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OPENSEQ.org
des
Genes: A B A+B
Length: 216 199 407
Sequences: 12368 37065 8488
Seq/Len: 57.26 186.26 20.86
MirrorTree (Pazo et al. 2001) 0.81
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 0.01 20.45
2 0.02 0.02 21.10
5 0.03 0.04 21.57
10 0.04 0.07 21.84
20 0.06 0.11 22.28
100 0.11 0.22 23.58
∞ 0.20 0.26 24.64
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
81_R 103_D 2.05 1.00 0.99
49_D 106_S 1.61 1.00 0.95
53_K 107_E 1.54 1.00 0.94
53_K 24_E 1.51 1.00 0.93
46_L 17_L 1.40 0.99 0.89
42_S 13_L 1.32 0.99 0.86
57_K 25_D 1.23 0.98 0.81
50_L 20_L 1.12 0.96 0.71
39_Q 10_Q 1.01 0.93 0.60
84_V 170_R 0.94 0.89 0.52
50_L 19_S 0.92 0.88 0.49
78_N 103_D 0.89 0.85 0.45
38_G 81_T 0.89 0.85 0.44
43_L 12_M 0.88 0.84 0.43
68_S 15_G 0.81 0.77 0.35
77_L 103_D 0.81 0.77 0.35
50_L 23_L 0.80 0.75 0.34
74_R 103_D 0.79 0.74 0.33
46_L 16_A 0.78 0.72 0.31
43_L 13_L 0.77 0.72 0.31
61_Q 22_N 0.77 0.71 0.30
52_R 107_E 0.74 0.67 0.26
54_L 23_L 0.71 0.62 0.23
49_D 105_P 0.70 0.60 0.22
39_Q 81_T 0.65 0.53 0.18
70_Q 105_P 0.65 0.52 0.18
42_S 81_T 0.65 0.52 0.17
46_L 20_L 0.65 0.51 0.17
65_E 19_S 0.63 0.49 0.16
84_V 81_T 0.62 0.47 0.15
49_D 20_L 0.58 0.41 0.13
57_K 24_E 0.58 0.40 0.12
80_V 82_F 0.57 0.39 0.12
49_D 107_E 0.57 0.39 0.12
38_G 170_R 0.57 0.38 0.11
39_Q 57_M 0.56 0.38 0.11
39_Q 8_E 0.55 0.36 0.11
53_K 110_A 0.55 0.36 0.11
45_G 103_D 0.55 0.36 0.11
45_G 105_P 0.55 0.35 0.10
53_K 23_L 0.55 0.35 0.10
77_L 81_T 0.55 0.35 0.10
39_Q 82_F 0.54 0.34 0.10
84_V 187_E 0.52 0.31 0.09
74_R 105_P 0.51 0.30 0.08
39_Q 55_I 0.50 0.28 0.08
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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