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OPENSEQ.org
covar HicAEC
Genes: A B A+B
Length: 58 138 196
Sequences: 2396 761 261
Seq/Len: 41.31 5.51 1.33
MirrorTree (Pazo et al. 2001) 0.68
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 0.00 1.28
2 0.00 0.01 1.29
5 0.01 0.01 1.31
10 0.02 0.01 1.31
20 0.03 0.01 1.33
100 0.05 0.02 1.49
∞ 0.10 0.07 2.05
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
44_K 28_Q 1.80 0.94 0.69
46_P 12_E 1.33 0.72 0.30
34_V 46_A 1.23 0.64 0.22
48_R 6_T 1.22 0.62 0.21
44_K 9_P 1.21 0.61 0.20
34_V 45_T 1.20 0.61 0.20
48_R 18_S 1.20 0.61 0.20
1_M 29_G 1.19 0.59 0.19
41_D 15_Y 1.17 0.58 0.18
47_L 2_R 1.10 0.51 0.14
32_R 53_D 1.08 0.49 0.13
1_M 96_L 1.07 0.48 0.13
4_S 17_V 1.05 0.46 0.12
54_Q 96_L 1.03 0.44 0.11
53_K 23_P 1.02 0.43 0.10
25_K 45_T 1.02 0.42 0.10
18_A 6_T 1.01 0.41 0.10
2_K 119_I 1.00 0.41 0.10
11_E 124_L 0.99 0.40 0.09
34_V 127_K 0.99 0.40 0.09
50_A 134_S 0.99 0.40 0.09
34_V 42_A 0.97 0.38 0.09
43_I 26_L 0.96 0.38 0.09
56_G 21_D 0.96 0.37 0.09
36_P 27_T 0.96 0.37 0.08
17_V 58_P 0.96 0.37 0.08
44_K 16_M 0.94 0.35 0.08
25_K 48_D 0.93 0.34 0.07
33_S 73_P 0.93 0.34 0.07
22_N 47_F 0.93 0.34 0.07
22_N 41_D 0.92 0.33 0.07
35_M 69_F 0.92 0.33 0.07
16_D 136_V 0.91 0.32 0.07
41_D 94_Q 0.90 0.32 0.07
22_N 38_A 0.90 0.32 0.06
1_M 35_A 0.90 0.31 0.06
57_L 89_S 0.89 0.30 0.06
12_S 135_L 0.88 0.30 0.06
39_P 106_E 0.86 0.28 0.06
44_K 14_G 0.86 0.28 0.06
21_S 7_L 0.85 0.28 0.05
11_E 99_R 0.85 0.27 0.05
3_Q 28_Q 0.84 0.27 0.05
13_Q 52_E 0.83 0.26 0.05
49_K 77_A 0.83 0.26 0.05
18_A 67_D 0.82 0.26 0.05
24_L 113_L 0.80 0.23 0.04
36_P 105_Q 0.80 0.23 0.04
41_D 125_A 0.79 0.23 0.04
35_M 40_K 0.79 0.23 0.04
16_D 31_T 0.79 0.23 0.04
39_P 27_T 0.79 0.23 0.04
49_K 12_E 0.78 0.22 0.04
40_C 67_D 0.78 0.22 0.04
4_S 4_P 0.77 0.22 0.04
32_R 49_F 0.77 0.22 0.04
44_K 1_M 0.77 0.21 0.04
49_K 126_A 0.75 0.20 0.03
25_K 49_F 0.75 0.20 0.03
50_A 8_T 0.75 0.20 0.03
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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