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OPENSEQ.org
RsfS-vs-L20
Genes: A B A+B
Length: 105 118 219
Sequences: 2682 1984 1140
Seq/Len: 25.54 16.81 5.21
MirrorTree (Pazo et al. 2001) 0.61
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 0.10 0.00
2 0.01 0.10 0.01
5 0.01 0.10 0.05
10 0.01 0.10 0.17
20 0.01 0.10 0.35
100 0.01 0.10 0.95
∞ 0.01 0.10 5.11
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_R 91_D 1.44 0.98 0.78
82_L 29_S 0.91 0.71 0.28
87_V 51_R 0.87 0.66 0.25
90_M 46_A 0.85 0.63 0.23
76_D 31_V 0.85 0.62 0.23
103_L 45_Y 0.81 0.57 0.19
26_D 96_A 0.80 0.56 0.19
14_I 51_R 0.80 0.56 0.19
87_V 36_F 0.79 0.55 0.18
36_C 19_K 0.79 0.54 0.18
45_S 14_H 0.78 0.54 0.17
87_V 86_A 0.77 0.52 0.17
44_S 16_K 0.77 0.52 0.17
14_I 38_A 0.75 0.49 0.15
74_S 97_D 0.75 0.49 0.15
103_L 9_I 0.72 0.45 0.14
30_K 91_D 0.72 0.45 0.14
9_F 90_I 0.71 0.44 0.13
32_S 91_D 0.69 0.41 0.12
40_C 33_R 0.69 0.40 0.11
19_G 86_A 0.68 0.39 0.11
84_D 20_Q 0.68 0.39 0.11
18_K 85_K 0.68 0.38 0.11
27_V 40_I 0.67 0.38 0.11
99_E 20_Q 0.67 0.38 0.10
25_L 21_A 0.66 0.36 0.10
74_S 108_A 0.66 0.36 0.10
61_A 90_I 0.66 0.36 0.10
64_L 53_R 0.65 0.35 0.10
67_L 27_A 0.65 0.34 0.09
27_V 10_A 0.64 0.34 0.09
74_S 25_Y 0.64 0.33 0.09
54_H 109_L 0.64 0.33 0.09
53_D 72_N 0.64 0.33 0.09
91_Q 79_F 0.63 0.33 0.09
102_K 90_I 0.63 0.33 0.09
59_S 75_S 0.63 0.32 0.09
78_I 78_K 0.62 0.31 0.08
18_K 77_S 0.62 0.31 0.08
29_G 2_A 0.62 0.30 0.08
78_I 100_V 0.61 0.30 0.08
3_G 88_V 0.61 0.30 0.08
32_S 38_A 0.61 0.30 0.08
19_G 35_A 0.60 0.29 0.07
10_V 30_R 0.60 0.29 0.07
49_M 47_Y 0.60 0.28 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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