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OPENSEQ.org
Sneha
Genes: A B A+B
Length: 228 567 709
Sequences: 35762 3416 1845
Seq/Len: 156.85 6.02 2.6
MirrorTree (Pazo et al. 2001) 0.62
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 1.98
2 0.02 0.00 2.00
5 0.04 0.01 2.07
10 0.06 0.01 2.16
20 0.10 0.01 2.32
100 0.20 0.04 3.04
∞ 0.25 0.14 3.79
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
19_E 334_R 1.62 0.97 0.82
108_K 319_D 1.27 0.85 0.55
17_L 312_T 1.13 0.74 0.41
20_M 316_M 1.11 0.72 0.39
85_K 301_S 1.09 0.70 0.37
8_I 461_K 0.92 0.51 0.22
86_T 358_R 0.92 0.51 0.21
155_T 317_A 0.91 0.49 0.20
57_L 350_L 0.90 0.48 0.20
79_I 449_R 0.87 0.45 0.17
137_E 444_V 0.86 0.44 0.17
53_V 445_A 0.85 0.43 0.16
14_D 313_T 0.84 0.42 0.16
116_V 492_A 0.83 0.40 0.15
11_V 486_A 0.83 0.40 0.15
63_N 495_H 0.83 0.40 0.15
14_D 345_R 0.82 0.39 0.14
11_V 273_V 0.81 0.39 0.14
15_A 41_R 0.81 0.37 0.13
79_I 209_T 0.80 0.37 0.13
186_R 513_L 0.80 0.37 0.13
8_I 241_V 0.80 0.37 0.13
182_V 465_S 0.79 0.36 0.13
14_D 476_R 0.79 0.35 0.12
31_D 402_E 0.79 0.35 0.12
20_M 317_A 0.78 0.35 0.12
182_V 228_G 0.78 0.34 0.12
22_T 515_L 0.78 0.34 0.12
8_I 54_I 0.77 0.34 0.12
79_I 38_L 0.77 0.33 0.11
196_V 346_F 0.76 0.33 0.11
8_I 421_I 0.76 0.32 0.11
137_E 421_I 0.75 0.32 0.11
216_L 225_L 0.75 0.32 0.11
205_V 496_Q 0.75 0.31 0.10
86_T 486_A 0.75 0.31 0.10
21_L 130_V 0.74 0.31 0.10
17_L 309_T 0.74 0.31 0.10
8_I 448_V 0.74 0.30 0.10
111_E 240_P 0.74 0.30 0.10
20_M 338_L 0.74 0.30 0.10
170_R 353_L 0.73 0.30 0.10
10_V 196_Y 0.73 0.30 0.10
79_I 51_L 0.73 0.29 0.10
110_K 321_I 0.73 0.29 0.09
11_V 336_T 0.72 0.28 0.09
86_T 491_D 0.72 0.28 0.09
35_I 455_L 0.72 0.28 0.09
16_S 338_L 0.72 0.28 0.09
42_L 256_L 0.71 0.28 0.09
113_V 403_Q 0.71 0.28 0.09
62_M 242_R 0.71 0.27 0.09
201_L 515_L 0.71 0.27 0.09
155_T 215_M 0.71 0.27 0.09
160_D 311_L 0.70 0.27 0.08
57_L 154_L 0.70 0.27 0.08
15_A 197_L 0.70 0.27 0.08
10_V 498_R 0.70 0.26 0.08
198_V 364_A 0.70 0.26 0.08
31_D 405_I 0.70 0.26 0.08
11_V 514_T 0.69 0.26 0.08
224_K 346_F 0.69 0.26 0.08
205_V 461_K 0.69 0.26 0.08
50_P 426_D 0.69 0.26 0.08
162_L 463_V 0.69 0.26 0.08
45_V 218_G 0.69 0.26 0.08
116_V 225_L 0.69 0.25 0.08
174_T 143_T 0.68 0.25 0.08
151_Q 243_S 0.68 0.25 0.07
40_Q 436_R 0.68 0.25 0.07
14_D 77_A 0.68 0.24 0.07
96_E 413_V 0.68 0.24 0.07
11_V 98_R 0.68 0.24 0.07
54_L 451_Y 0.68 0.24 0.07
184_G 301_S 0.68 0.24 0.07
198_V 502_W 0.68 0.24 0.07
198_V 513_L 0.67 0.24 0.07
91_V 357_S 0.67 0.24 0.07
144_K 224_V 0.67 0.24 0.07
54_L 195_L 0.67 0.24 0.07
182_V 226_L 0.67 0.24 0.07
62_M 421_I 0.67 0.24 0.07
199_Q 39_Q 0.67 0.24 0.07
104_M 349_L 0.67 0.24 0.07
205_V 253_E 0.67 0.24 0.07
170_R 377_V 0.67 0.23 0.07
215_V 506_G 0.67 0.23 0.07
137_E 404_V 0.67 0.23 0.07
23_I 335_S 0.67 0.23 0.07
203_A 302_D 0.67 0.23 0.07
200_R 313_T 0.66 0.23 0.07
177_V 459_E 0.66 0.23 0.07
198_V 191_A 0.66 0.23 0.07
157_L 503_G 0.66 0.23 0.07
54_L 192_N 0.66 0.23 0.07
81_M 241_V 0.66 0.23 0.07
79_I 518_V 0.66 0.23 0.07
69_R 133_V 0.66 0.23 0.07
215_V 358_R 0.66 0.23 0.07
41_A 350_L 0.65 0.22 0.07
69_R 59_F 0.65 0.22 0.07
21_L 393_I 0.65 0.22 0.06
165_L 228_G 0.65 0.22 0.06
152_I 179_A 0.65 0.22 0.06
34_V 40_L 0.65 0.22 0.06
198_V 134_P 0.64 0.22 0.06
127_P 392_G 0.64 0.22 0.06
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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