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OPENSEQ.org
Bs XE
Genes: A B A+B
Length: 296 228 511
Sequences: 2003 89438 1525
Seq/Len: 6.77 392.27 2.98
MirrorTree (Pazo et al. 2001) 0.60
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 0.08 2.76
2 0.00 0.09 2.77
5 0.01 0.14 2.81
10 0.01 0.19 2.85
20 0.01 0.24 2.91
100 0.01 0.35 3.20
∞ 0.01 0.37 3.37
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
203_E 89_K 1.93 0.99 0.97
211_T 75_P 1.62 0.97 0.91
207_L 89_K 1.48 0.95 0.86
4_I 108_G 1.40 0.93 0.82
10_R 105_E 1.31 0.89 0.76
211_T 76_F 1.26 0.87 0.72
121_L 84_V 1.22 0.84 0.68
34_L 173_S 1.22 0.84 0.68
208_V 106_V 1.20 0.83 0.67
43_I 174_W 1.17 0.81 0.64
207_L 49_Y 1.16 0.80 0.62
20_T 39_A 1.14 0.78 0.60
225_L 191_V 1.12 0.77 0.58
231_S 199_I 1.09 0.74 0.54
189_N 160_I 1.08 0.73 0.54
129_T 89_K 1.07 0.72 0.52
18_R 134_F 1.06 0.71 0.51
229_F 190_V 1.05 0.69 0.49
127_V 137_Q 1.03 0.68 0.47
295_R 158_V 1.02 0.67 0.46
148_V 66_L 1.01 0.66 0.45
289_S 39_A 1.01 0.65 0.45
198_R 114_I 1.00 0.64 0.44
288_T 62_N 1.00 0.64 0.43
252_K 25_I 0.99 0.64 0.43
97_E 32_Y 0.99 0.63 0.43
278_G 102_F 0.99 0.63 0.43
35_I 42_S 0.98 0.63 0.42
205_M 102_F 0.98 0.62 0.42
95_E 71_E 0.97 0.61 0.40
205_M 200_V 0.96 0.59 0.39
11_E 207_V 0.95 0.59 0.39
206_K 74_I 0.94 0.58 0.38
230_G 168_L 0.94 0.57 0.36
23_T 77_V 0.92 0.55 0.35
160_R 147_S 0.92 0.55 0.35
234_P 33_V 0.91 0.54 0.34
78_N 211_E 0.90 0.52 0.32
30_V 106_V 0.90 0.52 0.32
101_L 198_E 0.90 0.52 0.32
272_L 39_A 0.90 0.52 0.32
189_N 143_Q 0.89 0.52 0.32
84_K 22_S 0.89 0.51 0.32
172_G 39_A 0.89 0.51 0.31
186_L 177_M 0.89 0.51 0.31
21_W 81_I 0.89 0.51 0.31
280_V 61_I 0.87 0.49 0.29
204_I 89_K 0.87 0.49 0.29
122_N 44_F 0.85 0.46 0.27
287_L 95_T 0.85 0.46 0.27
21_W 33_V 0.84 0.45 0.26
15_S 147_S 0.84 0.45 0.26
296_V 89_K 0.84 0.45 0.26
84_K 112_S 0.83 0.44 0.26
128_K 8_Y 0.83 0.44 0.25
182_T 180_L 0.83 0.44 0.25
199_R 179_T 0.83 0.43 0.25
36_L 96_V 0.82 0.43 0.24
223_G 79_R 0.81 0.42 0.24
13_F 47_M 0.81 0.42 0.24
262_P 194_T 0.81 0.42 0.23
286_S 92_P 0.81 0.41 0.23
236_A 216_V 0.81 0.41 0.23
59_E 105_E 0.81 0.41 0.23
230_G 184_N 0.80 0.41 0.23
87_Q 68_T 0.80 0.40 0.22
9_L 95_T 0.80 0.40 0.22
