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OPENSEQ.org
1-5
Genes: A B A+B
Length: 388 285 597
Sequences: 4352 4913 592
Seq/Len: 11.22 17.24 0.99
MirrorTree (Pazo et al. 2001) 0.78
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 0.05 0.06 0.09
2 0.05 0.07 0.26
5 0.06 0.08 0.74
10 0.06 0.08 0.81
20 0.07 0.09 0.88
100 0.08 0.09 1.25
∞ 0.15 0.14 2.81
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
182_I 131_G 1.19 0.51 0.00
250_V 82_T 1.18 0.50 0.00
262_S 2_I 1.10 0.43 0.00
124_I 185_S 1.07 0.40 0.00
333_P 104_L 1.04 0.37 0.00
161_A 255_G 1.04 0.37 0.00
281_G 63_D 1.03 0.37 0.00
150_A 234_M 1.01 0.35 0.00
253_S 146_A 0.99 0.33 0.00
299_A 134_R 0.98 0.33 0.00
162_I 63_D 0.98 0.32 0.00
28_I 65_A 0.96 0.30 0.00
334_T 163_R 0.95 0.30 0.00
109_A 17_K 0.95 0.30 0.00
139_V 145_F 0.94 0.29 0.00
95_R 131_G 0.94 0.29 0.00
191_P 186_V 0.93 0.28 0.00
356_L 2_I 0.93 0.28 0.00
54_I 166_D 0.93 0.28 0.00
181_Y 187_V 0.93 0.28 0.00
361_V 250_V 0.91 0.27 0.00
147_T 145_F 0.90 0.26 0.00
116_I 154_S 0.90 0.26 0.00
94_S 260_Q 0.90 0.26 0.00
52_V 250_V 0.90 0.26 0.00
54_I 104_L 0.89 0.25 0.00
216_A 224_M 0.89 0.25 0.00
139_V 235_T 0.88 0.25 0.00
56_D 92_G 0.88 0.24 0.00
194_E 260_Q 0.88 0.24 0.00
314_V 252_A 0.87 0.24 0.00
53_L 183_M 0.87 0.24 0.00
151_M 78_I 0.87 0.24 0.00
284_Y 151_V 0.86 0.23 0.00
297_C 126_V 0.86 0.23 0.00
253_S 10_L 0.86 0.23 0.00
304_K 10_L 0.85 0.23 0.00
131_V 129_S 0.85 0.23 0.00
185_A 129_S 0.84 0.22 0.00
163_D 259_F 0.83 0.22 0.00
302_M 135_A 0.83 0.22 0.00
368_R 93_D 0.83 0.22 0.00
300_I 131_G 0.83 0.21 0.00
215_T 179_G 0.83 0.21 0.00
300_I 161_L 0.83 0.21 0.00
258_A 139_A 0.82 0.21 0.00
181_Y 65_A 0.82 0.21 0.00
262_S 189_S 0.82 0.21 0.00
326_L 140_L 0.82 0.21 0.00
64_V 263_T 0.82 0.21 0.00
26_D 184_P 0.82 0.21 0.00
92_S 131_G 0.82 0.21 0.00
24_K 231_T 0.81 0.20 0.00
166_M 75_V 0.80 0.20 0.00
382_Y 27_F 0.80 0.20 0.00
114_T 10_L 0.80 0.20 0.00
208_I 144_G 0.79 0.19 0.00
108_H 126_V 0.79 0.19 0.00
359_M 132_T 0.79 0.19 0.00
252_G 78_I 0.79 0.19 0.00
302_M 131_G 0.78 0.19 0.00
31_H 188_I 0.78 0.18 0.00
191_P 187_V 0.78 0.18 0.00
29_V 154_S 0.78 0.18 0.00
202_V 225_A 0.78 0.18 0.00
292_V 197_I 0.78 0.18 0.00
281_G 66_T 0.78 0.18 0.00
118_A 188_I 0.77 0.18 0.00
102_E 48_A 0.77 0.18 0.00
179_R 73_G 0.77 0.18 0.00
372_I 39_L 0.77 0.18 0.00
67_F 90_L 0.77 0.18 0.00
54_I 235_T 0.76 0.17 0.00
115_V 51_T 0.76 0.17 0.00
131_V 16_Y 0.76 0.17 0.00
139_V 36_L 0.75 0.17 0.00
334_T 144_G 0.75 0.17 0.00
250_V 188_I 0.75 0.17 0.00
118_A 237_A 0.75 0.17 0.00
148_L 92_G 0.74 0.17 0.00
155_S 52_I 0.74 0.17 0.00
89_G 191_I 0.74 0.17 0.00
296_E 74_A 0.74 0.16 0.00
91_Y 238_E 0.74 0.16 0.00
188_E 58_I 0.74 0.16 0.00
80_R 221_L 0.74 0.16 0.00
300_I 233_L 0.74 0.16 0.00
283_A 150_I 0.74 0.16 0.00
114_T 2_I 0.74 0.16 0.00
328_A 16_Y 0.74 0.16 0.00
370_K 29_T 0.74 0.16 0.00
109_A 56_L 0.73 0.16 0.00
86_I 196_P 0.73 0.16 0.00
162_I 39_L 0.73 0.16 0.00
182_I 148_I 0.73 0.16 0.00
107_S 18_T 0.73 0.16 0.00
148_L 66_T 0.73 0.16 0.00
116_I 79_I 0.73 0.16 0.00
155_S 6_R 0.73 0.16 0.00
92_S 50_V 0.72 0.16 0.00
281_G 20_L 0.72 0.16 0.00
81_L 233_L 0.72 0.15 0.00
86_I 181_D 0.72 0.15 0.00
374_L 193_A 0.72 0.15 0.00
335_S 176_P 0.72 0.15 0.00
303_V 34_K 0.72 0.15 0.00
353_D 127_V 0.72 0.15 0.00
210_N 11_H 0.72 0.15 0.00
245_I 260_Q 0.72 0.15 0.00
124_I 150_I 0.72 0.15 0.00
24_K 104_L 0.71 0.15 0.00
161_A 230_R 0.71 0.15 0.00
368_R 80_P 0.71 0.15 0.00
189_T 63_D 0.71 0.15 0.00
249_I 52_I 0.71 0.15 0.00
336_V 50_V 0.71 0.15 0.00
213_E 11_H 0.71 0.15 0.00
280_I 56_L 0.71 0.15 0.00
189_T 220_V 0.71 0.15 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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