May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
3OEI
Genes: A B A+B
Length: 91 85 165
Sequences: 1925 3190 707
Seq/Len: 21.15 37.53 4.28
MirrorTree (Pazo et al. 2001) 0.78
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 0.01 4.02
2 0.01 0.03 4.05
5 0.02 0.04 4.15
10 0.03 0.05 4.23
20 0.03 0.06 4.31
100 0.05 0.08 4.65
∞ 0.10 0.12 5.39
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
64_E 9_D 3.07 1.00 1.00
65_A 7_D 2.81 1.00 1.00
68_R 7_D 2.40 1.00 1.00
70_K 70_R 2.22 1.00 0.99
55_S 83_Y 2.16 1.00 0.99
68_R 8_P 2.12 1.00 0.99
66_V 56_Y 1.96 1.00 0.98
63_M 52_E 1.92 1.00 0.98
76_F 3_S 1.83 1.00 0.98
61_R 80_K 1.67 0.99 0.96
69_D 7_D 1.52 0.98 0.93
54_R 83_Y 1.49 0.98 0.92
77_T 6_F 1.48 0.98 0.92
74_S 7_D 1.46 0.97 0.91
58_N 83_Y 1.35 0.95 0.86
61_R 12_E 1.33 0.95 0.85
69_D 77_T 1.28 0.93 0.82
69_D 79_L 1.21 0.91 0.78
66_V 79_L 1.21 0.91 0.78
79_S 29_T 1.11 0.84 0.68
68_R 9_D 1.07 0.82 0.65
70_K 56_Y 1.07 0.82 0.65
51_Y 62_D 1.04 0.79 0.61
69_D 56_Y 1.03 0.78 0.60
74_S 5_N 1.01 0.76 0.58
50_V 51_G 1.01 0.76 0.57
52_L 68_V 0.97 0.72 0.53
74_S 77_T 0.88 0.61 0.42
66_V 70_R 0.88 0.60 0.41
63_M 53_L 0.86 0.59 0.40
36_V 14_F 0.85 0.57 0.38
53_L 53_L 0.84 0.55 0.36
37_L 30_R 0.83 0.55 0.36
19_V 83_Y 0.83 0.54 0.35
72_G 7_D 0.82 0.54 0.35
61_R 13_D 0.82 0.53 0.34
36_V 55_G 0.82 0.53 0.34
65_A 56_Y 0.81 0.51 0.32
41_D 9_D 0.78 0.47 0.29
8_A 6_F 0.77 0.46 0.28
32_A 19_A 0.77 0.46 0.28
78_K 6_F 0.77 0.46 0.28
12_L 53_L 0.77 0.45 0.28
7_E 35_I 0.76 0.45 0.27
65_A 53_L 0.76 0.44 0.27
30_S 81_A 0.74 0.42 0.25
4_S 21_D 0.73 0.40 0.23
52_L 82_R 0.71 0.38 0.22
46_W 41_S 0.70 0.37 0.21
64_E 4_V 0.70 0.37 0.21
74_S 79_L 0.70 0.36 0.21
76_F 6_F 0.70 0.36 0.21
18_Q 15_L 0.69 0.36 0.20
20_N 27_R 0.68 0.35 0.19
25_P 39_P 0.68 0.35 0.19
70_K 19_A 0.68 0.34 0.19
79_S 14_F 0.67 0.33 0.18
26_V 68_V 0.67 0.33 0.18
42_D 63_D 0.66 0.32 0.17
42_D 64_E 0.66 0.32 0.17
36_V 53_L 0.65 0.31 0.16
65_A 80_K 0.65 0.30 0.16
69_D 5_N 0.64 0.30 0.16
65_A 79_L 0.64 0.29 0.15
41_D 80_K 0.63 0.28 0.15
62_L 56_Y 0.63 0.28 0.15
17_E 81_A 0.62 0.28 0.14
8_A 39_P 0.62 0.27 0.14
58_N 82_R 0.62 0.27 0.14
33_G 39_P 0.62 0.27 0.14
53_L 11_W 0.61 0.26 0.13
31_R 23_K 0.61 0.26 0.13
68_R 12_E 0.60 0.25 0.13
57_E 45_K 0.60 0.25 0.12
50_V 67_L 0.59 0.24 0.12
15_L 51_G 0.58 0.23 0.11
73_H 72_G 0.58 0.23 0.11
82_E 22_R 0.58 0.23 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)
Page generated in 0.0292 seconds.