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1fm0_D_E

Genes: A B A+B
Length: 81 150 214
Sequences: 1868 1748 979
Seq/Len: 23.06 11.65 4.57
MirrorTree (Pazo et al. 2001) 0.74
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 3.89
2 0.01 0.01 4.09
5 0.01 0.01 4.14
10 0.01 0.02 4.19
20 0.01 0.02 4.24
100 0.01 0.02 4.29
0.03 0.02 4.78
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
11_R 53_E 2.31 1.00 0.99
58_T 61_K 1.84 1.00 0.98
59_L 62_A 1.15 0.89 0.73
79_T 54_H 1.14 0.88 0.72
78_V 59_T 1.12 0.87 0.70
57_Q 61_K 1.11 0.86 0.69
78_V 38_V 1.11 0.86 0.68
9_Q 37_K 1.09 0.85 0.67
75_F 58_M 1.01 0.78 0.58
57_Q 57_G 1.00 0.77 0.56
2_I 74_W 1.00 0.77 0.56
54_A 58_M 0.95 0.72 0.51
58_T 65_E 0.94 0.70 0.49
57_Q 55_Y 0.94 0.70 0.48
78_V 85_I 0.91 0.67 0.46
75_F 94_I 0.88 0.63 0.42
75_F 52_L 0.82 0.55 0.34
3_K 74_W 0.81 0.53 0.33
57_Q 58_M 0.80 0.52 0.32
46_L 101_S 0.79 0.51 0.31
79_T 70_A 0.79 0.51 0.30
12_E 127_R 0.78 0.49 0.29
54_A 123_P 0.78 0.49 0.29
30_A 20_P 0.77 0.48 0.28
15_G 81_V 0.77 0.48 0.28
30_A 14_S 0.76 0.46 0.27
50_K 92_D 0.76 0.46 0.27
8_A 63_L 0.75 0.45 0.26
10_V 94_I 0.75 0.45 0.26
2_I 71_R 0.74 0.44 0.25
35_M 136_W 0.74 0.44 0.25
10_V 37_K 0.74 0.43 0.25
65_P 69_E 0.74 0.43 0.24
51_L 111_G 0.72 0.41 0.23
47_E 59_T 0.72 0.41 0.23
73_A 55_Y 0.72 0.41 0.23
7_F 55_Y 0.71 0.40 0.22
24_D 92_D 0.71 0.39 0.22
59_L 59_T 0.70 0.39 0.21
79_T 8_V 0.70 0.39 0.21
72_V 76_L 0.70 0.39 0.21
19_T 28_D 0.70 0.39 0.21
1_M 65_E 0.70 0.38 0.21
78_V 88_L 0.70 0.38 0.21
79_T 124_F 0.69 0.37 0.20
79_T 56_P 0.69 0.36 0.20
5_L 50_L 0.68 0.36 0.19
53_A 79_V 0.68 0.36 0.19
8_A 123_P 0.68 0.36 0.19
5_L 105_S 0.68 0.36 0.19
58_T 50_L 0.68 0.35 0.19
75_F 53_E 0.67 0.35 0.18
71_E 58_M 0.67 0.34 0.18
29_E 11_Q 0.66 0.34 0.18
59_L 8_V 0.66 0.33 0.17
60_V 137_V 0.66 0.33 0.17
33_Q 133_G 0.66 0.33 0.17
10_V 58_M 0.65 0.32 0.16
1_M 66_I 0.64 0.31 0.16
52_L 47_V 0.64 0.31 0.16
59_L 32_V 0.64 0.31 0.16
13_L 37_K 0.64 0.31 0.16
78_V 74_W 0.64 0.31 0.16
21_V 96_F 0.64 0.31 0.16
59_L 130_T 0.64 0.31 0.16
8_A 84_R 0.64 0.31 0.15
3_K 32_V 0.64 0.31 0.15
4_V 89_W 0.64 0.30 0.15
3_K 12_P 0.64 0.30 0.15
40_D 111_G 0.64 0.30 0.15
76_P 127_R 0.63 0.30 0.15
79_T 52_L 0.63 0.30 0.15
19_T 19_Y 0.63 0.30 0.15
59_L 37_K 0.63 0.30 0.15
10_V 62_A 0.63 0.29 0.15
19_T 33_T 0.63 0.29 0.15
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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