0.06
10 0.05 0.07 0.21
20 0.05 0.07 0.37
100 0.07 0.07 0.83
∞ 0.13 0.08 2.35
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
143_Q 290_A 1.65 0.60 0.00
79_V 142_I 1.57 0.54 0.00
192_A 188_T 1.51 0.50 0.00
163_N 27_I 1.45 0.46 0.00
133_V 63_V 1.42 0.44 0.00
40_P 196_I 1.39 0.42 0.00
115_V 131_D 1.33 0.38 0.00
146_V 232_V 1.29 0.35 0.00
56_I 303_K 1.29 0.35 0.00
83_A 131_D 1.24 0.32 0.00
96_G 151_T 1.22 0.30 0.00
68_L 63_V 1.21 0.30 0.00
193_V 244_R 1.20 0.29 0.00
111_F 111_D 1.19 0.28 0.00
78_L 116_L 1.18 0.28 0.00
47_L 259_A 1.16 0.27 0.00
5_T 330_S 1.15 0.26 0.00
68_L 222_V 1.15 0.26 0.00
121_K 330_S 1.14 0.26 0.00
131_L 188_T 1.13 0.25 0.00
101_D 241_S 1.13 0.25 0.00
133_V 59_M 1.13 0.25 0.00
68_L 239_V 1.12 0.24 0.00
7_R 29_R 1.11 0.24 0.00
194_G 293_S 1.11 0.24 0.00
91_Q 183_L 1.11 0.24 0.00
7_R 7_K 1.11 0.24 0.00
13_D 40_T 1.11 0.24 0.00
68_L 293_S 1.09 0.23 0.00
104_L 54_A 1.09 0.23 0.00
71_E 239_V 1.08 0.23 0.00
192_A 59_M 1.08 0.22 0.00
169_P 151_T 1.07 0.22 0.00
40_P 107_K 1.07 0.22 0.00
83_A 226_I 1.06 0.21 0.00
193_V 229_I 1.05 0.21 0.00
89_L 242_E 1.04 0.20 0.00
25_P 243_T 1.03 0.20 0.00
34_R 306_A 1.03 0.20 0.00
20_S 257_K 1.03 0.20 0.00
76_L 182_N 1.02 0.20 0.00
123_I 288_A 1.02 0.20 0.00
116_S 206_N 1.02 0.20 0.00
155_V 59_M 1.01 0.19 0.00
27_T 305_N 1.01 0.19 0.00
41_N 54_A 1.01 0.19 0.00
83_A 132_A 1.01 0.19 0.00
124_G 83_A 1.01 0.19 0.00
150_D 62_I 1.01 0.19 0.00
62_A 186_S 1.00 0.19 0.00
186_F 83_A 1.00 0.19 0.00
98_Y 12_A 1.00 0.19 0.00
187_T 32_E 0.99 0.18 0.00
34_R 206_N 0.99 0.18 0.00
115_V 239_V 0.99 0.18 0.00
195_V 65_I 0.98 0.18 0.00
25_P 265_Y 0.98 0.18 0.00
28_R 214_N 0.96 0.17 0.00
150_D 292_Y 0.96 0.17 0.00
42_A 185_Q 0.96 0.17 0.00
76_L 107_K 0.96 0.17 0.00
14_L 330_S 0.96 0.17 0.00
15_I 196_I 0.95 0.17 0.00
157_R 252_I 0.95 0.17 0.00
104_L 219_Y 0.95 0.17 0.00
32_A 54_A 0.95 0.17 0.00
42_A 327_L 0.94 0.16 0.00
140_R 144_V 0.94 0.16 0.00
3_A 196_I 0.94 0.16 0.00
21_Q 62_I 0.94 0.16 0.00
52_R 42_S 0.94 0.16 0.00
91_Q 293_S 0.94 0.16 0.00
7_R 32_E 0.94 0.16 0.00
5_T 274_E 0.93 0.16 0.00
96_G 157_E 0.93 0.16 0.00
100_V 315_E 0.93 0.16 0.00
29_A 198_M 0.92 0.16 0.00
173_E 29_R 0.92 0.15 0.00
143_Q 186_S 0.92 0.15 0.00
17_D 220_A 0.92 0.15 0.00
121_K 27_I 0.91 0.15 0.00
146_V 259_A 0.91 0.15 0.00
72_E 106_R 0.91 0.15 0.00
159_K 185_Q 0.91 0.15 0.00
40_P 226_I 0.90 0.15 0.00
61_G 234_E 0.90 0.15 0.00
101_D 198_M 0.90 0.15 0.00
135_K 26_S 0.90 0.15 0.00
196_I 45_S 0.90 0.15 0.00
98_Y 141_V 0.89 0.14 0.00
170_E 252_I 0.89 0.14 0.00
5_T 4_D 0.89 0.14 0.00
149_I 228_R 0.89 0.14 0.00
194_G 19_E 0.89 0.14 0.00
186_F 283_K 0.89 0.14 0.00
37_F 165_M 0.89 0.14 0.00
