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OPENSEQ.org
1IXR-2
Genes: A B A+B
Length: 191 308 497
Sequences: 2889 2596 1698
Seq/Len: 15.13 8.43 3.42
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 3.06
2 0.09 0.08 3.21
5 0.09 0.08 3.34
10 0.09 0.08 3.38
20 0.09 0.08 3.40
100 0.09 0.08 3.49
∞ 0.09 0.09 4.07
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 72_K 3.38 1.00 1.00
84_V 129_R 1.14 0.82 0.68
125_L 204_K 1.09 0.78 0.64
155_A 117_I 1.07 0.76 0.61
148_E 163_Y 1.03 0.71 0.56
109_L 72_K 1.01 0.70 0.54
17_F 168_E 0.99 0.68 0.52
183_I 81_A 0.99 0.68 0.52
51_L 19_K 0.99 0.67 0.51
184_K 131_E 0.98 0.67 0.50
125_L 176_D 0.97 0.65 0.49
83_K 120_G 0.96 0.65 0.48
124_A 23_Y 0.96 0.65 0.48
185_E 277_L 0.96 0.64 0.47
57_L 70_I 0.95 0.62 0.46
128_K 61_N 0.94 0.62 0.45
128_K 222_I 0.92 0.60 0.43
3_R 163_Y 0.91 0.58 0.42
126_E 122_G 0.91 0.58 0.42
186_A 105_H 0.90 0.57 0.41
25_G 67_G 0.90 0.56 0.40
107_R 115_M 0.90 0.56 0.40
41_G 58_L 0.90 0.56 0.40
162_Q 22_V 0.89 0.55 0.39
20_L 51_A 0.89 0.55 0.39
106_A 158_V 0.88 0.54 0.38
118_R 70_I 0.88 0.54 0.38
156_L 38_L 0.88 0.54 0.37
80_V 98_L 0.87 0.53 0.36
188_K 21_R 0.86 0.52 0.36
78_S 176_D 0.86 0.52 0.35
76_S 265_T 0.85 0.50 0.34
27_F 208_R 0.85 0.50 0.34
80_V 54_I 0.85 0.50 0.34
113_S 120_G 0.84 0.49 0.33
122_R 30_R 0.84 0.49 0.33
49_H 40_F 0.84 0.49 0.33
80_V 115_M 0.84 0.48 0.32
6_R 286_I 0.82 0.47 0.31
148_E 126_R 0.82 0.46 0.30
156_L 67_G 0.82 0.46 0.30
158_F 72_K 0.82 0.46 0.30
119_L 130_L 0.81 0.45 0.29
117_R 215_Q 0.81 0.44 0.29
3_R 271_S 0.80 0.44 0.29
80_V 33_P 0.80 0.44 0.28
21_A 256_F 0.80 0.44 0.28
83_K 162_E 0.80 0.43 0.28
60_Y 54_I 0.80 0.43 0.28
2_I 126_R 0.80 0.43 0.28
115_V 64_V 0.79 0.42 0.27
68_L 10_Y 0.79 0.42 0.27
163_A 72_K 0.78 0.42 0.27
70_L 173_V 0.78 0.42 0.27
111_S 299_V 0.78 0.41 0.26
67_N 163_Y 0.78 0.41 0.26
125_L 110_M 0.78 0.41 0.26
147_E 165_T 0.77 0.40 0.25
92_L 179_L 0.77 0.40 0.25
159_K 129_R 0.77 0.40 0.25
187_L 74_G 0.77 0.39 0.25
53_K 268_T 0.76 0.39 0.24
84_V 114_V 0.76 0.39 0.24
106_A 291_L 0.76 0.39 0.24
68_L 256_F 0.76 0.39 0.24
70_L 62_L 0.76 0.39 0.24
162_Q 129_R 0.76 0.38 0.24
4_Y 121_Q 0.76 0.38 0.24
115_V 56_H 0.76 0.38 0.24
31_P 252_L 0.75 0.38 0.23
148_E 119_I 0.75 0.37 0.23
67_N 263_L 0.75 0.37 0.23
142_E 187_E 0.74 0.36 0.22
112_A 10_Y 0.74 0.36 0.22
116_G 97_R 0.74 0.36 0.22
78_S 204_K 0.74 0.36 0.22
25_G 38_L 0.74 0.36 0.22
87_A 78_A 0.74 0.36 0.22
183_I 246_R 0.73 0.36 0.22
127_L 211_R 0.73 0.35 0.21
156_L 277_L 0.73 0.35 0.21
126_E 123_P 0.73 0.35 0.21
162_Q 279_E 0.73 0.35 0.21
60_Y 163_Y 0.73 0.35 0.21
76_S 70_I 0.73 0.35 0.21
84_V 86_E 0.73 0.35 0.21
100_A 20_L 0.72 0.35 0.21
126_E 30_R 0.72 0.34 0.20
149_A 88_D 0.72 0.34 0.20
122_R 227_A 0.72 0.34 0.20
78_S 303_L 0.72 0.34 0.20
87_A 236_L 0.72 0.34 0.20
166_V 58_L 0.72 0.34 0.20
117_R 248_I 0.72 0.34 0.20
60_Y 108_P 0.71 0.33 0.20
28_L 275_G 0.71 0.33 0.20
42_K 161_L 0.71 0.33 0.19
121_E 149_A 0.71 0.33 0.19
153_L 136_T 0.71 0.33 0.19
113_S 133_P 0.70 0.32 0.19
190_L 148_T 0.70 0.32 0.19
84_V 162_E 0.70 0.32 0.19
123_I 51_A 0.70 0.32 0.19
82_P 204_K 0.70 0.32 0.18
107_R 113_F 0.70 0.32 0.18
70_L 204_K 0.70 0.32 0.18
31_P 292_K 0.70 0.32 0.18
83_K 10_Y 0.70 0.31 0.18
105_D 290_L 0.70 0.31 0.18
31_P 254_L 0.69 0.31 0.18
142_E 113_F 0.69 0.31 0.18
152_A 77_A 0.69 0.31 0.18
3_R 51_A 0.69 0.31 0.18
158_F 71_E 0.69 0.31 0.18
48_T 241_L 0.69 0.31 0.18
110_T 134_R 0.69 0.31 0.17
4_Y 40_F 0.69 0.30 0.17
87_A 188_A 0.69 0.30 0.17
80_V 79_I 0.69 0.30 0.17
5_L 286_I 0.69 0.30 0.17
152_A 117_I 0.69 0.30 0.17
25_G 74_G 0.69 0.30 0.17
127_L 39_L 0.68 0.30 0.17
178_R 16_L 0.68 0.30 0.17
89_L 138_I 0.68 0.30 0.17
113_S 30_R 0.68 0.30 0.17
10_L 70_I 0.68 0.30 0.17
148_E 244_R 0.68 0.29 0.17
114_G 122_G 0.68 0.29 0.17
105_D 115_M 0.68 0.29 0.17
130_K 236_L 0.68 0.29 0.16
48_T 239_L 0.68 0.29 0.16
100_A 179_L 0.68 0.29 0.16
180_Q 256_F 0.67 0.29 0.16
21_A 233_A 0.67 0.29 0.16
129_G 86_E 0.67 0.29 0.16
60_Y 67_G 0.67 0.29 0.16
167_V 134_R 0.67 0.29 0.16
33_P 300_A 0.67 0.28 0.16
79_G 108_P 0.67 0.28 0.16
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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