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OPENSEQ.org
Kenn
Genes: A B A+B
Length: 440 88 486
Sequences: 1666 152 122
Seq/Len: 3.79 1.73 0.25
MirrorTree (Pazo et al. 2001) 0.57
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 0.00 0.00 0.23
2 0.01 0.00 0.23
5 0.01 0.00 0.23
10 0.02 0.00 0.23
20 0.03 0.00 0.23
100 0.05 0.00 0.23
∞ 0.11 0.02 0.24
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
120_L 37_I 1.64 0.46 0.00
187_I 9_S 1.50 0.37 0.00
91_S 27_T 1.49 0.37 0.00
16_L 48_N 1.49 0.36 0.00
374_F 59_K 1.43 0.33 0.00
358_A 73_A 1.42 0.32 0.00
176_T 39_Q 1.35 0.29 0.00
340_L 42_I 1.35 0.28 0.00
10_N 17_M 1.32 0.27 0.00
328_T 13_L 1.31 0.27 0.00
110_V 68_M 1.30 0.26 0.00
87_F 7_I 1.30 0.26 0.00
218_P 45_F 1.28 0.25 0.00
126_E 58_F 1.27 0.24 0.00
218_P 17_M 1.25 0.24 0.00
364_T 14_A 1.23 0.23 0.00
41_L 17_M 1.22 0.22 0.00
75_I 23_Q 1.21 0.22 0.00
327_L 23_Q 1.20 0.22 0.00
218_P 26_W 1.20 0.21 0.00
145_N 60_I 1.19 0.21 0.00
26_F 35_I 1.18 0.21 0.00
86_P 69_T 1.18 0.20 0.00
101_V 41_T 1.17 0.20 0.00
180_I 18_K 1.16 0.20 0.00
36_R 29_S 1.16 0.20 0.00
126_E 40_A 1.16 0.20 0.00
122_E 77_S 1.15 0.19 0.00
279_M 58_F 1.14 0.19 0.00
53_T 18_K 1.14 0.19 0.00
269_S 54_L 1.14 0.19 0.00
262_P 61_L 1.13 0.18 0.00
301_F 27_T 1.13 0.18 0.00
202_N 39_Q 1.11 0.18 0.00
410_L 32_A 1.10 0.17 0.00
229_R 22_Q 1.10 0.17 0.00
93_I 11_T 1.08 0.17 0.00
295_F 30_E 1.08 0.17 0.00
25_T 53_T 1.08 0.17 0.00
58_F 32_A 1.07 0.16 0.00
428_R 50_D 1.06 0.16 0.00
151_V 56_T 1.05 0.16 0.00
233_V 57_F 1.05 0.16 0.00
292_R 58_F 1.04 0.15 0.00
305_I 57_F 1.04 0.15 0.00
26_F 53_T 1.03 0.15 0.00
169_I 27_T 1.03 0.15 0.00
300_V 64_L 1.02 0.15 0.00
305_I 77_S 1.02 0.15 0.00
395_F 18_K 1.02 0.14 0.00
269_S 9_S 1.01 0.14 0.00
71_V 26_W 1.01 0.14 0.00
103_L 49_P 1.00 0.14 0.00
59_N 8_Y 1.00 0.14 0.00
123_A 36_G 1.00 0.14 0.00
317_V 35_I 1.00 0.14 0.00
119_K 25_G 0.99 0.14 0.00
279_M 7_I 0.99 0.14 0.00
216_N 67_S 0.99 0.14 0.00
10_N 57_F 0.99 0.14 0.00
104_I 26_W 0.98 0.14 0.00
339_V 32_A 0.98 0.14 0.00
200_V 12_Q 0.98 0.13 0.00
364_T 63_S 0.98 0.13 0.00
207_L 66_L 0.98 0.13 0.00
306_G 48_N 0.97 0.13 0.00
209_L 31_L 0.97 0.13 0.00
218_P 27_T 0.97 0.13 0.00
325_Y 55_T 0.96 0.13 0.00
