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OPENSEQ.org
236
Genes: A B A+B
Length: 175 372 539
Sequences: 802 3494 956
Seq/Len: 4.58 9.39 1.77
MirrorTree (Pazo et al. 2001) 0.80
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 0.01 0.65
2 0.00 0.01 1.66
5 0.00 0.01 1.75
10 0.01 0.01 1.75
20 0.01 0.01 1.75
100 0.01 0.02 1.76
∞ 0.02 0.10 1.78
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
106_T 252_T 1.30 0.78 0.04
143_Y 156_F 1.14 0.64 0.03
83_E 164_M 1.11 0.60 0.02
29_M 176_L 1.10 0.59 0.02
15_M 216_G 1.03 0.52 0.02
146_V 70_V 1.03 0.52 0.02
83_E 142_N 1.02 0.51 0.02
63_M 214_L 0.99 0.48 0.02
23_I 25_K 0.98 0.47 0.01
9_E 243_E 0.97 0.46 0.01
84_L 320_R 0.95 0.43 0.01
94_A 194_L 0.94 0.42 0.01
86_E 51_T 0.93 0.42 0.01
144_A 357_V 0.92 0.41 0.01
81_V 156_F 0.92 0.41 0.01
154_N 279_K 0.92 0.40 0.01
40_E 330_A 0.91 0.39 0.01
143_Y 328_L 0.90 0.38 0.01
94_A 74_V 0.90 0.38 0.01
149_E 356_T 0.90 0.38 0.01
163_A 266_A 0.88 0.36 0.01
86_E 337_L 0.88 0.36 0.01
143_Y 169_T 0.88 0.36 0.01
160_F 340_H 0.88 0.36 0.01
50_V 134_M 0.87 0.35 0.01
54_Y 335_N 0.87 0.35 0.01
92_Q 240_K 0.87 0.35 0.01
138_S 164_M 0.86 0.35 0.01
113_D 266_A 0.86 0.34 0.01
143_Y 142_N 0.86 0.34 0.01
168_E 330_A 0.85 0.34 0.01
116_S 138_S 0.85 0.33 0.01
39_R 189_A 0.85 0.33 0.01
63_M 193_R 0.85 0.33 0.01
123_I 319_S 0.85 0.33 0.01
99_V 243_E 0.85 0.33 0.01
54_Y 296_P 0.84 0.33 0.01
118_I 241_Q 0.84 0.32 0.01
85_E 60_T 0.84 0.32 0.01
18_A 177_V 0.84 0.32 0.01
42_A 113_T 0.82 0.30 0.01
47_K 98_C 0.81 0.30 0.01
143_Y 157_A 0.81 0.29 0.01
82_F 261_I 0.81 0.29 0.01
154_N 6_P 0.80 0.29 0.01
10_D 65_L 0.80 0.29 0.01
151_F 138_S 0.80 0.28 0.01
76_V 351_K 0.79 0.28 0.01
100_I 334_L 0.79 0.28 0.01
79_D 141_S 0.78 0.27 0.01
89_S 170_V 0.78 0.27 0.01
144_A 253_D 0.78 0.27 0.01
97_A 154_Y 0.76 0.25 0.01
173_A 235_E 0.76 0.25 0.01
54_Y 150_I 0.76 0.25 0.01
174_M 298_S 0.76 0.25 0.01
29_M 200_A 0.75 0.25 0.01
138_S 265_P 0.75 0.25 0.01
158_M 138_S 0.75 0.25 0.01
146_V 120_Y 0.75 0.24 0.01
127_E 356_T 0.75 0.24 0.01
29_M 30_G 0.74 0.24 0.01
63_M 161_P 0.74 0.24 0.01
12_A 166_A 0.74 0.24 0.01
23_I 3_I 0.74 0.23 0.01
6_G 200_A 0.73 0.23 0.01
109_A 240_K 0.73 0.23 0.01
12_A 197_V 0.73 0.23 0.01
10_D 291_A 0.73 0.23 0.01
40_E 265_P 0.72 0.22 0.01
86_E 363_T 0.72 0.22 0.01
54_Y 30_G 0.72 0.22 0.01
160_F 100_L 0.72 0.22 0.01
86_E 48_D 0.72 0.22 0.01
41_M 255_A 0.72 0.22 0.01
15_M 338_T 0.72 0.22 0.01
119_Y 189_A 0.72 0.22 0.01
126_V 215_G 0.72 0.22 0.01
85_E 4_A 0.71 0.21 0.01
85_E 356_T 0.71 0.21 0.01
170_I 147_R 0.71 0.21 0.01
131_T 241_Q 0.71 0.21 0.01
155_N 163_M 0.71 0.21 0.01
37_A 94_A 0.70 0.21 0.01
143_Y 290_E 0.70 0.21 0.01
129_A 215_G 0.70 0.21 0.01
99_V 147_R 0.70 0.21 0.01
114_P 337_L 0.70 0.20 0.01
47_K 71_V 0.70 0.20 0.01
134_F 261_I 0.70 0.20 0.01
173_A 200_A 0.70 0.20 0.01
169_Q 311_I 0.69 0.20 0.01
123_I 199_M 0.69 0.20 0.01
42_A 271_T 0.69 0.20 0.01
48_E 143_L 0.69 0.20 0.01
127_E 151_D 0.69 0.20 0.01
106_T 199_M 0.69 0.20 0.01
17_N 210_Q 0.69 0.20 0.01
172_Q 287_L 0.69 0.20 0.01
91_F 130_R 0.69 0.20 0.01
131_T 224_E 0.69 0.20 0.01
79_D 110_E 0.69 0.20 0.01
29_M 248_E 0.69 0.20 0.01
138_S 341_V 0.69 0.20 0.01
56_I 139_S 0.68 0.20 0.01
83_E 328_L 0.68 0.19 0.01
17_N 18_I 0.68 0.19 0.01
29_M 125_M 0.68 0.19 0.01
76_V 69_D 0.68 0.19 0.01
51_E 348_L 0.68 0.19 0.01
143_Y 320_R 0.68 0.19 0.01
51_E 43_A 0.68 0.19 0.01
6_G 140_Q 0.68 0.19 0.01
155_N 270_I 0.68 0.19 0.01
75_N 189_A 0.67 0.19 0.01
164_K 241_Q 0.67 0.19 0.01
174_M 36_E 0.67 0.19 0.01
9_E 362_V 0.67 0.19 0.01
144_A 250_V 0.67 0.19 0.01
39_R 356_T 0.67 0.19 0.01
143_Y 359_G 0.67 0.19 0.01
135_I 235_E 0.67 0.18 0.01
144_A 219_I 0.67 0.18 0.01
4_K 129_S 0.67 0.18 0.01
10_D 91_K 0.67 0.18 0.01
45_L 152_G 0.67 0.18 0.01
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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