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OPENSEQ.org
4-5
Genes: A B A+B
Length: 234 285 473
Sequences: 1521 4913 286
Seq/Len: 6.5 17.24 0.6
MirrorTree (Pazo et al. 2001) 0.68
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 0.07 0.06 0.34
2 0.07 0.07 0.42
5 0.07 0.08 0.49
10 0.07 0.08 0.53
20 0.07 0.09 0.55
100 0.08 0.09 0.64
∞ 0.09 0.14 1.02
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
153_Y 262_W 1.42 0.56 0.00
54_Q 188_I 1.33 0.49 0.00
200_S 135_A 1.33 0.48 0.00
68_Y 148_I 1.21 0.39 0.00
217_S 244_T 1.21 0.38 0.00
208_T 49_S 1.20 0.38 0.00
149_K 78_I 1.20 0.38 0.00
200_S 127_V 1.12 0.32 0.00
226_A 29_T 1.11 0.31 0.00
25_I 133_A 1.11 0.31 0.00
227_T 188_I 1.10 0.31 0.00
75_Q 79_I 1.07 0.29 0.00
35_A 187_V 1.04 0.27 0.00
135_K 250_V 1.03 0.26 0.00
68_Y 252_A 1.02 0.26 0.00
55_V 51_T 1.02 0.25 0.00
84_Y 179_G 1.01 0.25 0.00
149_K 40_I 0.99 0.24 0.00
63_Q 238_E 0.99 0.24 0.00
120_K 238_E 0.99 0.23 0.00
99_V 51_T 0.98 0.23 0.00
35_A 66_T 0.97 0.22 0.00
67_V 241_G 0.97 0.22 0.00
128_S 262_W 0.96 0.22 0.00
72_T 245_V 0.96 0.22 0.00
200_S 26_R 0.95 0.22 0.00
133_Q 235_T 0.95 0.21 0.00
127_A 51_T 0.95 0.21 0.00
68_Y 72_I 0.95 0.21 0.00
172_L 165_F 0.95 0.21 0.00
160_V 144_G 0.94 0.21 0.00
104_L 56_L 0.94 0.21 0.00
200_S 90_L 0.92 0.20 0.00
148_N 133_A 0.92 0.20 0.00
174_N 260_Q 0.92 0.20 0.00
215_L 91_V 0.91 0.19 0.00
217_S 6_R 0.91 0.19 0.00
20_A 136_A 0.90 0.19 0.00
91_Y 236_L 0.90 0.19 0.00
36_V 73_G 0.90 0.19 0.00
229_I 135_A 0.90 0.19 0.00
204_N 154_S 0.90 0.19 0.00
159_L 211_H 0.89 0.18 0.00
202_V 246_G 0.89 0.18 0.00
156_V 64_S 0.88 0.18 0.00
56_A 244_T 0.88 0.18 0.00
161_G 246_G 0.88 0.18 0.00
104_L 78_I 0.87 0.18 0.00
21_D 103_A 0.87 0.17 0.00
168_D 5_S 0.87 0.17 0.00
63_Q 70_R 0.87 0.17 0.00
211_S 255_G 0.87 0.17 0.00
188_M 20_L 0.87 0.17 0.00
170_F 104_L 0.86 0.17 0.00
153_Y 163_R 0.86 0.17 0.00
197_G 99_G 0.86 0.17 0.00
20_A 106_H 0.86 0.17 0.00
104_L 239_D 0.86 0.17 0.00
127_A 162_V 0.86 0.17 0.00
170_F 129_S 0.85 0.16 0.00
165_E 34_K 0.84 0.16 0.00
168_D 99_G 0.84 0.16 0.00
159_L 74_A 0.84 0.16 0.00
54_Q 262_W 0.84 0.16 0.00
229_I 126_V 0.83 0.16 0.00
224_L 220_V 0.83 0.16 0.00
226_A 225_A 0.83 0.16 0.00
160_V 97_W 0.83 0.16 0.00
226_A 242_W 0.83 0.15 0.00
55_V 45_F 0.82 0.15 0.00
32_G 61_L 0.82 0.15 0.00
95_L 265_I 0.82 0.15 0.00
59_R 20_L 0.82 0.15 0.00
130_H 130_G 0.81 0.15 0.00
104_L 196_P 0.81 0.15 0.00
123_T 185_S 0.81 0.15 0.00
219_A 154_S 0.81 0.15 0.00
66_I 61_L 0.81 0.15 0.00
111_H 78_I 0.81 0.15 0.00
192_N 250_V 0.81 0.15 0.00
208_T 97_W 0.81 0.15 0.00
194_G 259_F 0.81 0.15 0.00
225_S 44_D 0.81 0.15 0.00
143_W 63_D 0.81 0.15 0.00
146_F 258_Q 0.81 0.15 0.00
94_G 41_R 0.81 0.15 0.00
189_I 44_D 0.81 0.15 0.00
226_A 78_I 0.81 0.15 0.00
102_L 58_I 0.80 0.14 0.00
66_I 244_T 0.80 0.14 0.00
142_S 188_I 0.80 0.14 0.00
202_V 202_R 0.80 0.14 0.00
58_L 133_A 0.80 0.14 0.00
72_T 225_A 0.80 0.14 0.00
130_H 53_P 0.79 0.14 0.00
130_H 55_K 0.79 0.14 0.00
130_H 76_N 0.79 0.14 0.00
130_H 96_D 0.79 0.14 0.00
130_H 128_G 0.79 0.14 0.00
130_H 247_G 0.79 0.14 0.00
168_D 4_A 0.79 0.14 0.00
129_H 54_L 0.79 0.14 0.00
58_L 98_R 0.79 0.14 0.00
228_E 264_G 0.79 0.14 0.00
230_R 241_G 0.79 0.14 0.00
177_A 58_I 0.79 0.14 0.00
160_V 246_G 0.78 0.14 0.00
94_G 133_A 0.78 0.14 0.00
131_D 143_L 0.78 0.14 0.00
214_A 61_L 0.78 0.14 0.00
197_G 250_V 0.78 0.14 0.00
172_L 246_G 0.78 0.14 0.00
95_L 188_I 0.78 0.14 0.00
211_S 256_W 0.78 0.14 0.00
36_V 20_L 0.77 0.13 0.00
44_E 230_R 0.77 0.13 0.00
152_Q 62_L 0.77 0.13 0.00
78_K 176_P 0.77 0.13 0.00
33_S 21_P 0.77 0.13 0.00
92_Q 34_K 0.77 0.13 0.00
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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