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OPENSEQ.org
AfQ2 AfO2VWA
Genes: A B A+B
Length: 272 199 457
Sequences: 6143 728 618
Seq/Len: 22.58 3.66 1.35
MirrorTree (Pazo et al. 2001) 0.88
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 0.00 1.13
2 0.01 0.00 1.20
5 0.01 0.00 1.29
10 0.01 0.00 1.30
20 0.03 0.01 1.31
100 0.05 0.01 1.32
∞ 0.16 0.05 1.36
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
160_S 31_T 1.68 0.92 0.46
176_F 102_M 1.63 0.90 0.41
141_L 122_L 1.39 0.77 0.24
145_H 138_L 1.34 0.73 0.21
184_E 115_D 1.33 0.72 0.20
100_A 39_A 1.31 0.71 0.19
146_P 102_M 1.28 0.69 0.18
184_E 175_R 1.28 0.69 0.18
98_T 159_I 1.23 0.64 0.15
269_M 36_S 1.22 0.63 0.14
40_V 123_T 1.22 0.63 0.14
244_A 7_A 1.20 0.61 0.13
209_A 12_L 1.19 0.60 0.13
143_R 154_I 1.18 0.59 0.13
225_T 96_T 1.17 0.58 0.12
119_T 158_C 1.14 0.55 0.11
165_L 190_L 1.13 0.54 0.11
206_T 147_N 1.12 0.53 0.10
183_A 44_A 1.12 0.53 0.10
267_I 137_L 1.10 0.51 0.10
249_L 74_G 1.09 0.50 0.09
66_V 82_V 1.09 0.50 0.09
53_F 159_I 1.09 0.50 0.09
68_V 86_R 1.08 0.49 0.09
196_V 12_L 1.08 0.49 0.09
143_R 117_K 1.08 0.49 0.09
62_G 154_I 1.08 0.49 0.09
126_L 39_A 1.07 0.48 0.09
97_L 56_I 1.06 0.47 0.08
69_A 14_L 1.04 0.46 0.08
10_N 159_I 1.03 0.45 0.07
183_A 28_D 1.03 0.44 0.07
262_T 45_W 1.03 0.44 0.07
249_L 165_A 1.03 0.44 0.07
110_D 73_K 1.02 0.44 0.07
139_G 159_I 1.02 0.44 0.07
32_A 51_G 1.02 0.43 0.07
60_R 90_L 1.01 0.43 0.07
227_L 198_T 1.01 0.42 0.07
177_E 78_P 1.01 0.42 0.07
260_R 116_K 1.01 0.42 0.07
250_V 115_D 1.00 0.41 0.07
39_P 145_A 0.99 0.40 0.06
125_P 49_Q 0.98 0.40 0.06
160_S 198_T 0.98 0.40 0.06
268_D 93_G 0.98 0.39 0.06
11_Q 3_G 0.97 0.38 0.06
23_Q 2_A 0.96 0.37 0.06
83_W 9_T 0.96 0.37 0.06
139_G 156_T 0.96 0.37 0.06
161_L 98_M 0.96 0.37 0.06
23_Q 30_Q 0.96 0.37 0.06
167_Q 90_L 0.96 0.37 0.06
71_N 61_S 0.96 0.37 0.06
207_V 117_K 0.95 0.36 0.05
188_G 85_G 0.94 0.36 0.05
198_P 51_G 0.94 0.36 0.05
265_H 133_Q 0.94 0.36 0.05
89_G 146_V 0.94 0.36 0.05
51_S 79_W 0.94 0.36 0.05
184_E 3_G 0.94 0.36 0.05
243_A 119_M 0.94 0.35 0.05
180_Y 134_D 0.94 0.35 0.05
269_M 5_D 0.94 0.35 0.05
139_G 60_N 0.94 0.35 0.05
254_T 12_L 0.93 0.35 0.05
140_E 96_T 0.93 0.34 0.05
189_I 59_F 0.93 0.34 0.05
86_D 146_V 0.93 0.34 0.05
96_P 193_L 0.93 0.34 0.05
267_I 48_E 0.92 0.34 0.05
143_R 113_K 0.92 0.34 0.05
239_V 123_T 0.91 0.33 0.05
140_E 128_S 0.91 0.33 0.05
123_I 58_G 0.91 0.33 0.05
19_F 20_E 0.91 0.33 0.05
82_R 64_R 0.91 0.33 0.05
128_D 172_I 0.91 0.33 0.05
135_L 138_L 0.91 0.33 0.05
106_I 56_I 0.91 0.32 0.04
19_F 185_R 0.90 0.32 0.04
239_V 160_S 0.90 0.32 0.04
239_V 12_L 0.90 0.32 0.04
253_I 194_F 0.89 0.31 0.04
68_V 189_K 0.89 0.31 0.04
191_V 119_M 0.89 0.31 0.04
75_T 8_V 0.89 0.31 0.04
143_R 53_P 0.89 0.31 0.04
199_S 110_A 0.89 0.31 0.04
122_V 67_V 0.89 0.31 0.04
218_G 56_I 0.89 0.31 0.04
12_Y 167_A 0.89 0.31 0.04
