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OPENSEQ.org
2oor
Genes: A B A+B
Length: 372 175 539
Sequences: 3494 802 962
Seq/Len: 9.39 4.58 1.78
MirrorTree (Pazo et al. 2001) 0.80
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 0.65
2 0.01 0.00 1.66
5 0.01 0.00 1.75
10 0.01 0.01 1.75
20 0.01 0.01 1.76
100 0.02 0.01 1.77
∞ 0.10 0.02 1.78
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
252_T 106_T 1.30 0.78 0.04
216_G 15_M 1.21 0.70 0.03
70_V 146_V 1.15 0.65 0.03
156_F 143_Y 1.11 0.61 0.02
176_L 29_M 1.08 0.57 0.02
164_M 83_E 1.07 0.56 0.02
164_M 138_S 1.04 0.53 0.02
356_T 149_E 1.00 0.49 0.02
214_L 63_M 0.99 0.48 0.02
241_Q 118_I 0.99 0.47 0.02
142_N 83_E 0.98 0.46 0.01
340_H 160_F 0.97 0.46 0.01
25_K 23_I 0.97 0.46 0.01
134_M 50_V 0.97 0.45 0.01
337_L 86_E 0.96 0.44 0.01
194_L 94_A 0.95 0.43 0.01
330_A 40_E 0.94 0.42 0.01
219_I 144_A 0.93 0.41 0.01
357_V 144_A 0.92 0.40 0.01
266_A 163_A 0.92 0.40 0.01
169_T 143_Y 0.91 0.39 0.01
320_R 84_L 0.90 0.39 0.01
243_E 99_V 0.90 0.38 0.01
240_K 92_Q 0.89 0.38 0.01
330_A 168_E 0.89 0.38 0.01
243_E 9_E 0.88 0.36 0.01
51_T 86_E 0.88 0.36 0.01
141_S 79_D 0.87 0.35 0.01
71_V 47_K 0.86 0.35 0.01
156_F 81_V 0.86 0.34 0.01
319_S 123_I 0.85 0.33 0.01
60_T 85_E 0.84 0.32 0.01
356_T 85_E 0.84 0.32 0.01
266_A 113_D 0.84 0.32 0.01
296_P 54_Y 0.84 0.32 0.01
65_L 10_D 0.83 0.31 0.01
265_P 138_S 0.82 0.31 0.01
235_E 173_A 0.82 0.31 0.01
334_L 100_I 0.81 0.30 0.01
328_L 143_Y 0.81 0.29 0.01
359_G 143_Y 0.81 0.29 0.01
279_K 154_N 0.81 0.29 0.01
265_P 40_E 0.81 0.29 0.01
170_V 89_S 0.80 0.29 0.01
74_V 94_A 0.80 0.28 0.01
200_A 173_A 0.80 0.28 0.01
193_R 63_M 0.79 0.28 0.01
351_K 76_V 0.79 0.28 0.01
253_D 144_A 0.79 0.28 0.01
113_T 42_A 0.77 0.26 0.01
335_N 54_Y 0.77 0.26 0.01
284_I 173_A 0.77 0.26 0.01
200_A 6_G 0.77 0.26 0.01
240_K 109_A 0.77 0.26 0.01
290_E 143_Y 0.77 0.26 0.01
338_T 15_M 0.76 0.26 0.01
4_A 85_E 0.76 0.26 0.01
363_T 86_E 0.76 0.26 0.01
250_V 144_A 0.76 0.25 0.01
142_N 143_Y 0.76 0.25 0.01
296_P 94_A 0.75 0.25 0.01
189_A 39_R 0.75 0.24 0.01
138_S 116_S 0.75 0.24 0.01
147_R 99_V 0.74 0.24 0.01
100_L 160_F 0.74 0.24 0.01
150_I 54_Y 0.74 0.24 0.01
291_A 10_D 0.74 0.24 0.01
30_G 29_M 0.74 0.24 0.01
147_R 170_I 0.74 0.23 0.01
30_G 54_Y 0.74 0.23 0.01
102_A 42_A 0.73 0.23 0.01
205_A 84_L 0.73 0.23 0.01
301_G 51_E 0.73 0.23 0.01
356_T 127_E 0.73 0.23 0.01
328_L 83_E 0.73 0.23 0.01
130_R 91_F 0.73 0.23 0.01
261_I 82_F 0.73 0.23 0.01
129_S 144_A 0.73 0.23 0.01
138_S 151_F 0.73 0.23 0.01
248_E 29_M 0.72 0.22 0.01
276_T 18_A 0.72 0.22 0.01
285_I 144_A 0.72 0.22 0.01
154_Y 97_A 0.72 0.22 0.01
151_D 127_E 0.71 0.22 0.01
36_E 174_M 0.71 0.22 0.01
112_L 141_S 0.71 0.22 0.01
72_W 169_Q 0.71 0.22 0.01
261_I 134_F 0.71 0.22 0.01
141_S 15_M 0.71 0.22 0.01
224_E 131_T 0.71 0.22 0.01
177_V 18_A 0.71 0.21 0.01
368_I 22_I 0.71 0.21 0.01
200_A 29_M 0.71 0.21 0.01
3_I 23_I 0.71 0.21 0.01
90_I 165_K 0.70 0.21 0.01
166_A 12_A 0.70 0.21 0.01
298_S 174_M 0.70 0.21 0.01
120_Y 146_V 0.70 0.21 0.01
215_G 126_V 0.70 0.21 0.01
143_L 48_E 0.70 0.21 0.01
210_Q 17_N 0.70 0.20 0.01
6_P 154_N 0.69 0.20 0.01
287_L 172_Q 0.69 0.20 0.01
224_E 143_Y 0.69 0.20 0.01
211_V 11_A 0.69 0.20 0.01
215_G 129_A 0.69 0.20 0.01
138_S 158_M 0.69 0.20 0.01
241_Q 164_K 0.69 0.20 0.01
98_C 47_K 0.69 0.20 0.01
362_V 9_E 0.68 0.20 0.01
140_Q 6_G 0.68 0.20 0.01
199_M 106_T 0.68 0.20 0.01
233_M 7_S 0.68 0.20 0.01
241_Q 131_T 0.68 0.19 0.01
139_S 56_I 0.68 0.19 0.01
266_A 119_Y 0.68 0.19 0.01
189_A 75_N 0.68 0.19 0.01
161_P 63_M 0.68 0.19 0.01
4_A 6_G 0.68 0.19 0.01
21_E 2_S 0.68 0.19 0.01
102_A 93_T 0.68 0.19 0.01
194_L 129_A 0.68 0.19 0.01
70_V 22_I 0.68 0.19 0.01
199_M 123_I 0.68 0.19 0.01
69_D 76_V 0.67 0.19 0.01
235_E 135_I 0.67 0.19 0.01
110_E 79_D 0.67 0.19 0.01
133_S 144_A 0.67 0.19 0.01
97_M 19_S 0.67 0.19 0.01
207_T 84_L 0.67 0.19 0.01
289_V 173_A 0.67 0.18 0.01
3_I 38_L 0.67 0.18 0.01
351_K 21_V 0.67 0.18 0.01
336_F 160_F 0.66 0.18 0.01
157_A 143_Y 0.66 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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