May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
1kf6_1_C_D
Genes: A B A+B
Length: 130 119 248
Sequences: 156 147 148
Seq/Len: 1.2 1.24 0.6
MirrorTree (Pazo et al. 2001) 0.91
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 0.07 0.07 0.59
2 0.07 0.07 0.59
5 0.07 0.07 0.59
10 0.07 0.07 0.59
20 0.07 0.07 0.59
100 0.07 0.07 0.59
∞ 0.07 0.07 0.59
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
36_V 79_G 2.01 0.89 0.35
46_L 33_I 1.78 0.80 0.21
26_M 90_L 1.56 0.66 0.12
111_S 31_V 1.56 0.66 0.12
47_F 38_I 1.52 0.63 0.10
109_I 16_G 1.44 0.57 0.08
68_I 91_K 1.43 0.56 0.08
33_V 83_M 1.43 0.56 0.08
56_W 98_K 1.43 0.56 0.08
54_E 110_V 1.36 0.51 0.07
16_W 37_G 1.36 0.51 0.06
4_R 88_H 1.35 0.50 0.06
83_T 25_S 1.35 0.50 0.06
62_F 91_K 1.34 0.49 0.06
83_T 14_F 1.33 0.49 0.06
56_W 77_W 1.33 0.48 0.06
49_L 52_Y 1.27 0.44 0.05
30_G 83_M 1.24 0.41 0.04
4_R 77_W 1.24 0.41 0.04
53_P 53_E 1.24 0.41 0.04
80_L 51_S 1.24 0.41 0.04
6_P 77_W 1.19 0.37 0.04
86_W 23_M 1.19 0.37 0.04
15_W 81_H 1.18 0.37 0.04
123_I 31_V 1.18 0.36 0.03
96_I 24_W 1.15 0.34 0.03
9_R 58_F 1.15 0.34 0.03
119_A 117_V 1.14 0.34 0.03
22_Y 69_F 1.14 0.34 0.03
59_F 65_R 1.14 0.33 0.03
127_A 68_L 1.13 0.33 0.03
86_W 14_F 1.12 0.32 0.03
90_A 14_F 1.10 0.30 0.03
104_G 45_F 1.09 0.30 0.03
119_A 28_I 1.09 0.30 0.03
91_P 26_A 1.09 0.30 0.03
94_A 68_L 1.09 0.30 0.02
16_W 9_S 1.08 0.29 0.02
39_S 29_A 1.07 0.29 0.02
6_P 13_V 1.07 0.29 0.02
93_A 29_A 1.07 0.29 0.02
117_V 62_F 1.06 0.28 0.02
36_V 27_I 1.05 0.27 0.02
34_P 91_K 1.05 0.27 0.02
5_K 117_V 1.05 0.27 0.02
34_P 84_H 1.04 0.27 0.02
72_N 35_L 1.04 0.27 0.02
90_A 78_C 1.04 0.27 0.02
93_A 86_A 1.04 0.27 0.02
122_V 44_L 1.04 0.27 0.02
12_T 105_A 1.03 0.26 0.02
28_R 11_E 1.02 0.26 0.02
75_T 78_C 1.02 0.26 0.02
30_G 23_M 1.02 0.26 0.02
113_W 91_K 1.02 0.25 0.02
90_A 23_M 1.02 0.25 0.02
125_F 62_F 1.02 0.25 0.02
5_K 16_G 1.01 0.25 0.02
112_L 27_I 1.01 0.25 0.02
30_G 107_I 1.01 0.25 0.02
4_R 84_H 1.00 0.24 0.02
38_F 36_V 0.99 0.24 0.02
10_P 106_A 0.99 0.24 0.02
69_V 99_W 0.99 0.24 0.02
45_G 64_G 0.98 0.23 0.02
48_A 36_V 0.98 0.23 0.02
82_H 22_G 0.97 0.23 0.02
32_A 119_I 0.97 0.23 0.02
38_F 91_K 0.97 0.23 0.02
48_A 106_A 0.97 0.23 0.01
56_W 52_Y 0.97 0.23 0.01
59_F 118_T 0.97 0.22 0.01
86_W 86_A 0.96 0.22 0.01
121_I 113_L 0.96 0.22 0.01
8_V 7_K 0.96 0.22 0.01
1_T 95_P 0.95 0.22 0.01
86_W 72_I 0.95 0.22 0.01
82_H 74_L 0.95 0.21 0.01
2_T 19_G 0.95 0.21 0.01
49_L 89_D 0.95 0.21 0.01
70_I 112_T 0.94 0.21 0.01
39_S 23_M 0.94 0.21 0.01
31_T 79_G 0.94 0.21 0.01
86_W 25_S 0.94 0.21 0.01
98_V 51_S 0.94 0.21 0.01