355_G 45_F 0.96 0.13 0.00
269_S 69_T 0.96 0.13 0.00
38_A 30_E 0.96 0.13 0.00
13_V 13_L 0.95 0.12 0.00
26_F 19_L 0.95 0.12 0.00
327_L 76_A 0.95 0.12 0.00
159_A 39_Q 0.94 0.12 0.00
376_A 60_I 0.94 0.12 0.00
305_I 36_G 0.94 0.12 0.00
101_V 8_Y 0.94 0.12 0.00
325_Y 62_Q 0.94 0.12 0.00
142_R 37_I 0.94 0.12 0.00
270_D 25_G 0.93 0.12 0.00
126_E 42_I 0.93 0.12 0.00
308_T 27_T 0.93 0.12 0.00
16_L 56_T 0.93 0.12 0.00
336_A 57_F 0.92 0.12 0.00
120_L 55_T 0.92 0.12 0.00
175_P 6_K 0.91 0.12 0.00
334_I 27_T 0.91 0.12 0.00
247_L 87_E 0.91 0.12 0.00
402_A 72_D 0.91 0.11 0.00
414_F 72_D 0.91 0.11 0.00
255_M 41_T 0.90 0.11 0.00
129_L 58_F 0.90 0.11 0.00
46_P 27_T 0.89 0.11 0.00
411_P 12_Q 0.89 0.11 0.00
259_F 14_A 0.89 0.11 0.00
406_V 32_A 0.89 0.11 0.00
223_I 42_I 0.89 0.11 0.00
49_R 19_L 0.89 0.11 0.00
171_K 31_L 0.89 0.11 0.00
362_K 27_T 0.89 0.11 0.00
356_L 8_Y 0.88 0.11 0.00
92_E 32_A 0.88 0.11 0.00
317_V 17_M 0.88 0.11 0.00
145_N 58_F 0.88 0.11 0.00
251_P 64_L 0.88 0.11 0.00
334_I 51_N 0.88 0.11 0.00
414_F 77_S 0.88 0.11 0.00
398_M 68_M 0.87 0.10 0.00
358_A 14_A 0.87 0.10 0.00
276_A 32_A 0.87 0.10 0.00
369_I 29_S 0.86 0.10 0.00
179_I 57_F 0.86 0.10 0.00
175_P 55_T 0.86 0.10 0.00
292_R 60_I 0.86 0.10 0.00
175_P 36_G 0.86 0.10 0.00
36_R 18_K 0.86 0.10 0.00
368_K 60_I 0.86 0.10 0.00
299_Q 35_I 0.86 0.10 0.00
287_E 19_L 0.85 0.10 0.00
132_Y 63_S 0.85 0.10 0.00
65_L 28_Q 0.85 0.10 0.00
293_Y 6_K 0.85 0.10 0.00
414_F 31_L 0.85 0.10 0.00
358_A 66_L 0.85 0.10 0.00
36_R 76_A 0.85 0.10 0.00
169_I 55_T 0.85 0.10 0.00
74_R 25_G 0.84 0.10 0.00
395_F 59_K 0.84 0.10 0.00
382_R 45_F 0.84 0.10 0.00
3_K 10_P 0.84 0.10 0.00
71_V 44_N 0.84 0.10 0.00
37_Y 25_G 0.83 0.10 0.00
263_S 14_A 0.83 0.10 0.00
107_D 25_G 0.83 0.10 0.00
199_S 12_Q 0.83 0.10 0.00
17_T 36_G 0.83 0.10 0.00
317_V 36_G 0.83 0.10 0.00
240_W 64_L 0.83 0.10 0.00
366_I 59_K 0.83 0.10 0.00
162_R 50_D 0.83 0.10 0.00
327_L 45_F 0.82 0.09 0.00
162_R 30_E 0.82 0.09 0.00
70_I 25_G 0.82 0.09 0.00
124_R 22_Q 0.82 0.09 0.00
78_R 26_W 0.81 0.09 0.00
70_I 10_P 0.81 0.09 0.00
388_M 9_S 0.81 0.09 0.00
107_D 36_G 0.81 0.09 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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