108_Y 145_A 0.89 0.31 0.04
71_N 58_G 0.89 0.31 0.04
129_H 194_F 0.88 0.31 0.04
250_V 72_I 0.88 0.30 0.04
189_I 101_A 0.88 0.30 0.04
42_V 76_S 0.88 0.30 0.04
93_Q 50_L 0.88 0.30 0.04
109_L 129_D 0.88 0.30 0.04
211_A 138_L 0.88 0.30 0.04
190_L 76_S 0.88 0.30 0.04
205_V 89_A 0.87 0.30 0.04
72_E 106_G 0.87 0.30 0.04
228_L 118_L 0.87 0.29 0.04
55_E 119_M 0.87 0.29 0.04
92_W 73_K 0.87 0.29 0.04
77_A 123_T 0.86 0.29 0.04
262_T 59_F 0.86 0.29 0.04
10_N 28_D 0.86 0.29 0.04
181_P 9_T 0.86 0.29 0.04
120_T 76_S 0.86 0.29 0.04
60_R 56_I 0.86 0.29 0.04
267_I 122_L 0.86 0.29 0.04
16_K 167_A 0.86 0.28 0.04
230_Y 43_L 0.86 0.28 0.04
83_W 43_L 0.86 0.28 0.04
189_I 179_V 0.85 0.28 0.04
188_G 76_S 0.85 0.28 0.04
113_V 100_A 0.85 0.28 0.04
183_A 140_E 0.85 0.28 0.04
45_P 153_G 0.85 0.27 0.04
240_A 164_H 0.84 0.27 0.04
243_A 180_I 0.84 0.27 0.04
201_A 49_Q 0.84 0.27 0.04
130_R 97_R 0.84 0.27 0.04
229_V 98_M 0.84 0.27 0.04
270_T 184_A 0.84 0.27 0.04
232_A 92_A 0.84 0.27 0.04
256_D 131_D 0.84 0.27 0.04
40_V 74_G 0.84 0.27 0.03
22_P 154_I 0.84 0.27 0.03
184_E 110_A 0.83 0.27 0.03
78_D 86_R 0.83 0.27 0.03
263_L 144_Q 0.83 0.27 0.03
36_K 161_L 0.83 0.26 0.03
68_V 40_V 0.83 0.26 0.03
135_L 159_I 0.83 0.26 0.03
125_P 80_G 0.83 0.26 0.03
182_N 48_E 0.83 0.26 0.03
266_A 16_E 0.83 0.26 0.03
216_G 183_I 0.83 0.26 0.03
38_L 195_I 0.83 0.26 0.03
42_V 153_G 0.83 0.26 0.03
15_G 23_K 0.83 0.26 0.03
192_Q 175_R 0.83 0.26 0.03
124_H 103_R 0.82 0.26 0.03
123_I 84_K 0.82 0.26 0.03
25_D 76_S 0.82 0.26 0.03
48_C 12_L 0.82 0.26 0.03
251_Q 31_T 0.82 0.26 0.03
16_K 102_M 0.82 0.25 0.03
243_A 76_S 0.82 0.25 0.03
232_A 89_A 0.82 0.25 0.03
210_T 2_A 0.82 0.25 0.03
227_L 142_A 0.82 0.25 0.03
259_I 150_D 0.82 0.25 0.03
237_D 7_A 0.82 0.25 0.03
90_T 73_K 0.82 0.25 0.03
190_L 125_G 0.81 0.25 0.03
250_V 120_L 0.81 0.25 0.03
182_N 78_P 0.81 0.25 0.03
259_I 170_A 0.81 0.25 0.03
263_L 82_V 0.81 0.25 0.03
179_D 9_T 0.81 0.25 0.03
59_W 60_N 0.81 0.25 0.03
232_A 192_E 0.81 0.25 0.03
191_V 147_N 0.81 0.24 0.03
62_G 108_Y 0.81 0.24 0.03
174_T 185_R 0.81 0.24 0.03
187_A 184_A 0.80 0.24 0.03
139_G 96_T 0.80 0.24 0.03
260_R 51_G 0.80 0.24 0.03
179_D 40_V 0.80 0.24 0.03
145_H 155_F 0.80 0.24 0.03
45_P 149_L 0.80 0.24 0.03
84_L 40_V 0.80 0.24 0.03
60_R 7_A 0.80 0.24 0.03
111_E 17_S 0.80 0.24 0.03
13_L 28_D 0.80 0.24 0.03
152_I 143_R 0.80 0.23 0.03
162_M 16_E 0.79 0.23 0.03
117_Q 198_T 0.79 0.23 0.03
41_M 122_L 0.79 0.23 0.03
118_D 129_D 0.79 0.23 0.03
25_D 72_I 0.79 0.23 0.03
85_L 44_A 0.79 0.23 0.03
244_A 121_V 0.79 0.23 0.03
51_S 42_L 0.79 0.23 0.03
13_L 199_R 0.79 0.23 0.03
16_K 115_D 0.79 0.23 0.03
142_I 102_M 0.79 0.23 0.03
128_D 97_R 0.79 0.23 0.03
189_I 169_V 0.79 0.23 0.03
201_A 78_P 0.79 0.23 0.03
142_I 130_V 0.79 0.23 0.03
53_F 69_Y 0.79 0.23 0.03
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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