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OPENSEQ.org
4488
Genes: A B A+B
Length: 95 103 189
Sequences: 2929 2277 897
Seq/Len: 30.83 22.11 4.75
MirrorTree (Pazo et al. 2001) 0.70
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.02 4.53
2 0.01 0.02 4.56
5 0.02 0.03 4.57
10 0.02 0.04 4.58
20 0.03 0.04 4.64
100 0.04 0.06 4.85
∞ 0.09 0.11 5.81
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_G 23_G 2.25 1.00 0.99
21_A 23_G 2.15 1.00 0.99
12_K 30_E 2.02 1.00 0.99
9_S 33_E 1.72 0.99 0.96
8_F 29_I 1.45 0.98 0.91
18_T 19_D 1.38 0.97 0.88
29_D 27_R 1.35 0.96 0.86
14_K 11_L 1.33 0.96 0.85
32_L 27_R 1.30 0.95 0.83
81_Y 52_F 1.24 0.93 0.80
18_T 22_R 1.18 0.91 0.75
21_A 26_A 1.17 0.90 0.74
36_E 34_Q 1.11 0.87 0.69
8_F 6_T 1.06 0.83 0.63
21_A 22_R 1.06 0.83 0.63
60_P 66_Y 1.05 0.82 0.63
25_Y 30_E 1.05 0.82 0.63
15_L 22_R 1.05 0.82 0.62
28_A 24_R 1.01 0.79 0.58
57_G 18_P 0.94 0.72 0.50
55_R 29_I 0.93 0.71 0.48
29_D 30_E 0.90 0.67 0.45
7_P 3_N 0.89 0.66 0.43
8_F 4_V 0.89 0.65 0.43
10_Q 12_D 0.86 0.62 0.40
62_A 10_A 0.86 0.62 0.39
12_K 33_E 0.85 0.60 0.38
38_L 66_Y 0.83 0.57 0.35
14_K 15_L 0.81 0.55 0.33
8_F 30_E 0.81 0.54 0.33
57_G 21_L 0.80 0.53 0.32
15_L 15_L 0.80 0.53 0.32
14_K 22_R 0.80 0.53 0.31
65_R 92_I 0.79 0.52 0.31
36_E 35_E 0.79 0.52 0.31
8_F 76_L 0.79 0.52 0.31
73_A 66_Y 0.78 0.50 0.29
85_C 79_A 0.78 0.50 0.29
66_L 59_K 0.78 0.50 0.29
6_V 11_L 0.76 0.48 0.28
48_T 83_K 0.73 0.43 0.24
54_E 34_Q 0.72 0.42 0.23
64_S 81_V 0.72 0.42 0.23
88_T 89_T 0.72 0.41 0.23
69_N 44_S 0.71 0.41 0.23
59_R 76_L 0.71 0.41 0.22
76_K 59_K 0.71 0.41 0.22
24_G 40_K 0.71 0.40 0.22
91_I 101_E 0.70 0.40 0.21
66_L 43_H 0.70 0.39 0.21
22_V 16_E 0.70 0.39 0.21
38_L 13_E 0.70 0.39 0.21
23_K 89_T 0.69 0.38 0.20
13_Q 87_T 0.69 0.38 0.20
37_M 91_A 0.69 0.38 0.20
35_V 102_M 0.69 0.38 0.20
11_V 100_K 0.68 0.37 0.20
51_A 18_P 0.68 0.37 0.19
75_M 49_G 0.68 0.37 0.19
16_L 26_A 0.68 0.36 0.19
71_L 22_R 0.66 0.35 0.18
26_E 50_G 0.66 0.34 0.18
77_T 65_L 0.66 0.34 0.18
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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