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OPENSEQ.org
114
Genes: A B A+B
Length: 343 204 490
Sequences: 3035 8547 127
Seq/Len: 8.85 41.9 0.26
MirrorTree (Pazo et al. 2001) 0.33
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 0.04 0.02
2 0.06 0.04 0.04
5 0.07 0.05 0.08
10 0.08 0.07 0.13
20 0.08 0.09 0.23
100 0.11 0.17 0.74
∞ 0.16 0.24 1.50
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
206_L 66_G 1.73 0.53 0.00
257_A 90_T 1.53 0.40 0.00
54_N 17_T 1.29 0.26 0.00
328_F 90_T 1.26 0.25 0.00
38_L 17_T 1.22 0.23 0.00
248_L 112_L 1.17 0.21 0.00
52_S 18_T 1.16 0.20 0.00
246_R 122_R 1.16 0.20 0.00
43_I 28_F 1.13 0.19 0.00
217_L 83_F 1.13 0.19 0.00
239_L 31_K 1.11 0.18 0.00
266_A 17_T 1.09 0.17 0.00
250_L 17_T 1.07 0.17 0.00
302_P 17_T 1.07 0.17 0.00
248_L 86_T 1.07 0.17 0.00
117_L 31_K 1.06 0.17 0.00
193_M 116_K 1.05 0.16 0.00
71_T 40_V 1.04 0.16 0.00
145_L 136_N 1.03 0.15 0.00
305_L 90_T 1.03 0.15 0.00
33_V 128_S 1.02 0.15 0.00
206_L 36_L 1.01 0.15 0.00
236_A 66_G 1.01 0.15 0.00
227_F 136_N 1.01 0.15 0.00
248_L 115_N 1.00 0.14 0.00
48_A 101_L 1.00 0.14 0.00
142_A 17_T 1.00 0.14 0.00
247_E 96_N 1.00 0.14 0.00
17_T 17_T 0.99 0.14 0.00
243_P 17_T 0.99 0.14 0.00
188_L 28_F 0.97 0.14 0.00
294_K 52_I 0.97 0.13 0.00
170_L 119_I 0.96 0.13 0.00
222_L 127_K 0.96 0.13 0.00
215_Q 81_I 0.96 0.13 0.00
119_K 113_C 0.95 0.13 0.00
131_N 116_K 0.95 0.13 0.00
296_V 8_L 0.95 0.13 0.00
289_A 64_K 0.95 0.13 0.00
202_G 87_S 0.95 0.13 0.00
20_E 149_N 0.94 0.13 0.00
220_L 86_T 0.94 0.13 0.00
68_D 83_F 0.94 0.13 0.00
95_L 18_T 0.94 0.13 0.00
34_K 76_A 0.94 0.12 0.00
201_E 26_G 0.93 0.12 0.00
250_L 49_R 0.93 0.12 0.00
206_L 54_F 0.93 0.12 0.00
36_I 108_I 0.93 0.12 0.00
293_L 12_G 0.93 0.12 0.00
191_V 85_V 0.92 0.12 0.00
178_W 56_V 0.92 0.12 0.00
85_L 159_R 0.92 0.12 0.00
231_G 94_V 0.92 0.12 0.00
64_A 12_G 0.91 0.12 0.00
251_N 17_T 0.91 0.12 0.00
110_Q 126_A 0.91 0.12 0.00
61_L 102_V 0.91 0.12 0.00
291_R 45_F 0.91 0.12 0.00
171_E 152_K 0.91 0.12 0.00
33_V 115_N 0.91 0.12 0.00
289_A 6_L 0.91 0.12 0.00
269_K 145_K 0.90 0.12 0.00
136_Q 8_L 0.90 0.11 0.00
46_E 113_C 0.89 0.11 0.00
89_L 8_L 0.89 0.11 0.00
210_G 160_K 0.89 0.11 0.00
245_L 10_G 0.89 0.11 0.00
243_P 124_V 0.89 0.11 0.00
126_L 118_D 0.89 0.11 0.00
160_L 143_S 0.88 0.11 0.00
165_C 101_L 0.88 0.11 0.00
95_L 23_H 0.88 0.11 0.00
274_G 105_C 0.88 0.11 0.00
176_K 17_T 0.88 0.11 0.00
110_Q 8_L 0.88 0.11 0.00
199_R 12_G 0.88 0.11 0.00
58_K 91_Y 0.88 0.11 0.00
160_L 124_V 0.88 0.11 0.00
141_I 161_L 0.88 0.11 0.00
263_V 72_Y 0.88 0.11 0.00
288_D 94_V 0.88 0.11 0.00
98_V 47_T 0.87 0.11 0.00
95_L 15_G 0.87 0.11 0.00
95_L 16_K 0.87 0.11 0.00
126_L 83_F 0.87 0.11 0.00
220_L 118_D 0.87 0.11 0.00
165_C 113_C 0.86 0.10 0.00
211_L 144_A 0.86 0.10 0.00
43_I 90_T 0.86 0.10 0.00
177_E 9_V 0.86 0.10 0.00
217_L 17_T 0.86 0.10 0.00
112_P 63_E 0.86 0.10 0.00
103_N 101_L 0.86 0.10 0.00
321_V 90_T 0.86 0.10 0.00
248_L 18_T 0.85 0.10 0.00
245_L 14_T 0.85 0.10 0.00
61_L 58_D 0.85 0.10 0.00
312_N 149_N 0.85 0.10 0.00
285_I 114_G 0.84 0.10 0.00
256_S 115_N 0.84 0.10 0.00
181_T 81_I 0.84 0.10 0.00
44_G 69_R 0.84 0.10 0.00
127_Y 7_V 0.84 0.10 0.00
27_L 150_F 0.84 0.10 0.00
328_F 91_Y 0.84 0.10 0.00
92_C 17_T 0.83 0.10 0.00
214_C 36_L 0.83 0.10 0.00
102_D 113_C 0.83 0.10 0.00
123_L 15_G 0.83 0.10 0.00
123_L 16_K 0.83 0.10 0.00
191_V 39_E 0.83 0.10 0.00
220_L 58_D 0.83 0.10 0.00
56_A 17_T 0.83 0.10 0.00
202_G 77_Q 0.82 0.10 0.00
55_I 90_T 0.82 0.10 0.00
91_K 85_V 0.82 0.10 0.00
187_L 136_N 0.82 0.10 0.00
41_N 48_N 0.82 0.10 0.00
82_L 85_V 0.82 0.10 0.00
214_C 40_V 0.82 0.09 0.00
263_V 83_F 0.82 0.09 0.00
110_Q 89_V 0.81 0.09 0.00
328_F 150_F 0.81 0.09 0.00
264_V 111_V 0.81 0.09 0.00
235_L 9_V 0.80 0.09 0.00
289_A 13_G 0.80 0.09 0.00
49_R 125_K 0.80 0.09 0.00
263_V 133_R 0.80 0.09 0.00
193_M 144_A 0.80 0.09 0.00
221_D 30_K 0.80 0.09 0.00
160_L 64_K 0.80 0.09 0.00
126_L 15_G 0.80 0.09 0.00
126_L 16_K 0.80 0.09 0.00
117_L 137_L 0.80 0.09 0.00
87_Q 34_A 0.80 0.09 0.00
245_L 15_G 0.80 0.09 0.00
245_L 16_K 0.80 0.09 0.00
211_L 76_A 0.80 0.09 0.00
179_A 122_R 0.79 0.09 0.00
190_T 101_L 0.79 0.09 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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