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OPENSEQ.org
atpbdad
Genes: A B A+B
Length: 287 113 398
Sequences: 19844 12276 115
Seq/Len: 69.14 108.64 0.29
MirrorTree (Pazo et al. 2001) 0.54
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.05 0.04 0.24
2 0.07 0.05 0.25
5 0.10 0.08 0.26
10 0.11 0.09 0.27
20 0.13 0.11 0.29
100 0.17 0.14 0.32
∞ 0.23 0.21 0.40
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
197_S 104_I 1.70 0.54 0.00
234_I 66_P 1.55 0.44 0.00
209_V 96_G 1.49 0.40 0.00
186_T 60_S 1.45 0.38 0.00
165_K 101_L 1.45 0.37 0.00
222_Q 99_T 1.36 0.32 0.00
70_A 45_P 1.34 0.31 0.00
68_A 25_V 1.29 0.28 0.00
209_V 60_S 1.27 0.27 0.00
265_I 3_I 1.25 0.26 0.00
192_S 37_I 1.21 0.24 0.00
229_F 10_Q 1.19 0.23 0.00
265_I 30_V 1.15 0.21 0.00
196_I 5_K 1.14 0.21 0.00
209_V 11_A 1.11 0.20 0.00
165_K 60_S 1.11 0.20 0.00
168_A 9_L 1.10 0.19 0.00
119_L 3_I 1.10 0.19 0.00
227_V 81_T 1.08 0.18 0.00
259_S 66_P 1.08 0.18 0.00
182_V 101_L 1.08 0.18 0.00
165_K 79_G 1.07 0.18 0.00
212_H 50_V 1.04 0.17 0.00
56_L 78_F 1.04 0.17 0.00
248_A 16_V 1.04 0.17 0.00
68_A 14_A 1.03 0.17 0.00
249_V 80_A 1.03 0.16 0.00
156_G 66_P 1.03 0.16 0.00
209_V 61_M 1.03 0.16 0.00
238_P 66_P 1.03 0.16 0.00
189_N 82_I 1.02 0.16 0.00
91_I 29_E 1.02 0.16 0.00
156_G 23_I 1.01 0.16 0.00
86_A 108_V 1.01 0.16 0.00
160_V 80_A 1.01 0.16 0.00
165_K 52_E 1.01 0.15 0.00
33_T 55_S 1.01 0.15 0.00
125_V 94_R 1.00 0.15 0.00
280_R 57_V 1.00 0.15 0.00
249_V 78_F 1.00 0.15 0.00
127_V 98_E 1.00 0.15 0.00
208_E 58_D 1.00 0.15 0.00
167_S 62_I 0.99 0.15 0.00
238_P 80_A 0.98 0.15 0.00
146_V 27_V 0.98 0.15 0.00
228_A 107_L 0.97 0.14 0.00
269_L 59_E 0.97 0.14 0.00
280_R 49_V 0.96 0.14 0.00
11_R 30_V 0.96 0.14 0.00
196_I 83_N 0.96 0.14 0.00
273_V 103_Q 0.96 0.14 0.00
69_I 30_V 0.96 0.14 0.00
120_M 54_E 0.96 0.14 0.00
196_I 109_E 0.95 0.14 0.00
259_S 79_G 0.95 0.14 0.00
110_D 8_G 0.95 0.14 0.00
207_A 34_D 0.94 0.13 0.00
273_V 43_K 0.94 0.13 0.00
245_L 8_G 0.94 0.13 0.00
259_S 60_S 0.94 0.13 0.00
165_K 92_A 0.94 0.13 0.00
282_T 40_P 0.93 0.13 0.00
209_V 2_A 0.92 0.13 0.00
218_V 21_K 0.92 0.13 0.00
21_K 106_K 0.92 0.13 0.00
256_A 58_D 0.92 0.13 0.00
105_E 62_I 0.91 0.13 0.00
165_K 4_K 0.91 0.12 0.00
230_V 100_L 0.91 0.12 0.00
164_L 66_P 0.91 0.12 0.00
249_V 2_A 0.91 0.12 0.00
197_S 79_G 0.91 0.12 0.00
209_V 86_G 0.91 0.12 0.00
79_A 54_E 0.91 0.12 0.00
228_A 109_E 0.90 0.12 0.00
269_L 10_Q 0.90 0.12 0.00
158_I 75_D 0.90 0.12 0.00
32_V 57_V 0.90 0.12 0.00
177_R 21_K 0.90 0.12 0.00
178_M 49_V 0.89 0.12 0.00
185_I 36_V 0.89 0.12 0.00
