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OPENSEQ.org
GerAA-SpoVAC
Genes: A B A+B
Length: 482 150 615
Sequences: 1718 557 275
Seq/Len: 3.56 3.71 0.45
MirrorTree (Pazo et al. 2001) 0.21
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 0.00
2 0.01 0.00 0.01
5 0.01 0.00 0.14
10 0.02 0.00 0.16
20 0.06 0.00 0.17
100 0.13 0.01 0.22
∞ 0.20 0.07 0.44
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
296_I 68_I 1.69 0.67 0.00
301_V 120_M 1.44 0.48 0.00
442_F 138_V 1.33 0.40 0.00
140_V 66_I 1.19 0.31 0.00
111_Y 68_I 1.19 0.30 0.00
376_S 75_F 1.16 0.29 0.00
196_K 36_C 1.13 0.27 0.00
431_L 89_S 1.09 0.25 0.00
165_M 134_A 1.07 0.24 0.00
413_A 67_L 1.06 0.23 0.00
11_H 75_F 1.05 0.23 0.00
179_I 37_A 1.02 0.21 0.00
341_L 138_V 1.00 0.20 0.00
252_V 130_F 1.00 0.20 0.00
179_I 89_S 1.00 0.20 0.00
357_G 82_G 0.99 0.20 0.00
429_T 30_L 0.99 0.20 0.00
203_I 113_V 0.96 0.18 0.00
195_L 72_L 0.95 0.18 0.00
398_G 57_A 0.95 0.18 0.00
284_F 75_F 0.95 0.18 0.00
282_L 58_G 0.95 0.18 0.00
328_I 42_L 0.94 0.17 0.00
224_I 129_V 0.94 0.17 0.00
448_F 109_S 0.93 0.17 0.00
249_S 112_L 0.92 0.17 0.00
265_S 82_G 0.92 0.17 0.00
89_K 65_L 0.92 0.17 0.00
358_L 141_I 0.92 0.17 0.00
364_I 103_A 0.92 0.16 0.00
45_F 30_L 0.92 0.16 0.00
391_T 57_A 0.91 0.16 0.00
242_V 137_I 0.91 0.16 0.00
339_E 117_A 0.90 0.16 0.00
59_K 46_Y 0.90 0.16 0.00
112_I 100_M 0.89 0.15 0.00
90_K 134_A 0.89 0.15 0.00
62_I 77_I 0.87 0.15 0.00
245_L 140_M 0.87 0.15 0.00
238_F 117_A 0.86 0.14 0.00
193_A 14_T 0.86 0.14 0.00
237_L 24_N 0.86 0.14 0.00
160_I 38_I 0.85 0.14 0.00
325_F 120_M 0.85 0.14 0.00
384_V 77_I 0.85 0.14 0.00
410_F 99_S 0.85 0.14 0.00
227_T 71_L 0.85 0.14 0.00
114_T 89_S 0.85 0.14 0.00
367_A 84_F 0.85 0.14 0.00
362_V 70_A 0.85 0.14 0.00
79_Q 66_I 0.84 0.14 0.00
308_L 118_T 0.84 0.14 0.00
108_D 66_I 0.84 0.13 0.00
189_K 100_M 0.84 0.13 0.00
145_T 128_I 0.84 0.13 0.00
363_V 61_T 0.84 0.13 0.00
271_E 105_L 0.83 0.13 0.00
199_Q 102_S 0.83 0.13 0.00
303_F 141_I 0.82 0.13 0.00
12_D 120_M 0.82 0.13 0.00
313_A 117_A 0.82 0.13 0.00
364_I 132_V 0.82 0.13 0.00
407_I 75_F 0.82 0.13 0.00
15_A 65_L 0.82 0.13 0.00
435_T 108_K 0.82 0.13 0.00
434_Q 42_L 0.82 0.13 0.00
277_S 128_I 0.82 0.13 0.00
92_I 89_S 0.81 0.13 0.00
439_S 81_I 0.81 0.13 0.00
322_N 85_A 0.81 0.13 0.00
95_I 68_I 0.81 0.12 0.00
360_G 39_G 0.81 0.12 0.00
258_S 82_G 0.81 0.12 0.00
27_L 30_L 0.80 0.12 0.00
410_F 67_L 0.80 0.12 0.00
82_A 141_I 0.80 0.12 0.00
175_A 66_I 0.80 0.12 0.00
242_V 37_A 0.79 0.12 0.00
351_P 66_I 0.79 0.12 0.00
361_G 27_K 0.79 0.12 0.00
431_L 138_V 0.78 0.12 0.00
199_Q 137_I 0.78 0.12 0.00
415_L 129_V 0.77 0.11 0.00
140_V 13_K 0.77 0.11 0.00
234_S 66_I 0.77 0.11 0.00
29_K 75_F 0.77 0.11 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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