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OPENSEQ.org
Cd spoIIIAC-AD
Genes: A B A+B
Length: 65 128 192
Sequences: 278 389 369
Seq/Len: 4.28 3.04 1.92
MirrorTree (Pazo et al. 2001) 0.27
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 0.00 1.91
2 0.01 0.00 1.91
5 0.01 0.00 1.91
10 0.01 0.00 1.91
20 0.01 0.00 1.91
100 0.01 0.00 1.91
∞ 0.01 0.00 1.91
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
24_E 79_Y 1.88 0.98 0.92
59_R 80_L 1.56 0.93 0.78
57_T 105_K 1.46 0.89 0.71
36_T 103_G 1.44 0.88 0.69
59_R 25_P 1.34 0.82 0.60
8_K 84_A 1.32 0.81 0.58
22_I 36_G 1.26 0.77 0.52
22_I 95_N 1.25 0.76 0.52
42_I 71_I 1.22 0.74 0.48
47_V 75_I 1.22 0.73 0.48
49_T 31_I 1.18 0.70 0.43
11_G 85_I 1.17 0.69 0.43
42_I 102_F 1.16 0.68 0.41
3_I 108_V 1.15 0.67 0.40
22_I 87_L 1.14 0.66 0.40
12_V 83_F 1.14 0.66 0.39
50_E 70_L 1.13 0.65 0.38
6_I 45_F 1.12 0.64 0.38
64_L 20_I 1.12 0.64 0.37
22_I 67_Y 1.11 0.63 0.37
61_M 61_A 1.06 0.58 0.32
8_K 85_I 1.04 0.56 0.30
7_L 77_I 1.02 0.54 0.28
43_V 11_I 1.02 0.53 0.28
15_L 69_S 1.02 0.53 0.28
19_L 97_A 1.01 0.53 0.27
29_K 2_E 1.01 0.52 0.27
28_R 71_I 1.00 0.51 0.26
3_I 42_S 0.99 0.50 0.25
50_E 115_I 0.98 0.49 0.24
41_I 37_V 0.98 0.49 0.24
58_V 58_A 0.98 0.49 0.24
38_A 84_A 0.97 0.48 0.24
17_S 102_F 0.96 0.47 0.23
58_V 91_C 0.96 0.47 0.22
49_T 99_K 0.96 0.47 0.22
14_I 71_I 0.95 0.46 0.22
58_V 116_L 0.95 0.46 0.22
29_K 87_L 0.95 0.46 0.22
28_R 125_N 0.95 0.45 0.21
59_R 44_M 0.94 0.45 0.21
42_I 19_V 0.94 0.44 0.20
18_V 50_I 0.93 0.44 0.20
42_I 64_P 0.93 0.43 0.20
7_L 123_V 0.93 0.43 0.20
34_L 7_I 0.92 0.42 0.19
48_I 44_M 0.92 0.42 0.19
15_L 120_V 0.91 0.41 0.18
9_V 119_I 0.90 0.40 0.18
25_K 82_E 0.90 0.40 0.18
10_A 76_G 0.90 0.40 0.17
20_N 104_G 0.89 0.39 0.17
36_T 93_E 0.89 0.39 0.17
61_M 51_V 0.88 0.38 0.17
15_L 116_L 0.88 0.38 0.17
38_A 47_L 0.88 0.38 0.16
43_V 109_M 0.88 0.38 0.16
57_T 118_S 0.88 0.38 0.16
5_L 13_S 0.88 0.38 0.16
60_T 94_G 0.88 0.38 0.16
30_D 26_E 0.87 0.37 0.16
4_S 5_Q 0.87 0.37 0.16
60_T 41_L 0.87 0.37 0.16
10_A 82_E 0.87 0.37 0.16
60_T 116_L 0.87 0.37 0.16
64_L 95_N 0.87 0.37 0.15
51_I 96_I 0.87 0.37 0.15
59_R 98_S 0.86 0.36 0.15
8_K 88_C 0.86 0.36 0.15
45_G 74_L 0.86 0.36 0.15
24_E 106_I 0.86 0.36 0.15
59_R 9_I 0.86 0.36 0.15
48_I 84_A 0.85 0.35 0.15
48_I 124_V 0.85 0.35 0.15
22_I 96_I 0.85 0.35 0.14
9_V 80_L 0.85 0.35 0.14
17_S 67_Y 0.85 0.35 0.14
40_V 104_G 0.85 0.35 0.14
24_E 37_V 0.84 0.34 0.14
28_R 7_I 0.84 0.34 0.14
15_L 127_I 0.84 0.34 0.14
38_A 88_C 0.83 0.33 0.13
56_N 120_V 0.83 0.33 0.13
20_N 36_G 0.83 0.33 0.13
28_R 13_S 0.83 0.33 0.13
3_I 58_A 0.83 0.33 0.13
58_V 22_K 0.83 0.33 0.13
18_V 34_I 0.83 0.33 0.13
44_L 114_P 0.82 0.33 0.13
29_K 80_L 0.82 0.32 0.13
25_K 79_Y 0.82 0.32 0.13
42_I 112_S 0.82 0.32 0.13
35_T 75_I 0.82 0.32 0.12
29_K 17_C 0.82 0.32 0.12
41_I 104_G 0.82 0.32 0.12
45_G 81_M 0.81 0.32 0.12
30_D 47_L 0.81 0.31 0.12
11_G 38_I 0.81 0.31 0.12
22_I 35_T 0.81 0.31 0.12
48_I 42_S 0.81 0.31 0.12
46_M 86_Q 0.80 0.30 0.12
25_K 99_K 0.80 0.30 0.12
22_I 47_L 0.80 0.30 0.12
47_V 34_I 0.80 0.30 0.11
58_V 120_V 0.80 0.30 0.11
37_L 97_A 0.79 0.29 0.11
26_T 128_P 0.79 0.29 0.11
29_K 5_Q 0.79 0.29 0.11
35_T 68_I 0.79 0.29 0.11
29_K 16_L 0.79 0.29 0.11
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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