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OPENSEQ.org
NCRTp66s184
Genes: A B A+B
Length: 53 559 611
Sequences: 640 416 95
Seq/Len: 12.08 0.74 0.16
MirrorTree (Pazo et al. 2001) 0.79
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 0.16
2 0.02 0.01 0.16
5 0.02 0.01 0.16
10 0.02 0.01 0.16
20 0.02 0.01 0.16
100 0.02 0.01 0.16
∞ 0.02 0.01 0.16
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 1.51 0.28 0.00
46_L 116_F 1.41 0.24 0.00
46_L 146_Y 1.33 0.21 0.00
16_F 360_A 1.33 0.20 0.00
16_F 503_L 1.32 0.20 0.00
25_A 195_I 1.25 0.18 0.00
37_W 146_Y 1.16 0.15 0.00
25_A 178_I 1.16 0.15 0.00
32_R 82_K 1.15 0.15 0.00
20_K 79_E 1.12 0.14 0.00
32_R 79_E 1.10 0.13 0.00
37_W 116_F 1.10 0.13 0.00
29_K 391_L 1.09 0.13 0.00
42_E 70_K 1.09 0.13 0.00
48_D 167_I 1.07 0.13 0.00
37_W 282_L 1.06 0.12 0.00
35_G 171_F 1.05 0.12 0.00
10_R 360_A 1.05 0.12 0.00
26_R 162_S 1.05 0.12 0.00
20_K 531_V 1.03 0.12 0.00
35_G 146_Y 1.03 0.12 0.00
20_K 132_I 1.02 0.11 0.00
33_K 371_A 1.02 0.11 0.00
25_A 233_E 1.02 0.11 0.00
27_N 132_I 1.00 0.11 0.00
42_E 484_L 1.00 0.11 0.00
26_R 36_E 1.00 0.11 0.00
42_E 21_V 0.99 0.11 0.00
35_G 116_F 0.99 0.11 0.00
11_K 312_E 0.99 0.11 0.00
20_K 329_I 0.98 0.10 0.00
37_W 380_I 0.98 0.10 0.00
26_R 534_A 0.98 0.10 0.00
6_F 417_V 0.97 0.10 0.00
26_R 17_D 0.97 0.10 0.00
24_I 502_A 0.97 0.10 0.00
30_A 79_E 0.97 0.10 0.00
38_K 517_I 0.97 0.10 0.00
14_K 167_I 0.97 0.10 0.00
47_K 291_E 0.96 0.10 0.00
11_K 409_T 0.96 0.10 0.00
34_K 101_K 0.96 0.10 0.00
45_Q 189_V 0.96 0.10 0.00
4_G 550_K 0.96 0.10 0.00
20_K 82_K 0.96 0.10 0.00
47_K 350_K 0.95 0.10 0.00
48_D 82_K 0.95 0.10 0.00
11_K 502_A 0.94 0.10 0.00
26_R 315_H 0.94 0.10 0.00
50_T 49_K 0.94 0.10 0.00
37_W 523_E 0.94 0.10 0.00
33_K 201_K 0.92 0.09 0.00
26_R 50_I 0.92 0.09 0.00
25_A 371_A 0.92 0.09 0.00
35_G 205_L 0.92 0.09 0.00
29_K 531_V 0.92 0.09 0.00
14_K 122_E 0.92 0.09 0.00
7_R 203_E 0.92 0.09 0.00
48_D 341_I 0.91 0.09 0.00
14_K 527_K 0.91 0.09 0.00
29_K 414_W 0.91 0.09 0.00
37_W 329_I 0.91 0.09 0.00
47_K 513_S 0.91 0.09 0.00
48_D 399_D 0.90 0.09 0.00
9_Q 291_E 0.89 0.09 0.00
26_R 261_V 0.89 0.09 0.00
20_K 177_D 0.88 0.09 0.00
29_K 171_F 0.88 0.09 0.00
20_K 311_K 0.88 0.09 0.00
30_A 82_K 0.87 0.08 0.00
12_I 517_I 0.87 0.08 0.00
20_K 391_L 0.87 0.08 0.00
30_A 391_L 0.86 0.08 0.00
12_I 296_T 0.86 0.08 0.00
26_R 312_E 0.85 0.08 0.00
38_K 256_D 0.85 0.08 0.00
38_K 243_P 0.85 0.08 0.00
11_K 360_A 0.85 0.08 0.00
48_D 424_K 0.85 0.08 0.00
7_R 200_T 0.85 0.08 0.00
16_F 64_K 0.85 0.08 0.00
8_N 476_K 0.85 0.08 0.00
8_N 6_E 0.84 0.08 0.00
50_T 531_V 0.84 0.08 0.00
47_K 390_R 0.84 0.08 0.00
10_R 375_I 0.84 0.08 0.00
47_K 512_K 0.83 0.08 0.00
38_K 297_E 0.83 0.08 0.00
42_E 314_V 0.83 0.08 0.00
50_T 178_I 0.82 0.07 0.00
21_E 377_T 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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