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OPENSEQ.org
3rrl_ab
Genes: A B A+B
Length: 230 207 425
Sequences: 2534 2567 1609
Seq/Len: 11.02 12.4 3.79
MirrorTree (Pazo et al. 2001) 0.94
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 0.01 0.01 3.57
2 0.01 0.01 3.62
5 0.01 0.01 3.64
10 0.01 0.01 3.68
20 0.02 0.02 3.68
100 0.04 0.04 3.68
∞ 0.12 0.13 3.69
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
169_K 78_F 1.90 1.00 0.97
112_A 86_A 1.88 1.00 0.97
170_T 46_L 1.76 0.99 0.96
177_L 80_N 1.61 0.98 0.93
177_L 82_A 1.36 0.94 0.83
170_T 72_V 1.26 0.91 0.77
168_R 61_D 1.19 0.88 0.70
209_Y 87_M 1.15 0.85 0.66
211_Q 92_H 1.13 0.83 0.65
140_E 161_K 1.13 0.83 0.64
127_I 122_M 1.12 0.82 0.63
208_I 18_Y 1.08 0.80 0.60
209_Y 83_D 1.08 0.79 0.59
180_M 83_D 1.06 0.78 0.57
170_T 49_I 1.01 0.72 0.51
208_I 93_I 0.96 0.67 0.45
126_L 113_M 0.91 0.61 0.39
155_K 61_D 0.91 0.60 0.38
169_K 62_L 0.89 0.58 0.36
162_L 39_V 0.85 0.53 0.32
214_Y 102_E 0.85 0.53 0.32
161_T 37_N 0.85 0.53 0.32
53_N 67_K 0.83 0.50 0.29
121_T 127_D 0.82 0.49 0.29
135_E 197_E 0.81 0.49 0.28
207_G 18_Y 0.81 0.48 0.28
121_T 130_H 0.79 0.45 0.25
207_G 77_S 0.78 0.43 0.24
116_A 201_A 0.78 0.43 0.24
21_I 118_L 0.77 0.43 0.23
215_K 102_E 0.76 0.42 0.23
78_V 122_M 0.75 0.40 0.21
133_S 155_S 0.72 0.37 0.19
85_E 33_V 0.72 0.37 0.19
198_L 181_M 0.72 0.36 0.18
79_G 122_M 0.71 0.36 0.18
135_E 15_E 0.71 0.36 0.18
208_I 87_M 0.71 0.35 0.18
80_E 120_K 0.71 0.35 0.18
90_N 193_D 0.71 0.35 0.18
162_L 37_N 0.70 0.34 0.17
136_F 130_H 0.70 0.34 0.17
133_S 144_K 0.70 0.34 0.17
207_G 109_L 0.69 0.33 0.16
216_G 200_E 0.69 0.33 0.16
155_K 1_M 0.68 0.32 0.16
213_I 171_L 0.68 0.31 0.15
45_K 174_F 0.68 0.31 0.15
15_L 174_F 0.67 0.30 0.14
169_K 59_D 0.66 0.29 0.14
60_G 149_K 0.65 0.28 0.14
90_N 197_E 0.65 0.28 0.13
134_R 181_M 0.65 0.28 0.13
190_E 61_D 0.65 0.28 0.13
183_K 28_L 0.65 0.28 0.13
55_G 59_D 0.64 0.27 0.13
97_L 132_A 0.64 0.27 0.13
193_V 144_K 0.63 0.27 0.12
126_L 60_A 0.63 0.27 0.12
119_T 127_D 0.63 0.27 0.12
183_K 153_E 0.63 0.26 0.12
76_S 98_L 0.63 0.26 0.12
120_P 92_H 0.62 0.26 0.12
143_L 197_E 0.62 0.26 0.12
77_Y 120_K 0.62 0.25 0.12
120_P 5_I 0.62 0.25 0.12
181_A 94_D 0.62 0.25 0.12
158_K 144_K 0.62 0.25 0.11
117_Y 77_S 0.61 0.25 0.11
42_K 206_R 0.61 0.24 0.11
18_G 51_A 0.61 0.24 0.11
169_K 72_V 0.61 0.24 0.11
46_D 197_E 0.61 0.24 0.11
114_I 76_A 0.61 0.24 0.11
147_I 141_H 0.61 0.24 0.11
83_I 6_I 0.61 0.24 0.11
104_A 84_S 0.60 0.24 0.10
46_D 150_V 0.60 0.23 0.10
121_T 131_G 0.60 0.23 0.10
102_T 141_H 0.60 0.23 0.10
138_G 92_H 0.59 0.23 0.10
79_G 116_K 0.59 0.23 0.10
77_Y 67_K 0.59 0.23 0.10
76_S 85_F 0.59 0.23 0.10
10_K 186_L 0.59 0.23 0.10
12_L 39_V 0.59 0.22 0.10
198_L 151_K 0.59 0.22 0.10
185_C 104_S 0.59 0.22 0.10
95_V 93_I 0.59 0.22 0.10
183_K 197_E 0.59 0.22 0.10
75_A 100_G 0.59 0.22 0.10
173_N 81_S 0.59 0.22 0.10
7_D 148_S 0.58 0.22 0.09
174_F 27_T 0.58 0.22 0.09
89_L 100_G 0.58 0.22 0.09
219_F 61_D 0.58 0.21 0.09
169_K 83_D 0.58 0.21 0.09
197_E 202_E 0.58 0.21 0.09
199_D 78_F 0.58 0.21 0.09
52_N 128_L 0.58 0.21 0.09
79_G 121_G 0.58 0.21 0.09
108_H 90_G 0.57 0.21 0.09
71_K 145_Y 0.57 0.21 0.09
175_N 115_P 0.57 0.21 0.09
176_P 109_L 0.57 0.21 0.09
7_D 197_E 0.57 0.21 0.09
101_G 85_F 0.57 0.21 0.09
97_L 70_I 0.57 0.21 0.09
109_A 151_K 0.57 0.21 0.09
10_K 153_E 0.57 0.21 0.09
19_D 93_I 0.57 0.21 0.09
9_D 200_E 0.57 0.20 0.09
8_L 33_V 0.57 0.20 0.09
104_A 83_D 0.57 0.20 0.09
23_V 136_I 0.57 0.20 0.09
170_T 76_A 0.57 0.20 0.09
147_I 155_S 0.56 0.20 0.08
59_F 145_Y 0.56 0.20 0.08
46_D 155_S 0.56 0.20 0.08
13_S 200_E 0.56 0.20 0.08
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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