253_S 109_E 0.89 0.12 0.00
281_K 32_V 0.89 0.12 0.00
151_N 87_V 0.89 0.12 0.00
63_L 20_G 0.89 0.12 0.00
202_L 58_D 0.89 0.12 0.00
193_A 60_S 0.89 0.12 0.00
260_G 8_G 0.89 0.12 0.00
45_K 57_V 0.89 0.12 0.00
171_A 9_L 0.89 0.12 0.00
43_L 44_I 0.89 0.12 0.00
201_N 44_I 0.89 0.12 0.00
146_V 19_D 0.87 0.12 0.00
101_V 55_S 0.87 0.11 0.00
116_N 90_I 0.87 0.11 0.00
234_I 7_V 0.87 0.11 0.00
10_S 81_T 0.87 0.11 0.00
171_A 16_V 0.87 0.11 0.00
168_A 104_I 0.86 0.11 0.00
242_Q 101_L 0.86 0.11 0.00
78_I 46_V 0.86 0.11 0.00
103_A 31_A 0.86 0.11 0.00
277_Q 44_I 0.86 0.11 0.00
83_V 13_T 0.86 0.11 0.00
59_D 26_P 0.85 0.11 0.00
193_A 69_V 0.85 0.11 0.00
54_V 81_T 0.85 0.11 0.00
21_K 92_A 0.85 0.11 0.00
205_V 96_G 0.85 0.11 0.00
92_E 44_I 0.85 0.11 0.00
172_V 40_P 0.85 0.11 0.00
271_D 103_Q 0.85 0.11 0.00
267_D 58_D 0.85 0.11 0.00
99_V 103_Q 0.85 0.11 0.00
165_K 78_F 0.85 0.11 0.00
98_K 93_T 0.85 0.11 0.00
220_K 92_A 0.85 0.11 0.00
250_G 104_I 0.85 0.11 0.00
226_V 87_V 0.85 0.11 0.00
272_V 59_E 0.84 0.11 0.00
255_V 59_E 0.84 0.11 0.00
246_G 14_A 0.84 0.11 0.00
55_P 25_V 0.84 0.11 0.00
243_A 66_P 0.84 0.11 0.00
209_V 103_Q 0.84 0.11 0.00
165_K 12_K 0.84 0.11 0.00
259_S 11_A 0.84 0.11 0.00
190_W 26_P 0.84 0.11 0.00
284_S 35_I 0.84 0.10 0.00
173_Q 81_T 0.84 0.10 0.00
81_A 6_L 0.83 0.10 0.00
216_E 112_M 0.83 0.10 0.00
255_V 29_E 0.83 0.10 0.00
216_E 30_V 0.82 0.10 0.00
190_W 19_D 0.82 0.10 0.00
62_E 35_I 0.82 0.10 0.00
246_G 107_L 0.82 0.10 0.00
251_S 59_E 0.82 0.10 0.00
192_S 55_S 0.82 0.10 0.00
54_V 99_T 0.82 0.10 0.00
249_V 103_Q 0.82 0.10 0.00
165_K 44_I 0.82 0.10 0.00
208_E 7_V 0.81 0.10 0.00
153_R 51_V 0.81 0.10 0.00
156_G 31_A 0.81 0.10 0.00
156_G 32_V 0.81 0.10 0.00
111_G 16_V 0.81 0.10 0.00
240_L 44_I 0.81 0.10 0.00
187_G 47_D 0.81 0.10 0.00
187_G 64_G 0.81 0.10 0.00
187_G 65_E 0.81 0.10 0.00
188_D 47_D 0.81 0.10 0.00
188_D 64_G 0.81 0.10 0.00
188_D 65_E 0.81 0.10 0.00
214_K 47_D 0.81 0.10 0.00
214_K 64_G 0.81 0.10 0.00
214_K 65_E 0.81 0.10 0.00
231_G 47_D 0.81 0.10 0.00
231_G 64_G 0.81 0.10 0.00
231_G 65_E 0.81 0.10 0.00
267_D 57_V 0.81 0.10 0.00
203_D 3_I 0.81 0.10 0.00
125_V 19_D 0.81 0.10 0.00
120_M 32_V 0.81 0.10 0.00
111_G 32_V 0.81 0.10 0.00
53_L 90_I 0.81 0.10 0.00
258_E 82_I 0.81 0.10 0.00
202_L 104_I 0.80 0.10 0.00
249_V 12_K 0.80 0.10 0.00
92_E 99_T 0.80 0.10 0.00
196_I 50_V 0.80 0.10 0.00
266_R 81_T 0.80 0.10 0.00
30_E 66_P 0.80 0.10 0.00
87_L 36_V 0.80 0.10 0.00
234_I 67_V 0.80 0.10 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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