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OPENSEQ.org
2air_G_H
Genes: A B A+B
Length: 310 153 432
Sequences: 4513 690 540
Seq/Len: 14.56 4.51 1.25
MirrorTree (Pazo et al. 2001) 0.50
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 0.07 1.09
2 0.05 0.07 1.14
5 0.07 0.07 1.16
10 0.07 0.07 1.16
20 0.08 0.07 1.17
100 0.09 0.07 1.19
∞ 0.17 0.08 1.27
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
88_L 115_I 1.57 0.86 0.15
132_N 43_T 1.49 0.82 0.12
289_A 83_V 1.34 0.71 0.08
69_S 104_D 1.27 0.65 0.06
49_F 62_E 1.26 0.64 0.06
61_T 9_V 1.25 0.63 0.06
264_L 86_I 1.19 0.58 0.05
75_D 9_V 1.19 0.58 0.05
87_T 120_P 1.18 0.57 0.05
236_D 45_G 1.10 0.49 0.04
74_S 65_F 1.10 0.49 0.04
299_L 62_E 1.09 0.48 0.04
259_A 53_M 1.09 0.48 0.04
175_A 106_V 1.04 0.43 0.03
293_I 7_L 1.03 0.43 0.03
71_V 14_R 1.02 0.41 0.03
114_L 121_V 1.02 0.41 0.03
247_F 116_S 1.01 0.40 0.03
293_I 27_F 0.99 0.38 0.03
165_Y 86_I 0.99 0.38 0.03
154_N 85_R 0.99 0.38 0.03
242_N 61_I 0.98 0.38 0.03
250_R 12_I 0.98 0.38 0.02
68_A 144_E 0.98 0.37 0.02
305_N 107_L 0.97 0.37 0.02
19_D 142_E 0.96 0.36 0.02
178_K 116_S 0.96 0.36 0.02
237_P 117_H 0.96 0.35 0.02
43_V 120_P 0.95 0.34 0.02
274_A 85_R 0.94 0.34 0.02
49_F 91_V 0.93 0.33 0.02
302_L 18_I 0.93 0.33 0.02
227_M 11_A 0.92 0.32 0.02
289_A 9_V 0.91 0.32 0.02
297_Q 48_L 0.91 0.31 0.02
47_C 45_G 0.91 0.31 0.02
49_F 118_A 0.91 0.31 0.02
95_I 142_E 0.90 0.31 0.02
37_E 61_I 0.89 0.30 0.02
65_R 7_L 0.89 0.30 0.02
49_F 143_K 0.89 0.30 0.02
97_T 78_A 0.89 0.29 0.02
20_L 130_R 0.89 0.29 0.02
254_L 48_L 0.88 0.29 0.02
303_V 5_N 0.88 0.29 0.02
117_E 124_S 0.88 0.29 0.02
20_L 32_L 0.88 0.28 0.02
144_T 24_Q 0.88 0.28 0.02
275_T 18_I 0.88 0.28 0.02
263_V 124_S 0.87 0.28 0.02
87_T 16_T 0.87 0.28 0.02
263_V 55_R 0.87 0.28 0.02
75_D 26_G 0.87 0.28 0.02
125_L 93_G 0.86 0.28 0.02
39_L 91_V 0.86 0.27 0.01
24_L 11_A 0.86 0.27 0.01
154_N 88_N 0.85 0.27 0.01
232_K 134_I 0.85 0.27 0.01
116_T 88_N 0.85 0.26 0.01
263_V 42_I 0.85 0.26 0.01
186_F 48_L 0.85 0.26 0.01
23_V 83_V 0.84 0.26 0.01
133_Q 86_I 0.84 0.26 0.01
116_T 90_E 0.84 0.26 0.01
125_L 90_E 0.84 0.26 0.01
297_Q 43_T 0.84 0.26 0.01
124_V 31_S 0.84 0.25 0.01
136_T 82_T 0.83 0.25 0.01
92_I 80_Q 0.83 0.25 0.01
219_M 44_I 0.82 0.24 0.01
89_A 26_G 0.82 0.24 0.01
65_R 120_P 0.82 0.24 0.01
76_S 104_D 0.82 0.24 0.01
111_A 125_F 0.82 0.24 0.01
23_V 66_L 0.82 0.24 0.01
214_S 103_I 0.82 0.24 0.01
190_D 90_E 0.82 0.24 0.01
124_V 7_L 0.82 0.24 0.01
70_V 142_E 0.81 0.24 0.01
230_V 116_S 0.81 0.24 0.01
293_I 76_L 0.81 0.24 0.01
213_S 53_M 0.81 0.24 0.01
104_M 126_A 0.81 0.24 0.01
108_Q 117_H 0.81 0.24 0.01
238_S 143_K 0.81 0.23 0.01
282_H 89_Y 0.80 0.23 0.01
49_F 32_L 0.80 0.23 0.01
277_V 61_I 0.80 0.23 0.01
291_N 91_V 0.80 0.23 0.01
179_F 71_V 0.80 0.23 0.01
47_C 112_S 0.80 0.23 0.01
261_M 13_K 0.80 0.22 0.01
169_V 10_E 0.79 0.22 0.01
10_I 116_S 0.78 0.22 0.01
116_T 108_V 0.78 0.22 0.01
24_L 62_E 0.78 0.22 0.01
250_R 108_V 0.78 0.21 0.01
287_Q 88_N 0.78 0.21 0.01
235_L 29_L 0.78 0.21 0.01
93_S 118_A 0.78 0.21 0.01
127_A 54_G 0.78 0.21 0.01
186_F 45_G 0.77 0.21 0.01
191_A 116_S 0.77 0.21 0.01
111_A 121_V 0.77 0.21 0.01
304_L 42_I 0.77 0.21 0.01
264_L 112_S 0.77 0.20 0.01
294_F 29_L 0.76 0.20 0.01
87_T 119_E 0.76 0.20 0.01
303_V 116_S 0.76 0.20 0.01
293_I 10_E 0.76 0.20 0.01
294_F 74_L 0.76 0.20 0.01
185_Y 135_A 0.76 0.20 0.01
131_S 43_T 0.76 0.20 0.01
166_G 38_T 0.76 0.20 0.01
187_I 99_L 0.76 0.20 0.01
139_L 63_N 0.75 0.20 0.01
49_F 7_L 0.75 0.20 0.01
155_L 18_I 0.75 0.20 0.01
87_T 92_V 0.75 0.20 0.01
247_F 48_L 0.75 0.20 0.01
133_Q 45_G 0.75 0.20 0.01
16_S 146_S 0.75 0.20 0.01
221_E 52_E 0.75 0.19 0.01
187_I 58_L 0.75 0.19 0.01
236_D 48_L 0.74 0.19 0.01
18_D 93_G 0.74 0.19 0.01
147_E 103_I 0.74 0.19 0.01
154_N 13_K 0.74 0.19 0.01
264_L 22_P 0.74 0.19 0.01
241_A 117_H 0.74 0.19 0.01
56_R 28_K 0.74 0.19 0.01
179_F 22_P 0.74 0.19 0.01
108_Q 118_A 0.74 0.19 0.01
93_S 24_Q 0.74 0.19 0.01
61_T 106_V 0.74 0.19 0.01
145_I 55_R 0.73 0.18 0.01
40_K 14_R 0.73 0.18 0.01
122_V 105_N 0.73 0.18 0.01
232_K 102_R 0.73 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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