141_N 181_G 0.89 0.14 0.00
122_D 63_V 0.88 0.14 0.00
152_E 230_G 0.88 0.14 0.00
159_K 309_W 0.88 0.14 0.00
40_P 117_C 0.88 0.14 0.00
186_F 307_T 0.88 0.14 0.00
76_L 79_Q 0.88 0.14 0.00
157_R 293_S 0.88 0.14 0.00
21_Q 12_A 0.88 0.14 0.00
40_P 285_I 0.87 0.14 0.00
48_K 316_T 0.87 0.14 0.00
56_I 186_S 0.86 0.13 0.00
78_L 113_D 0.86 0.13 0.00
91_Q 200_I 0.86 0.13 0.00
63_S 288_A 0.86 0.13 0.00
68_L 191_I 0.86 0.13 0.00
42_A 284_L 0.86 0.13 0.00
195_V 87_E 0.86 0.13 0.00
186_F 41_I 0.85 0.13 0.00
9_Q 116_L 0.85 0.13 0.00
144_V 151_T 0.85 0.13 0.00
62_A 57_L 0.85 0.13 0.00
175_K 241_S 0.85 0.13 0.00
172_S 63_V 0.85 0.13 0.00
105_F 238_V 0.84 0.13 0.00
82_V 107_K 0.84 0.13 0.00
127_D 62_I 0.84 0.13 0.00
130_L 320_I 0.84 0.13 0.00
195_V 117_C 0.84 0.13 0.00
123_I 76_L 0.84 0.13 0.00
133_V 81_I 0.84 0.13 0.00
49_A 200_I 0.84 0.13 0.00
16_R 131_D 0.84 0.12 0.00
143_Q 275_L 0.83 0.12 0.00
98_Y 54_A 0.83 0.12 0.00
42_A 117_C 0.83 0.12 0.00
149_I 261_F 0.83 0.12 0.00
157_R 298_K 0.83 0.12 0.00
199_G 275_L 0.83 0.12 0.00
199_G 188_T 0.83 0.12 0.00
1_M 206_N 0.83 0.12 0.00
172_S 187_N 0.83 0.12 0.00
168_L 181_G 0.83 0.12 0.00
170_E 298_K 0.83 0.12 0.00
68_L 84_A 0.83 0.12 0.00
61_G 303_K 0.83 0.12 0.00
96_G 274_E 0.82 0.12 0.00
56_I 313_N 0.82 0.12 0.00
131_L 232_V 0.82 0.12 0.00
86_E 111_D 0.82 0.12 0.00
145_V 126_A 0.82 0.12 0.00
192_A 130_C 0.82 0.12 0.00
99_Q 113_D 0.82 0.12 0.00
115_V 319_E 0.82 0.12 0.00
75_G 116_L 0.82 0.12 0.00
46_H 22_F 0.82 0.12 0.00
45_E 305_N 0.82 0.12 0.00
168_L 307_T 0.82 0.12 0.00
55_V 230_G 0.82 0.12 0.00
103_S 54_A 0.82 0.12 0.00
40_P 200_I 0.81 0.12 0.00
135_K 164_H 0.81 0.12 0.00
194_G 298_K 0.81 0.12 0.00
13_D 324_V 0.81 0.12 0.00
58_I 184_K 0.81 0.12 0.00
115_V 126_A 0.81 0.12 0.00
189_E 113_D 0.81 0.12 0.00
24_M 159_E 0.81 0.12 0.00
159_K 298_K 0.81 0.12 0.00
44_E 252_I 0.81 0.12 0.00
7_R 15_L 0.81 0.12 0.00
131_L 282_E 0.81 0.12 0.00
145_V 257_K 0.81 0.12 0.00
12_F 228_R 0.80 0.12 0.00
60_S 258_Q 0.80 0.12 0.00
83_A 76_L 0.80 0.11 0.00
174_F 62_I 0.80 0.11 0.00
35_L 220_A 0.79 0.11 0.00
166_E 298_K 0.79 0.11 0.00
38_R 139_V 0.79 0.11 0.00
36_G 94_I 0.79 0.11 0.00
195_V 153_K 0.79 0.11 0.00
74_E 134_A 0.79 0.11 0.00
122_D 221_S 0.79 0.11 0.00
135_K 224_L 0.79 0.11 0.00
177_I 93_F 0.79 0.11 0.00
19_I 106_R 0.79 0.11 0.00
79_V 320_I 0.79 0.11 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
14190 2.49 LexAfun2 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9704 0.4 LexAfun Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
3611 2.48 lexA-recA Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done
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