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OPENSEQ.org
2wwv_A_D
Genes: A B A+B
Length: 103 103 202
Sequences: 1122 1109 869
Seq/Len: 10.89 10.77 4.3
MirrorTree (Pazo et al. 2001) 0.47
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 2.19
2 0.01 0.01 3.53
5 0.04 0.06 4.20
10 0.05 0.06 4.21
20 0.06 0.07 4.22
100 0.08 0.10 4.27
∞ 0.15 0.17 4.34
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
24_A 59_A 1.56 0.98 0.88
53_L 41_L 1.07 0.81 0.49
21_L 59_A 1.03 0.79 0.46
17_Q 79_S 0.99 0.74 0.41
42_D 44_E 0.91 0.65 0.32
27_K 63_P 0.86 0.59 0.27
74_L 38_P 0.75 0.43 0.17
15_S 75_E 0.74 0.42 0.16
27_K 64_E 0.71 0.38 0.14
19_R 10_A 0.71 0.38 0.14
59_I 90_V 0.70 0.37 0.14
9_M 84_K 0.70 0.36 0.14
11_L 81_L 0.67 0.33 0.12
53_L 59_A 0.66 0.32 0.11
80_H 57_Q 0.66 0.32 0.11
31_Q 63_P 0.66 0.32 0.11
17_Q 61_M 0.66 0.32 0.11
15_S 42_A 0.65 0.31 0.11
9_M 79_S 0.65 0.31 0.11
64_G 16_L 0.65 0.30 0.11
88_R 61_M 0.64 0.30 0.10
69_K 40_T 0.63 0.28 0.10
84_S 57_Q 0.63 0.28 0.10
35_A 96_A 0.61 0.26 0.09
92_T 64_E 0.61 0.26 0.09
59_I 42_A 0.60 0.25 0.08
22_A 59_A 0.60 0.25 0.08
42_D 43_G 0.58 0.23 0.08
72_L 35_E 0.58 0.23 0.08
71_S 65_I 0.58 0.23 0.07
92_T 61_M 0.58 0.23 0.07
59_I 85_V 0.58 0.23 0.07
18_A 41_L 0.58 0.23 0.07
20_S 53_L 0.58 0.23 0.07
41_M 46_G 0.57 0.22 0.07
12_I 62_L 0.57 0.22 0.07
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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