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OPENSEQ.org
FliMCheY
Genes: A B A+B
Length: 334 129 442
Sequences: 1471 1614 331
Seq/Len: 4.4 12.51 0.75
MirrorTree (Pazo et al. 2001) 0.67
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 0.26 0.01 0.12
2 0.26 0.02 0.14
5 0.27 0.05 0.17
10 0.27 0.09 0.26
20 0.27 0.10 0.52
100 0.31 0.12 0.71
∞ 0.32 0.19 1.16
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
165_Y 114_A 1.25 0.48 0.00
275_I 96_I 1.23 0.47 0.00
105_I 55_I 1.21 0.45 0.00
127_V 73_R 1.19 0.43 0.00
270_L 97_A 1.19 0.43 0.00
322_N 42_A 1.17 0.41 0.00
18_D 81_L 1.16 0.41 0.00
284_L 67_E 1.15 0.40 0.00
127_V 116_L 1.12 0.38 0.00
69_L 7_K 1.12 0.37 0.00
165_Y 54_V 1.12 0.37 0.00
78_D 107_V 1.11 0.36 0.00
254_V 51_Y 1.11 0.36 0.00
191_I 116_L 1.11 0.36 0.00
57_I 74_A 1.09 0.35 0.00
312_Q 22_R 1.07 0.34 0.00
297_D 97_A 1.07 0.33 0.00
153_V 68_L 1.07 0.33 0.00
294_A 22_R 1.07 0.33 0.00
279_N 107_V 1.06 0.33 0.00
316_R 27_E 1.06 0.32 0.00
40_P 7_K 1.06 0.32 0.00
172_I 15_S 1.05 0.32 0.00
11_I 41_D 1.01 0.29 0.00
123_V 120_L 1.01 0.28 0.00
252_R 10_V 1.00 0.28 0.00
271_R 6_L 0.98 0.27 0.00
130_L 64_D 0.98 0.27 0.00
104_L 54_V 0.98 0.27 0.00
69_L 10_V 0.97 0.26 0.00
314_A 42_A 0.96 0.26 0.00
210_N 8_F 0.95 0.25 0.00
118_F 67_E 0.95 0.25 0.00
267_D 44_N 0.94 0.24 0.00
321_I 50_G 0.94 0.24 0.00
314_A 53_F 0.94 0.24 0.00
60_R 90_A 0.94 0.24 0.00
19_S 41_D 0.93 0.24 0.00
218_C 54_V 0.93 0.24 0.00
310_N 84_L 0.93 0.23 0.00
235_P 56_S 0.92 0.23 0.00
272_L 21_V 0.92 0.23 0.00
79_I 71_T 0.92 0.23 0.00
170_K 70_K 0.91 0.23 0.00
202_T 9_L 0.91 0.23 0.00
304_S 97_A 0.91 0.23 0.00
76_S 114_A 0.91 0.22 0.00
256_H 30_F 0.91 0.22 0.00
133_G 29_G 0.91 0.22 0.00
165_Y 51_Y 0.90 0.22 0.00
185_Q 63_M 0.90 0.22 0.00
141_V 66_L 0.90 0.22 0.00
215_F 33_V 0.90 0.21 0.00
275_I 114_A 0.89 0.21 0.00
296_V 120_L 0.89 0.21 0.00
95_N 103_A 0.89 0.21 0.00
292_I 120_L 0.89 0.21 0.00
65_F 95_I 0.89 0.21 0.00
276_L 71_T 0.89 0.21 0.00
157_M 54_V 0.89 0.21 0.00
21_V 83_V 0.89 0.21 0.00
171_A 113_A 0.88 0.21 0.00
278_L 83_V 0.88 0.20 0.00
188_F 101_A 0.87 0.20 0.00
268_I 114_A 0.87 0.20 0.00
93_A 7_K 0.87 0.20 0.00
58_N 84_L 0.86 0.20 0.00
155_N 72_I 0.86 0.19 0.00
322_N 70_K 0.86 0.19 0.00
18_D 67_E 0.86 0.19 0.00
272_L 96_I 0.85 0.19 0.00
130_L 103_A 0.85 0.19 0.00
206_V 55_I 0.85 0.19 0.00
281_G 39_G 0.85 0.19 0.00
315_L 81_L 0.85 0.19 0.00
192_T 22_R 0.84 0.18 0.00
230_L 41_D 0.84 0.18 0.00
310_N 8_F 0.84 0.18 0.00
316_R 19_R 0.84 0.18 0.00
222_S 72_I 0.84 0.18 0.00
101_N 108_V 0.84 0.18 0.00
318_E 97_A 0.83 0.18 0.00
254_V 121_N 0.83 0.18 0.00
260_E 107_V 0.83 0.18 0.00
157_M 33_V 0.83 0.18 0.00
220_P 102_G 0.83 0.18 0.00
278_L 31_N 0.83 0.18 0.00
153_V 51_Y 0.83 0.18 0.00
304_S 15_S 0.83 0.18 0.00
168_A 37_E 0.83 0.18 0.00
311_G 15_S 0.83 0.18 0.00
234_P 15_S 0.83 0.18 0.00
62_A 24_L 0.83 0.18 0.00
283_V 10_V 0.83 0.18 0.00
147_T 43_L 0.82 0.18 0.00
267_D 45_K 0.82 0.18 0.00
236_L 38_D 0.82 0.18 0.00
13_A 8_F 0.82 0.17 0.00
9_A 15_S 0.82 0.17 0.00
320_L 10_V 0.82 0.17 0.00
301_V 38_D 0.82 0.17 0.00
96_L 8_F 0.82 0.17 0.00
250_L 38_D 0.81 0.17 0.00
118_F 121_N 0.81 0.17 0.00
115_L 38_D 0.81 0.17 0.00
273_S 55_I 0.81 0.17 0.00
175_L 42_A 0.81 0.17 0.00
135_G 101_A 0.81 0.17 0.00
122_L 56_S 0.80 0.17 0.00
259_L 52_G 0.80 0.16 0.00
206_V 107_V 0.80 0.16 0.00
272_L 73_R 0.80 0.16 0.00
273_S 121_N 0.80 0.16 0.00
273_S 71_T 0.80 0.16 0.00
73_L 52_G 0.79 0.16 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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