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OPENSEQ.org
358-359
Genes: A B A+B
Length: 205 307 486
Sequences: 2862 2007 1684
Seq/Len: 13.96 6.54 3.47
MirrorTree (Pazo et al. 2001) 0.79
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 0.06 0.08 2.97
2 0.06 0.08 3.10
5 0.06 0.08 3.21
10 0.06 0.08 3.27
20 0.06 0.08 3.29
100 0.06 0.08 3.38
∞ 0.06 0.10 3.95
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
166_E 76_K 3.20 1.00 1.00
152_E 129_K 1.00 0.69 0.53
159_S 120_V 0.98 0.67 0.51
146_V 190_N 0.97 0.65 0.49
17_I 251_N 0.94 0.62 0.46
3_T 166_Y 0.93 0.61 0.44
88_T 132_E 0.93 0.60 0.44
152_E 122_I 0.92 0.59 0.43
151_D 168_S 0.91 0.58 0.41
152_E 166_Y 0.91 0.58 0.41
27_W 211_R 0.89 0.56 0.40
188_E 273_I 0.89 0.56 0.39
48_C 44_Y 0.89 0.55 0.39
128_S 207_I 0.88 0.55 0.39
109_Y 287_I 0.87 0.54 0.37
17_I 171_E 0.87 0.54 0.37
129_L 125_D 0.86 0.52 0.36
87_K 123_G 0.86 0.52 0.35
46_I 60_N 0.85 0.50 0.34
133_E 65_K 0.82 0.47 0.31
152_E 44_Y 0.82 0.47 0.31
20_E 55_A 0.81 0.46 0.30
127_L 27_S 0.81 0.46 0.30
84_I 118_I 0.80 0.45 0.29
189_V 108_L 0.80 0.44 0.29
74_W 176_V 0.80 0.44 0.28
186_V 85_S 0.80 0.44 0.28
84_I 58_I 0.80 0.44 0.28
111_A 141_I 0.79 0.43 0.28
187_A 134_K 0.79 0.43 0.28
50_I 23_Q 0.79 0.43 0.28
146_V 116_F 0.79 0.43 0.27
61_E 74_L 0.79 0.42 0.27
37_E 248_E 0.78 0.42 0.27
91_N 234_I 0.78 0.41 0.26
112_L 76_K 0.78 0.41 0.26
84_I 37_Q 0.77 0.41 0.26
108_N 113_M 0.77 0.41 0.25
172_K 287_I 0.77 0.40 0.25
191_K 25_Q 0.76 0.39 0.24
98_E 199_S 0.76 0.39 0.24
122_I 133_M 0.76 0.39 0.24
109_Y 161_I 0.75 0.38 0.23
71_E 166_Y 0.75 0.38 0.23
46_I 170_A 0.75 0.38 0.23
3_T 55_A 0.75 0.38 0.23
37_E 273_I 0.74 0.37 0.23
125_A 34_N 0.74 0.37 0.22
25_S 71_G 0.74 0.37 0.22
114_G 141_I 0.74 0.37 0.22
186_V 250_L 0.74 0.36 0.22
80_E 74_L 0.73 0.36 0.22
179_D 188_N 0.73 0.36 0.22
82_N 299_S 0.73 0.36 0.22
95_N 275_N 0.73 0.36 0.22
37_E 170_A 0.73 0.36 0.21
108_N 118_I 0.73 0.35 0.21
59_I 274_E 0.73 0.35 0.21
80_E 261_S 0.72 0.35 0.21
104_I 224_D 0.72 0.35 0.21
95_N 182_Q 0.72 0.34 0.20
33_N 296_I 0.72 0.34 0.20
103_Y 24_I 0.72 0.34 0.20
83_G 111_P 0.72 0.34 0.20
84_I 196_T 0.72 0.34 0.20
98_E 62_L 0.71 0.34 0.20
132_F 214_F 0.71 0.34 0.20
108_N 286_M 0.71 0.33 0.19
159_S 13_E 0.71 0.33 0.19
109_Y 141_I 0.71 0.33 0.19
114_G 295_I 0.71 0.33 0.19
77_R 24_I 0.70 0.33 0.19
84_I 134_K 0.70 0.32 0.19
129_L 34_N 0.70 0.32 0.19
166_E 26_L 0.70 0.32 0.18
162_Y 76_K 0.70 0.32 0.18
28_F 271_H 0.70 0.32 0.18
114_G 252_R 0.69 0.32 0.18
39_N 62_L 0.69 0.31 0.18
156_T 120_V 0.69 0.31 0.18
84_I 83_A 0.69 0.31 0.18
9_V 304_L 0.69 0.31 0.18
144_V 186_E 0.69 0.31 0.18
128_S 179_Y 0.69 0.31 0.17
5_I 165_N 0.69 0.30 0.17
110_S 118_I 0.68 0.30 0.17
157_L 139_T 0.68 0.30 0.17
158_K 263_S 0.68 0.30 0.17
124_R 33_L 0.68 0.30 0.17
124_R 124_K 0.68 0.29 0.17
104_I 36_T 0.68 0.29 0.16
140_N 287_I 0.67 0.29 0.16
108_N 161_I 0.67 0.29 0.16
73_E 35_K 0.67 0.29 0.16
48_C 282_L 0.67 0.29 0.16
94_N 207_I 0.67 0.29 0.16
186_V 244_V 0.67 0.28 0.16
162_Y 78_S 0.67 0.28 0.16
72_K 14_F 0.66 0.28 0.15
48_C 161_I 0.66 0.28 0.15
5_I 282_L 0.66 0.28 0.15
170_A 295_I 0.66 0.28 0.15
2_I 129_K 0.66 0.28 0.15
91_N 191_E 0.66 0.28 0.15
190_I 78_S 0.66 0.28 0.15
116_N 123_G 0.66 0.28 0.15
86_S 142_G 0.66 0.28 0.15
10_T 57_L 0.66 0.28 0.15
139_K 151_I 0.66 0.27 0.15
41_E 264_S 0.66 0.27 0.15
164_Q 205_I 0.65 0.27 0.15
77_R 74_L 0.65 0.27 0.15
47_F 237_N 0.65 0.27 0.15
64_F 58_I 0.65 0.27 0.15
37_E 181_K 0.65 0.27 0.15
118_V 60_N 0.65 0.27 0.14
143_G 35_K 0.65 0.27 0.14
81_L 232_L 0.65 0.27 0.14
191_K 88_K 0.65 0.27 0.14
6_F 287_I 0.65 0.27 0.14
124_R 183_M 0.65 0.26 0.14
168_Q 53_T 0.65 0.26 0.14
153_L 91_D 0.65 0.26 0.14
82_N 151_I 0.65 0.26 0.14
97_L 103_P 0.65 0.26 0.14
186_V 262_I 0.64 0.26 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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