74_I 54_R 0.94 0.21 0.01
89_L 11_E 0.94 0.21 0.01
112_L 78_C 0.94 0.21 0.01
81_L 68_L 0.93 0.20 0.01
39_S 14_F 0.93 0.20 0.01
31_T 33_I 0.93 0.20 0.01
47_F 106_A 0.92 0.20 0.01
43_I 25_S 0.92 0.20 0.01
121_I 34_L 0.91 0.20 0.01
83_T 16_G 0.91 0.19 0.01
11_M 119_I 0.91 0.19 0.01
22_Y 66_V 0.91 0.19 0.01
82_H 23_M 0.91 0.19 0.01
77_A 113_L 0.91 0.19 0.01
63_L 9_S 0.90 0.19 0.01
9_R 77_W 0.90 0.19 0.01
48_A 116_V 0.90 0.19 0.01
62_F 116_V 0.90 0.19 0.01
17_K 119_I 0.90 0.19 0.01
123_I 53_E 0.89 0.18 0.01
62_F 36_V 0.89 0.18 0.01
38_F 116_V 0.89 0.18 0.01
95_N 14_F 0.89 0.18 0.01
46_L 57_A 0.89 0.18 0.01
113_W 84_H 0.89 0.18 0.01
73_L 96_A 0.89 0.18 0.01
61_D 42_L 0.89 0.18 0.01
78_A 95_P 0.89 0.18 0.01
45_G 89_D 0.89 0.18 0.01
33_V 62_F 0.88 0.18 0.01
6_P 111_V 0.88 0.18 0.01
16_W 75_P 0.88 0.18 0.01
58_G 109_T 0.88 0.18 0.01
56_W 16_G 0.88 0.18 0.01
26_M 86_A 0.88 0.18 0.01
41_E 37_G 0.87 0.17 0.01
5_K 34_L 0.87 0.17 0.01
114_A 61_S 0.87 0.17 0.01
65_N 70_L 0.87 0.17 0.01
86_W 19_G 0.86 0.17 0.01
23_R 39_L 0.86 0.17 0.01
34_P 83_M 0.86 0.17 0.01
91_P 17_L 0.86 0.17 0.01
81_L 42_L 0.86 0.17 0.01
50_K 100_V 0.86 0.17 0.01
38_F 84_H 0.86 0.17 0.01
12_T 5_N 0.86 0.17 0.01
67_V 109_T 0.86 0.17 0.01
28_R 39_L 0.85 0.17 0.01
75_T 17_L 0.85 0.17 0.01
63_L 14_F 0.85 0.17 0.01
30_G 35_L 0.85 0.17 0.01
48_A 6_P 0.85 0.17 0.01
13_S 59_A 0.85 0.16 0.01
41_E 69_F 0.85 0.16 0.01
35_A 78_C 0.85 0.16 0.01
33_V 38_I 0.85 0.16 0.01
31_T 68_L 0.84 0.16 0.01
103_M 68_L 0.84 0.16 0.01
33_V 34_L 0.84 0.16 0.01
115_V 27_I 0.84 0.16 0.01
114_A 109_T 0.84 0.16 0.01
119_A 112_T 0.84 0.16 0.01
113_W 75_P 0.84 0.16 0.01
40_I 28_I 0.84 0.16 0.01
118_V 57_A 0.83 0.16 0.01
48_A 91_K 0.83 0.16 0.01
124_L 88_H 0.83 0.16 0.01
18_K 87_M 0.83 0.16 0.01
125_F 7_K 0.83 0.16 0.01
126_V 68_L 0.83 0.16 0.01
86_W 74_L 0.83 0.15 0.01
21_F 88_H 0.82 0.15 0.01
45_G 88_H 0.82 0.15 0.01
11_M 93_H 0.82 0.15 0.01
62_F 6_P 0.82 0.15 0.01
36_V 61_S 0.82 0.15 0.01
122_V 86_A 0.82 0.15 0.01
73_L 115_G 0.82 0.15 0.01
86_W 78_C 0.82 0.15 0.01
89_L 16_G 0.82 0.15 0.01
105_P 76_L 0.81 0.15 0.01
7_Y 8_R 0.81 0.15 0.01
41_E 43_G 0.81 0.15 0.01
82_H 30_P 0.81 0.15 0.01
56_W 67_F 0.81 0.15 0.01
30_G 109_T 0.81 0.15 0.01
91_P 87_M 0.81 0.15 0.01
22_Y 11_E 0.81 0.15 0.01
46_L 69_F 0.81 0.15 0.01
21_F 58_F 0.81 0.15 0.01
52_G 22_G 0.81 0.15 0.01
93_A 70_L 0.81 0.15 0.01
11_M 8_R 0.81 0.15 0.01
74_I 71_M 0.80 0.14 0.01
118_V 37_G 0.80 0.14 0.01
32_A 86_A 0.80 0.14 0.01
93_A 24_W 0.80 0.14 0.01
12_T 80_L 0.80 0.14 0.01
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 0.5548 seconds.