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OPENSEQ.org
1IXR_A_C
Genes: A B A+B
Length: 191 312 500
Sequences: 2889 2672 1703
Seq/Len: 15.13 8.56 3.41
MirrorTree (Pazo et al. 2001) 0.75
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 0.08 3.04
2 0.09 0.08 3.18
5 0.09 0.08 3.30
10 0.09 0.08 3.36
20 0.09 0.08 3.39
100 0.09 0.08 3.47
∞ 0.09 0.09 4.04
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
162_Q 76_K 3.15 1.00 1.00
155_A 121_I 0.99 0.68 0.51
148_E 130_R 0.97 0.65 0.49
142_E 191_E 0.97 0.65 0.48
84_V 133_R 0.96 0.64 0.48
128_K 226_I 0.95 0.63 0.46
17_F 172_E 0.93 0.60 0.44
184_K 135_E 0.92 0.58 0.42
3_R 167_Y 0.91 0.58 0.42
126_E 126_G 0.91 0.58 0.42
106_A 295_L 0.91 0.57 0.41
147_E 169_T 0.90 0.57 0.40
148_E 167_Y 0.90 0.56 0.40
128_K 65_N 0.89 0.55 0.38
78_S 307_L 0.86 0.52 0.35
185_E 281_L 0.86 0.52 0.35
124_A 27_Y 0.86 0.51 0.35
148_E 123_I 0.86 0.51 0.35
83_K 124_G 0.84 0.49 0.33
188_K 25_R 0.84 0.49 0.33
49_H 44_F 0.83 0.48 0.32
125_L 208_K 0.83 0.47 0.31
27_F 212_R 0.81 0.46 0.30
180_Q 260_F 0.81 0.45 0.30
186_A 109_H 0.81 0.45 0.29
80_V 119_M 0.81 0.44 0.29
37_A 254_E 0.80 0.43 0.28
41_G 62_L 0.80 0.43 0.28
142_E 117_F 0.80 0.43 0.28
119_L 134_L 0.79 0.42 0.27
109_L 76_K 0.78 0.41 0.26
95_R 200_S 0.77 0.40 0.25
183_I 85_A 0.77 0.40 0.25
105_D 114_M 0.77 0.40 0.25
47_H 60_H 0.77 0.40 0.25
162_Q 26_V 0.76 0.39 0.24
51_L 23_K 0.76 0.39 0.24
20_L 55_A 0.76 0.39 0.24
57_L 74_I 0.76 0.39 0.24
106_A 162_V 0.75 0.38 0.23
138_G 191_E 0.75 0.37 0.23
100_A 24_L 0.74 0.37 0.22
92_L 183_L 0.74 0.36 0.22
76_S 269_T 0.74 0.36 0.22
111_S 142_I 0.73 0.35 0.21
148_E 44_F 0.73 0.35 0.21
127_L 215_R 0.73 0.35 0.21
60_Y 58_I 0.73 0.35 0.21
68_L 14_Y 0.73 0.35 0.21
158_F 76_K 0.73 0.35 0.21
122_R 34_R 0.73 0.35 0.21
80_V 58_I 0.72 0.34 0.20
80_V 37_P 0.72 0.34 0.20
25_G 71_G 0.72 0.34 0.20
125_L 180_D 0.72 0.34 0.20
87_A 240_L 0.71 0.33 0.19
80_V 135_E 0.71 0.33 0.19
67_N 167_Y 0.71 0.32 0.19
170_L 190_E 0.70 0.32 0.18
57_L 119_M 0.70 0.32 0.18
121_E 33_A 0.70 0.32 0.18
105_D 294_L 0.70 0.32 0.18
2_I 130_R 0.70 0.32 0.18
33_P 304_A 0.70 0.31 0.18
187_L 78_G 0.69 0.31 0.18
105_D 162_V 0.69 0.31 0.18
126_E 34_R 0.69 0.31 0.18
101_L 36_E 0.69 0.31 0.18
188_K 89_E 0.69 0.31 0.18
163_A 76_K 0.69 0.31 0.17
183_I 250_R 0.69 0.30 0.17
40_E 170_P 0.69 0.30 0.17
77_V 238_L 0.69 0.30 0.17
68_L 260_F 0.69 0.30 0.17
70_L 177_V 0.69 0.30 0.17
48_T 243_L 0.68 0.30 0.17
155_A 13_E 0.68 0.30 0.17
115_V 60_H 0.68 0.30 0.17
55_E 282_E 0.68 0.29 0.17
76_S 74_I 0.68 0.29 0.17
183_I 256_L 0.68 0.29 0.17
139_E 187_R 0.68 0.29 0.16
111_S 68_V 0.68 0.29 0.16
79_G 112_P 0.68 0.29 0.16
166_V 74_I 0.68 0.29 0.16
73_L 74_I 0.67 0.29 0.16
183_I 134_L 0.67 0.29 0.16
152_A 121_I 0.67 0.28 0.16
190_L 78_G 0.67 0.28 0.16
153_L 140_T 0.67 0.28 0.15
149_A 92_D 0.66 0.28 0.15
73_L 24_L 0.66 0.27 0.15
48_T 284_V 0.66 0.27 0.15
47_H 171_E 0.66 0.27 0.15
82_P 143_G 0.66 0.27 0.15
80_V 197_G 0.66 0.27 0.15
107_R 119_M 0.66 0.27 0.15
178_R 20_L 0.66 0.27 0.15
49_H 162_V 0.65 0.27 0.14
84_V 90_E 0.65 0.27 0.14
6_R 290_I 0.65 0.27 0.14
185_E 184_L 0.65 0.26 0.14
63_P 83_I 0.65 0.26 0.14
6_R 169_T 0.65 0.26 0.14
167_V 138_R 0.65 0.26 0.14
78_S 152_T 0.65 0.26 0.14
109_L 75_E 0.65 0.26 0.14
92_L 283_E 0.65 0.26 0.14
159_K 212_R 0.65 0.26 0.14
113_S 137_P 0.65 0.26 0.14
111_S 303_V 0.65 0.26 0.14
124_A 46_P 0.65 0.26 0.14
108_L 142_I 0.65 0.26 0.14
3_R 55_A 0.64 0.26 0.14
115_V 68_V 0.64 0.26 0.14
117_R 219_Q 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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