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OPENSEQ.org
NC2RTp66s184
Genes: A B A+B
Length: 55 559 613
Sequences: 584 416 93
Seq/Len: 10.62 0.74 0.15
MirrorTree (Pazo et al. 2001) 0.78
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 0.02 0.01 0.15
2 0.02 0.01 0.15
5 0.02 0.01 0.15
10 0.02 0.01 0.15
20 0.02 0.01 0.15
100 0.02 0.01 0.15
∞ 0.02 0.01 0.15
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
25_A 62_A 1.49 0.26 0.00
46_L 116_F 1.46 0.25 0.00
16_F 503_L 1.45 0.24 0.00
16_F 360_A 1.45 0.24 0.00
46_L 146_Y 1.37 0.21 0.00
25_A 195_I 1.29 0.18 0.00
20_K 79_E 1.25 0.17 0.00
20_K 531_V 1.23 0.16 0.00
11_K 502_A 1.22 0.16 0.00
53_Q 548_V 1.20 0.15 0.00
25_A 178_I 1.19 0.15 0.00
29_K 391_L 1.18 0.15 0.00
48_D 82_K 1.16 0.14 0.00
42_E 484_L 1.16 0.14 0.00
11_K 312_E 1.15 0.14 0.00
20_K 329_I 1.15 0.14 0.00
35_G 171_F 1.14 0.14 0.00
37_W 146_Y 1.13 0.14 0.00
14_K 527_K 1.13 0.14 0.00
32_R 82_K 1.11 0.13 0.00
20_K 82_K 1.11 0.13 0.00
33_K 371_A 1.09 0.13 0.00
37_W 282_L 1.08 0.12 0.00
37_W 116_F 1.08 0.12 0.00
35_G 146_Y 1.05 0.12 0.00
20_K 132_I 1.05 0.12 0.00
32_R 79_E 1.04 0.12 0.00
27_N 132_I 1.04 0.12 0.00
42_E 70_K 1.03 0.11 0.00
35_G 116_F 1.03 0.11 0.00
8_N 476_K 1.03 0.11 0.00
24_I 502_A 1.00 0.11 0.00
6_F 417_V 0.99 0.10 0.00
26_R 315_H 0.97 0.10 0.00
50_T 49_K 0.97 0.10 0.00
37_W 380_I 0.97 0.10 0.00
25_A 233_E 0.97 0.10 0.00
7_R 203_E 0.96 0.10 0.00
50_T 531_V 0.95 0.10 0.00
11_K 250_D 0.95 0.10 0.00
37_W 329_I 0.95 0.10 0.00
33_K 201_K 0.94 0.09 0.00
14_K 167_I 0.94 0.09 0.00
10_R 360_A 0.94 0.09 0.00
42_E 21_V 0.93 0.09 0.00
16_F 550_K 0.92 0.09 0.00
35_G 158_A 0.92 0.09 0.00
48_D 167_I 0.92 0.09 0.00
48_D 341_I 0.92 0.09 0.00
38_K 297_E 0.91 0.09 0.00
37_W 523_E 0.90 0.09 0.00
47_K 291_E 0.90 0.09 0.00
14_K 122_E 0.90 0.09 0.00
16_F 546_E 0.90 0.09 0.00
30_A 531_V 0.90 0.09 0.00
48_D 399_D 0.90 0.09 0.00
48_D 424_K 0.90 0.09 0.00
25_A 371_A 0.88 0.08 0.00
8_N 388_K 0.88 0.08 0.00
47_K 350_K 0.88 0.08 0.00
20_K 338_T 0.87 0.08 0.00
45_Q 189_V 0.87 0.08 0.00
21_E 377_T 0.86 0.08 0.00
35_G 241_V 0.86 0.08 0.00
30_A 391_L 0.86 0.08 0.00
11_K 409_T 0.86 0.08 0.00
29_K 414_W 0.85 0.08 0.00
35_G 205_L 0.85 0.08 0.00
47_K 189_V 0.85 0.08 0.00
11_K 360_A 0.84 0.08 0.00
46_L 73_K 0.84 0.08 0.00
29_K 171_F 0.84 0.08 0.00
26_R 534_A 0.84 0.08 0.00
42_E 452_L 0.84 0.08 0.00
7_R 200_T 0.84 0.07 0.00
47_K 390_R 0.83 0.07 0.00
27_N 60_V 0.83 0.07 0.00
4_G 476_K 0.83 0.07 0.00
30_A 79_E 0.83 0.07 0.00
12_I 296_T 0.83 0.07 0.00
21_E 90_V 0.82 0.07 0.00
26_R 437_A 0.82 0.07 0.00
27_N 177_D 0.82 0.07 0.00
46_L 445_A 0.82 0.07 0.00
32_R 414_W 0.82 0.07 0.00
4_G 334_E 0.82 0.07 0.00
4_G 550_K 0.82 0.07 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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