May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
L33-vs-S10
Genes: A B A+B
Length: 55 103 153
Sequences: 1895 1460 672
Seq/Len: 34.45 14.17 4.39
MirrorTree (Pazo et al. 2001) 0.44
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 0.08 0.09 0.01
2 0.08 0.09 0.01
5 0.08 0.09 0.06
10 0.08 0.09 0.12
20 0.08 0.09 1.03
100 0.10 0.09 2.15
∞ 0.13 0.09 4.25
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
33_K 46_K 1.55 0.98 0.87
7_E 18_I 1.29 0.94 0.71
44_R 94_A 1.27 0.93 0.69
22_T 102_L 1.03 0.79 0.45
53_K 18_I 0.96 0.72 0.37
30_K 13_F 0.95 0.71 0.36
41_P 18_I 0.94 0.69 0.35
44_R 73_L 0.83 0.55 0.24
36_L 55_P 0.82 0.54 0.23
33_K 98_V 0.82 0.53 0.23
44_R 22_T 0.81 0.52 0.22
46_H 12_A 0.79 0.50 0.20
45_Q 19_D 0.79 0.49 0.20
22_T 52_L 0.77 0.47 0.19
28_R 51_V 0.76 0.45 0.18
35_E 68_R 0.75 0.44 0.17
19_H 82_K 0.75 0.44 0.17
44_R 40_I 0.73 0.41 0.16
7_E 54_S 0.73 0.41 0.16
52_A 75_D 0.73 0.41 0.15
42_V 47_E 0.72 0.40 0.15
52_A 16_R 0.72 0.40 0.15
19_H 83_T 0.72 0.39 0.15
14_S 74_V 0.71 0.38 0.14
11_L 62_R 0.69 0.36 0.13
37_K 85_D 0.69 0.36 0.13
27_K 36_V 0.69 0.36 0.13
40_D 65_Y 0.69 0.36 0.13
27_K 78_E 0.68 0.35 0.13
12_V 61_A 0.67 0.34 0.12
33_K 53_I 0.66 0.33 0.12
20_F 63_D 0.66 0.33 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 0.2263 seconds.