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OPENSEQ.org
smut
Genes: A B A+B
Length: 65 110 175
Sequences: 7176 84129 4314
Seq/Len: 110.4 764.81 24.65
MirrorTree (Pazo et al. 2001) 0.49
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 0.10 24.65
2 0.00 0.13 25.41
5 0.01 0.16 26.53
10 0.02 0.19 28.29
20 0.04 0.23 30.41
100 0.10 0.31 36.40
∞ 0.18 0.34 39.03
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
38_S 12_D 2.87 1.00 1.00
21_S 13_I 2.73 1.00 1.00
24_E 101_S 2.24 1.00 0.99
17_T 10_I 2.04 1.00 0.99
45_D 9_P 1.90 1.00 0.98
46_E 9_P 1.86 1.00 0.98
25_A 17_N 1.84 1.00 0.98
22_Y 13_I 1.50 1.00 0.93
39_F 16_F 1.37 0.99 0.89
29_G 20_K 1.16 0.97 0.76
14_T 7_E 1.08 0.95 0.69
42_V 9_P 1.06 0.95 0.68
28_D 103_R 1.02 0.94 0.63
13_R 97_T 1.01 0.93 0.62
28_D 17_N 0.99 0.92 0.59
18_S 10_I 0.89 0.85 0.47
35_V 19_A 0.88 0.84 0.45
22_Y 12_D 0.86 0.82 0.43
6_S 78_K 0.77 0.72 0.32
25_A 16_F 0.77 0.72 0.32
35_V 16_F 0.77 0.71 0.32
17_T 100_F 0.75 0.68 0.29
42_V 12_D 0.73 0.65 0.27
28_D 102_N 0.71 0.62 0.25
18_S 9_P 0.69 0.59 0.23
5_V 5_D 0.67 0.55 0.20
11_E 76_S 0.61 0.45 0.15
25_A 102_N 0.60 0.44 0.15
13_R 79_D 0.59 0.43 0.14
28_D 20_K 0.58 0.40 0.13
24_E 81_E 0.56 0.38 0.12
24_E 102_N 0.54 0.34 0.10
2_R 82_F 0.53 0.33 0.10
62_R 79_D 0.53 0.33 0.10
46_E 7_E 0.53 0.32 0.10
37_P 24_D 0.52 0.30 0.09
2_R 80_S 0.51 0.30 0.09
14_T 51_M 0.49 0.27 0.08
42_V 13_I 0.47 0.24 0.07
8_V 58_L 0.47 0.23 0.06
1_R 81_E 0.46 0.23 0.06
41_K 67_N 0.46 0.23 0.06
55_T 79_D 0.46 0.23 0.06
46_E 51_M 0.45 0.22 0.06
22_Y 16_F 0.45 0.22 0.06
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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