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OPENSEQ.org
RsfS-vs-S4
Genes: A B A+B
Length: 105 206 309
Sequences: 2682 1236 560
Seq/Len: 25.54 6 1.81
MirrorTree (Pazo et al. 2001) 0.52
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 0.09 0.00
2 0.01 0.09 0.00
5 0.01 0.09 0.01
10 0.01 0.09 0.01
20 0.01 0.09 0.02
100 0.01 0.09 0.17
∞ 0.01 0.09 1.80
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
97_L 76_Y 1.30 0.78 0.04
50_S 200_I 1.10 0.61 0.02
20_Q 128_R 1.08 0.58 0.02
80_V 132_I 1.05 0.54 0.02
78_I 143_V 1.04 0.54 0.02
78_I 156_K 1.04 0.54 0.02
26_D 102_V 0.98 0.47 0.02
53_D 206_K 0.96 0.45 0.02
30_K 155_V 0.96 0.45 0.02
37_M 50_D 0.94 0.43 0.01
7_Q 147_E 0.93 0.42 0.01
38_I 46_P 0.92 0.41 0.01
3_G 10_K 0.91 0.40 0.01
86_I 157_A 0.90 0.38 0.01
23_I 150_K 0.88 0.37 0.01
80_V 169_T 0.88 0.36 0.01
50_S 166_E 0.87 0.36 0.01
47_H 132_I 0.87 0.35 0.01
21_D 153_S 0.86 0.35 0.01
25_L 181_T 0.84 0.33 0.01
47_H 133_A 0.83 0.32 0.01
87_V 138_S 0.83 0.32 0.01
19_G 109_A 0.83 0.32 0.01
76_D 123_I 0.82 0.31 0.01
55_V 184_R 0.82 0.31 0.01
15_D 187_E 0.81 0.30 0.01
97_L 85_N 0.81 0.30 0.01
94_S 50_D 0.81 0.29 0.01
25_L 138_S 0.81 0.29 0.01
39_I 75_Y 0.80 0.29 0.01
19_G 201_V 0.80 0.29 0.01
96_R 145_I 0.79 0.28 0.01
22_I 156_K 0.79 0.28 0.01
26_D 186_P 0.78 0.27 0.01
59_S 143_V 0.78 0.27 0.01
71_G 49_S 0.78 0.27 0.01
12_D 191_L 0.77 0.27 0.01
63_G 128_R 0.77 0.27 0.01
24_A 102_V 0.77 0.27 0.01
16_D 145_I 0.77 0.26 0.01
101_E 198_H 0.77 0.26 0.01
88_H 81_R 0.77 0.26 0.01
51_I 153_S 0.75 0.25 0.01
81_D 58_K 0.75 0.25 0.01
47_H 180_G 0.75 0.25 0.01
86_I 172_E 0.74 0.24 0.01
16_D 10_K 0.73 0.23 0.01
86_I 144_S 0.73 0.23 0.01
69_V 155_V 0.73 0.23 0.01
24_A 182_F 0.73 0.23 0.01
85_V 28_I 0.72 0.22 0.01
82_L 57_E 0.71 0.22 0.01
5_A 148_K 0.71 0.22 0.01
76_D 92_A 0.71 0.22 0.01
103_L 48_L 0.71 0.22 0.01
83_G 156_K 0.71 0.21 0.01
44_S 63_R 0.71 0.21 0.01
52_A 145_I 0.71 0.21 0.01
33_I 11_L 0.70 0.21 0.01
40_C 169_T 0.70 0.21 0.01
29_G 169_T 0.70 0.21 0.01
92_E 123_I 0.70 0.21 0.01
40_C 86_T 0.70 0.21 0.01
46_R 50_D 0.69 0.20 0.01
105_S 206_K 0.69 0.20 0.01
46_R 158_A 0.69 0.20 0.01
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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