May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
3i1o_J_N
Genes: A B A+B
Length: 103 101 201
Sequences: 1166 1732 423
Seq/Len: 11.32 17.15 2.1
MirrorTree (Pazo et al. 2001) 0.70
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 0.09 0.09 0.01
2 0.09 0.09 0.01
5 0.09 0.09 0.02
10 0.09 0.09 0.12
20 0.09 0.09 2.07
100 0.09 0.09 2.39
∞ 0.09 0.09 3.23
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
48_R 99_A 2.79 1.00 1.00
50_T 74_L 1.70 0.96 0.92
60_D 89_M 1.59 0.94 0.89
89_R 54_D 1.44 0.89 0.81
56_H 55_S 1.39 0.87 0.78
64_Q 93_I 1.37 0.86 0.77
47_E 76_K 1.36 0.86 0.76
13_F 29_A 1.33 0.84 0.73
80_T 79_L 1.26 0.79 0.67
53_I 87_A 1.22 0.76 0.63
52_L 10_E 1.22 0.76 0.63
63_D 89_M 1.19 0.73 0.60
67_I 96_L 1.17 0.71 0.58
18_I 74_L 1.17 0.71 0.57
65_Y 89_M 1.15 0.69 0.55
63_D 10_E 1.14 0.69 0.54
22_T 80_S 1.09 0.64 0.49
58_N 83_K 1.09 0.63 0.48
58_N 72_G 1.08 0.62 0.47
22_T 55_S 1.04 0.58 0.42
69_T 70_P 1.04 0.58 0.42
22_T 6_M 1.03 0.57 0.41
52_L 4_Q 1.01 0.54 0.39
74_V 97_K 1.00 0.54 0.39
20_Q 72_G 1.00 0.54 0.38
53_I 96_L 0.98 0.52 0.36
20_Q 97_K 0.97 0.50 0.34
66_E 61_R 0.95 0.49 0.33
60_D 87_A 0.95 0.48 0.33
12_A 73_F 0.94 0.47 0.31
77_V 92_E 0.93 0.46 0.30
61_A 87_A 0.93 0.46 0.30
55_P 11_V 0.92 0.45 0.29
81_E 89_M 0.92 0.44 0.29
58_N 6_M 0.91 0.44 0.28
66_E 99_A 0.91 0.43 0.28
65_Y 87_A 0.90 0.43 0.28
61_A 83_K 0.90 0.43 0.27
18_I 49_Q 0.88 0.40 0.25
18_I 12_K 0.87 0.40 0.24
60_D 6_M 0.87 0.40 0.24
74_V 98_K 0.87 0.39 0.24
17_L 12_K 0.87 0.39 0.24
38_G 94_P 0.86 0.39 0.24
79_P 76_K 0.86 0.39 0.23
52_L 34_V 0.85 0.38 0.23
78_E 21_F 0.85 0.38 0.23
64_Q 82_I 0.85 0.37 0.22
61_A 89_M 0.85 0.37 0.22
77_V 58_S 0.84 0.36 0.22
70_H 88_A 0.84 0.36 0.22
17_L 49_Q 0.84 0.36 0.21
58_N 55_S 0.83 0.35 0.21
40_I 53_R 0.83 0.35 0.21
45_R 21_F 0.83 0.35 0.20
18_I 92_E 0.82 0.34 0.20
57_V 43_N 0.81 0.33 0.19
40_I 96_L 0.80 0.32 0.18
53_I 82_I 0.80 0.32 0.18
20_Q 99_A 0.80 0.32 0.18
49_F 62_N 0.79 0.31 0.17
73_L 18_D 0.79 0.31 0.17
65_Y 88_A 0.79 0.30 0.17
77_V 21_F 0.78 0.30 0.16
101_S 72_G 0.78 0.30 0.16
22_T 57_P 0.78 0.30 0.16
46_K 66_Q 0.78 0.30 0.16
18_I 87_A 0.77 0.29 0.16
58_N 67_T 0.77 0.29 0.16
27_E 89_M 0.77 0.29 0.16
53_I 89_M 0.77 0.29 0.16
96_V 53_R 0.77 0.29 0.15
84_V 76_K 0.76 0.28 0.15
46_K 71_H 0.76 0.28 0.15
63_D 9_R 0.76 0.28 0.15
39_P 94_P 0.75 0.28 0.14
18_I 83_K 0.75 0.28 0.14
37_R 80_S 0.75 0.28 0.14
13_F 43_N 0.75 0.27 0.14
101_S 42_W 0.75 0.27 0.14
92_L 94_P 0.75 0.27 0.14
91_D 84_V 0.75 0.27 0.14
13_F 8_A 0.74 0.27 0.14
17_L 9_R 0.74 0.27 0.14
8_I 70_P 0.74 0.27 0.14
74_V 89_M 0.74 0.26 0.14
45_R 23_K 0.74 0.26 0.13
61_A 92_E 0.74 0.26 0.13
57_V 78_G 0.73 0.26 0.13
67_I 11_V 0.73 0.26 0.13
64_Q 87_A 0.73 0.26 0.13
61_A 6_M 0.73 0.26 0.13
69_T 76_K 0.73 0.25 0.13
65_Y 10_E 0.73 0.25 0.13
12_A 18_D 0.73 0.25 0.13
37_R 50_T 0.73 0.25 0.13
5_R 75_R 0.73 0.25 0.13
35_Q 12_K 0.73 0.25 0.13
17_L 19_K 0.73 0.25 0.13
39_P 44_A 0.72 0.25 0.12
53_I 60_Q 0.72 0.25 0.12
62_R 74_L 0.72 0.25 0.12
100_I 13_R 0.72 0.25 0.12
18_I 89_M 0.72 0.24 0.12
58_N 71_H 0.72 0.24 0.12
63_D 58_S 0.71 0.24 0.12
95_G 99_A 0.71 0.24 0.12
89_R 12_K 0.71 0.24 0.12
56_H 51_L 0.71 0.24 0.12
86_A 28_K 0.71 0.24 0.12
59_K 69_R 0.71 0.24 0.12
46_K 10_E 0.71 0.24 0.12
30_K 91_G 0.71 0.24 0.12
71_L 73_F 0.70 0.23 0.11
61_A 96_L 0.70 0.23 0.11
3_N 26_E 0.70 0.23 0.11
12_A 87_A 0.70 0.23 0.11
101_S 66_Q 0.70 0.23 0.11
87_L 2_A 0.70 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)
ID Seq/Len Name Options I_Prob Status
7673 2.1 3i1o_J_N Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done - Shared
2502 1.96 S10_S14_test Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 1.00 Done
Page generated in 0.0235 seconds.