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OPENSEQ.org
NstoN 3
Genes: A B A+B
Length: 73 220 270
Sequences: 1026 7026 142
Seq/Len: 14.05 31.94 0.53
MirrorTree (Pazo et al. 2001) 0.17
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 0.07 0.06 0.03
2 0.08 0.07 0.05
5 0.08 0.08 0.06
10 0.08 0.08 0.09
20 0.09 0.09 0.16
100 0.12 0.11 0.31
∞ 0.14 0.15 0.48
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
57_C 117_P 1.37 0.48 0.00
65_T 80_P 1.21 0.36 0.00
55_C 134_W 1.20 0.35 0.00
55_C 117_P 1.20 0.35 0.00
44_Y 69_L 1.17 0.33 0.00
26_C 18_W 1.17 0.33 0.00
28_C 18_W 1.17 0.33 0.00
37_C 18_W 1.17 0.33 0.00
40_C 18_W 1.17 0.33 0.00
61_C 117_P 1.15 0.32 0.00
57_C 134_W 1.10 0.28 0.00
65_T 67_I 1.09 0.28 0.00
65_T 7_V 1.05 0.25 0.00
32_V 177_V 1.03 0.24 0.00
29_K 12_T 1.02 0.23 0.00
34_G 18_W 1.02 0.23 0.00
52_C 18_W 1.01 0.23 0.00
43_G 62_S 1.00 0.23 0.00
47_F 131_R 1.00 0.22 0.00
26_C 134_W 0.98 0.21 0.00
28_C 134_W 0.98 0.21 0.00
37_C 134_W 0.98 0.21 0.00
40_C 134_W 0.98 0.21 0.00
54_P 155_W 0.97 0.21 0.00
66_G 117_P 0.95 0.20 0.00
68_C 117_P 0.94 0.19 0.00
31_G 10_L 0.94 0.19 0.00
54_P 160_P 0.93 0.19 0.00
45_W 136_D 0.92 0.18 0.00
52_C 151_Y 0.91 0.18 0.00
68_C 151_Y 0.88 0.17 0.00
41_M 173_L 0.88 0.17 0.00
61_C 134_W 0.87 0.16 0.00
57_C 73_N 0.85 0.15 0.00
46_G 4_S 0.84 0.15 0.00
39_R 111_P 0.84 0.15 0.00
43_G 11_V 0.83 0.15 0.00
62_D 45_I 0.83 0.14 0.00
45_W 175_Y 0.82 0.14 0.00
9_A 56_I 0.82 0.14 0.00
55_C 18_W 0.81 0.14 0.00
56_D 179_G 0.81 0.14 0.00
62_D 117_P 0.81 0.14 0.00
52_C 134_W 0.80 0.13 0.00
48_G 148_S 0.79 0.13 0.00
68_C 18_W 0.79 0.13 0.00
34_G 134_W 0.78 0.13 0.00
26_C 186_Y 0.78 0.13 0.00
28_C 186_Y 0.78 0.13 0.00
37_C 186_Y 0.78 0.13 0.00
40_C 186_Y 0.78 0.13 0.00
8_S 75_V 0.78 0.13 0.00
44_Y 1_V 0.78 0.12 0.00
24_G 18_W 0.78 0.12 0.00
64_I 119_G 0.77 0.12 0.00
45_W 85_A 0.77 0.12 0.00
54_P 120_V 0.77 0.12 0.00
58_A 208_T 0.76 0.12 0.00
44_Y 159_I 0.76 0.12 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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