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OPENSEQ.org
6173
Genes: A B A+B
Length: 94 106 190
Sequences: 3305 2354 856
Seq/Len: 35.16 22.21 4.51
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 4.28
2 0.01 0.02 4.32
5 0.02 0.03 4.34
10 0.02 0.04 4.36
20 0.03 0.04 4.43
100 0.05 0.06 4.65
∞ 0.10 0.11 5.71
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
12_K 30_E 2.00 1.00 0.98
21_V 23_A 1.97 1.00 0.98
24_A 23_A 1.95 1.00 0.98
9_S 33_E 1.72 0.99 0.96
18_N 19_P 1.57 0.99 0.93
14_K 11_E 1.44 0.97 0.89
8_F 29_L 1.40 0.97 0.87
18_N 22_Q 1.35 0.96 0.85
81_Y 52_F 1.33 0.95 0.84
32_E 27_K 1.28 0.94 0.81
29_T 27_K 1.27 0.94 0.80
60_Q 66_F 1.20 0.91 0.75
15_A 22_Q 1.14 0.87 0.69
21_V 26_L 1.13 0.87 0.68
6_I 11_E 1.12 0.87 0.68
11_V 6_F 1.09 0.84 0.64
14_K 15_Y 1.01 0.78 0.56
36_A 34_A 0.99 0.76 0.53
48_T 83_K 0.99 0.75 0.53
55_R 29_L 0.97 0.74 0.51
21_V 22_Q 0.95 0.71 0.47
8_F 30_E 0.93 0.69 0.45
57_G 18_E 0.91 0.66 0.43
42_K 53_E 0.90 0.65 0.41
48_T 17_L 0.89 0.64 0.41
8_F 4_L 0.89 0.64 0.41
16_L 26_L 0.89 0.63 0.40
55_R 22_Q 0.88 0.63 0.40
54_A 34_A 0.87 0.61 0.38
83_A 16_D 0.86 0.60 0.37
62_A 10_A 0.85 0.59 0.36
12_K 33_E 0.85 0.59 0.36
41_M 36_G 0.84 0.57 0.35
14_K 22_Q 0.83 0.55 0.33
24_A 40_R 0.82 0.55 0.33
7_K 3_E 0.81 0.53 0.31
25_Y 30_E 0.81 0.53 0.31
41_M 84_T 0.81 0.53 0.31
28_A 24_K 0.80 0.51 0.30
67_E 53_E 0.79 0.51 0.29
66_L 43_D 0.79 0.50 0.28
66_L 59_K 0.78 0.49 0.28
11_V 15_Y 0.78 0.49 0.28
26_D 50_G 0.78 0.49 0.28
17_A 76_I 0.77 0.47 0.26
59_S 76_I 0.77 0.47 0.26
68_R 70_K 0.77 0.47 0.26
69_N 44_T 0.77 0.47 0.26
81_Y 13_E 0.76 0.46 0.25
64_S 97_S 0.75 0.45 0.24
26_D 100_E 0.74 0.44 0.24
36_A 35_K 0.74 0.44 0.24
67_E 47_I 0.72 0.41 0.22
87_M 52_F 0.72 0.41 0.21
31_E 24_K 0.72 0.40 0.21
23_K 89_K 0.72 0.40 0.21
78_L 23_A 0.72 0.40 0.21
37_V 91_E 0.71 0.39 0.21
51_E 18_E 0.71 0.39 0.20
15_A 15_Y 0.70 0.39 0.20
8_F 6_F 0.70 0.38 0.20
50_T 62_S 0.70 0.38 0.19
88_H 89_K 0.69 0.36 0.18
25_Y 23_A 0.68 0.36 0.18
21_V 15_Y 0.68 0.36 0.18
48_T 12_S 0.68 0.36 0.18
85_C 79_T 0.68 0.36 0.18
19_P 22_Q 0.67 0.35 0.17
35_R 102_L 0.67 0.34 0.17
12_K 19_P 0.67 0.34 0.17
86_G 61_I 0.66 0.33 0.17
62_A 52_F 0.66 0.33 0.16
47_L 100_E 0.66 0.33 0.16
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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