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OPENSEQ.org
NCRTp66c184
Genes: A B A+B
Length: 54 558 612
Sequences: 586 441 94
Seq/Len: 10.85 0.79 0.15
MirrorTree (Pazo et al. 2001) 0.80
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
46_M 116_F 1.51 0.27 0.00
25_A 62_A 1.48 0.26 0.00
46_M 146_Y 1.44 0.24 0.00
20_K 530_V 1.42 0.23 0.00
16_F 502_L 1.38 0.21 0.00
16_F 359_A 1.36 0.21 0.00
48_E 82_K 1.23 0.17 0.00
24_L 501_A 1.23 0.16 0.00
25_A 195_I 1.22 0.16 0.00
29_R 390_L 1.22 0.16 0.00
53_Q 547_V 1.21 0.16 0.00
42_E 483_L 1.20 0.16 0.00
35_G 171_F 1.15 0.14 0.00
26_K 36_E 1.13 0.14 0.00
41_K 21_V 1.12 0.13 0.00
11_R 501_A 1.12 0.13 0.00
37_W 282_L 1.11 0.13 0.00
37_W 146_Y 1.11 0.13 0.00
33_K 370_A 1.08 0.12 0.00
20_K 329_V 1.07 0.12 0.00
25_A 178_I 1.05 0.12 0.00
37_W 116_F 1.04 0.11 0.00
8_N 475_K 1.04 0.11 0.00
48_E 167_I 1.03 0.11 0.00
11_R 312_E 1.02 0.11 0.00
30_A 390_L 1.01 0.11 0.00
26_K 533_A 1.01 0.11 0.00
50_T 530_V 1.00 0.11 0.00
37_W 329_V 1.00 0.11 0.00
25_A 233_E 1.00 0.11 0.00
42_E 70_K 0.99 0.10 0.00
26_K 87_F 0.99 0.10 0.00
37_W 379_I 0.98 0.10 0.00
35_G 146_Y 0.98 0.10 0.00
20_K 79_E 0.97 0.10 0.00
16_F 28_E 0.96 0.10 0.00
7_R 203_E 0.96 0.10 0.00
10_K 359_A 0.95 0.10 0.00
27_N 291_E 0.94 0.09 0.00
38_K 297_A 0.94 0.09 0.00
35_G 116_F 0.93 0.09 0.00
35_G 158_A 0.93 0.09 0.00
37_W 522_E 0.93 0.09 0.00
27_N 132_I 0.92 0.09 0.00
47_K 189_V 0.92 0.09 0.00
33_K 201_K 0.92 0.09 0.00
47_K 529_K 0.92 0.09 0.00
26_K 312_E 0.92 0.09 0.00
48_E 341_I 0.92 0.09 0.00
32_R 82_K 0.91 0.09 0.00
42_E 21_V 0.91 0.09 0.00
48_E 423_K 0.91 0.09 0.00
14_R 122_K 0.90 0.09 0.00
26_K 17_D 0.90 0.09 0.00
25_A 370_A 0.90 0.09 0.00
35_G 205_L 0.89 0.09 0.00
26_K 261_V 0.89 0.09 0.00
29_R 413_W 0.89 0.09 0.00
26_K 315_H 0.89 0.08 0.00
32_R 79_E 0.89 0.08 0.00
35_G 241_V 0.89 0.08 0.00
4_G 334_Q 0.88 0.08 0.00
46_M 73_K 0.88 0.08 0.00
11_R 359_A 0.88 0.08 0.00
13_I 215_S 0.87 0.08 0.00
48_E 398_E 0.87 0.08 0.00
29_R 171_F 0.87 0.08 0.00
47_K 385_I 0.87 0.08 0.00
50_T 139_T 0.86 0.08 0.00
8_N 387_K 0.86 0.08 0.00
47_K 291_E 0.86 0.08 0.00
9_Q 470_D 0.86 0.08 0.00
33_K 173_K 0.86 0.08 0.00
11_R 408_T 0.85 0.08 0.00
47_K 326_I 0.85 0.08 0.00
16_F 545_K 0.85 0.08 0.00
47_K 463_Q 0.85 0.08 0.00
47_K 7_T 0.85 0.08 0.00
4_G 475_K 0.85 0.08 0.00
32_R 36_E 0.85 0.08 0.00
34_K 101_K 0.85 0.08 0.00
4_G 549_K 0.85 0.08 0.00
30_A 79_E 0.84 0.08 0.00
20_K 338_T 0.84 0.08 0.00
21_E 90_V 0.84 0.08 0.00
7_R 292_V 0.83 0.07 0.00
45_Q 189_V 0.83 0.07 0.00
27_N 60_I 0.83 0.07 0.00
46_M 444_A 0.83 0.07 0.00
12_T 296_T 0.83 0.07 0.00
12_T 516_L 0.83 0.07 0.00
32_R 194_E 0.83 0.07 0.00
12_T 359_A 0.83 0.07 0.00
20_K 340_Q 0.83 0.07 0.00
7_R 200_T 0.82 0.07 0.00
48_E 320_D 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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