193_I 114_I 0.80 0.40 0.22
292_K 61_I 0.80 0.40 0.22
227_G 46_K 0.80 0.40 0.22
214_F 179_T 0.80 0.40 0.22
74_D 215_I 0.80 0.40 0.22
215_I 134_F 0.79 0.39 0.22
272_L 66_L 0.79 0.39 0.21
199_R 59_I 0.79 0.39 0.21
32_V 191_V 0.79 0.38 0.21
87_Q 62_N 0.78 0.38 0.20
170_N 190_V 0.78 0.38 0.20
187_I 42_S 0.78 0.37 0.20
107_D 180_L 0.78 0.37 0.20
214_F 198_E 0.77 0.37 0.20
194_T 33_V 0.77 0.37 0.20
113_T 93_K 0.77 0.37 0.20
22_M 192_M 0.77 0.37 0.20
203_E 49_Y 0.77 0.36 0.19
127_V 28_G 0.77 0.36 0.19
182_T 30_F 0.76 0.36 0.19
194_T 49_Y 0.76 0.36 0.19
155_K 190_V 0.76 0.36 0.19
42_V 69_I 0.76 0.35 0.19
142_I 46_K 0.76 0.35 0.19
249_V 69_I 0.76 0.35 0.19
140_K 6_E 0.76 0.35 0.19
27_I 175_E 0.76 0.35 0.18
171_I 67_A 0.76 0.35 0.18
230_G 159_V 0.75 0.34 0.18
99_D 47_M 0.75 0.34 0.18
12_S 147_S 0.75 0.34 0.18
136_P 68_T 0.75 0.34 0.18
274_L 95_T 0.74 0.33 0.17
80_I 24_T 0.74 0.33 0.17
37_V 36_P 0.74 0.33 0.17
240_S 24_T 0.74 0.33 0.17
45_L 39_A 0.74 0.33 0.17
142_I 52_E 0.74 0.33 0.17
120_P 152_I 0.74 0.33 0.17
229_F 24_T 0.73 0.32 0.17
185_F 17_A 0.73 0.32 0.16
217_W 191_V 0.73 0.32 0.16
238_V 118_V 0.73 0.32 0.16
245_V 84_V 0.73 0.32 0.16
224_L 175_E 0.73 0.32 0.16
250_V 180_L 0.73 0.32 0.16
187_I 184_N 0.72 0.32 0.16
53_N 66_L 0.72 0.32 0.16
167_V 94_L 0.72 0.31 0.16
54_A 121_V 0.72 0.31 0.16
237_L 81_I 0.72 0.31 0.16
34_L 53_K 0.72 0.31 0.16
24_F 20_G 0.72 0.31 0.15
141_K 84_V 0.72 0.31 0.15
249_V 100_V 0.72 0.31 0.15
171_I 98_E 0.72 0.31 0.15
15_S 47_M 0.71 0.30 0.15
48_N 97_F 0.71 0.30 0.15
122_N 104_L 0.71 0.30 0.15
232_V 60_L 0.71 0.30 0.15
180_V 6_E 0.71 0.30 0.15
263_Y 159_V 0.71 0.30 0.15
103_D 19_N 0.71 0.30 0.15
285_G 39_A 0.71 0.30 0.15
40_F 108_G 0.71 0.30 0.15
165_V 104_L 0.71 0.30 0.15
80_I 6_E 0.71 0.30 0.15
77_Q 22_S 0.71 0.30 0.15
114_M 76_F 0.71 0.30 0.15
294_L 34_V 0.71 0.30 0.15
217_W 103_A 0.71 0.30 0.15
206_K 34_V 0.71 0.30 0.15
217_W 104_L 0.71 0.30 0.15
136_P 21_I 0.71 0.30 0.15
43_I 4_M 0.70 0.29 0.14
187_I 25_I 0.70 0.29 0.14
30_V 168_L 0.70 0.29 0.14
24_F 159_V 0.70 0.29 0.14
50_M 42_S 0.70 0.29 0.14
231_S 91_L 0.70 0.29 0.14
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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