May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
GREM
Genes: A B A+B
Length: 131 119 249
Sequences: 152 147 146
Seq/Len: 1.16 1.24 0.59
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 0.58
2 0.07 0.07 0.58
5 0.07 0.07 0.58
10 0.07 0.07 0.58
20 0.07 0.07 0.58
100 0.07 0.07 0.58
∞ 0.07 0.07 0.58
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
37_V 79_G 1.93 0.86 0.19
47_L 33_I 1.74 0.77 0.12
112_S 31_V 1.63 0.71 0.09
27_M 90_L 1.58 0.67 0.08
55_E 110_V 1.49 0.61 0.06
57_W 98_K 1.44 0.57 0.05
110_I 16_G 1.43 0.55 0.05
69_I 91_K 1.41 0.55 0.05
34_V 83_M 1.37 0.51 0.04
5_R 88_H 1.37 0.51 0.04
17_W 37_G 1.36 0.50 0.04
48_F 38_I 1.35 0.50 0.04
84_T 25_S 1.34 0.48 0.04
84_T 14_F 1.33 0.48 0.04
63_F 91_K 1.31 0.47 0.03
97_I 24_W 1.30 0.46 0.03
81_L 51_S 1.29 0.45 0.03
57_W 77_W 1.28 0.44 0.03
31_G 83_M 1.24 0.41 0.03
5_R 77_W 1.23 0.40 0.03
50_L 52_Y 1.21 0.38 0.02
68_V 109_T 1.20 0.38 0.02
118_V 62_F 1.20 0.37 0.02
105_G 45_F 1.17 0.35 0.02
16_W 81_H 1.17 0.35 0.02
128_A 68_L 1.16 0.35 0.02
7_P 77_W 1.16 0.35 0.02
94_A 86_A 1.16 0.35 0.02
23_Y 69_F 1.14 0.33 0.02
60_F 65_R 1.14 0.33 0.02
10_R 58_F 1.13 0.33 0.02
37_V 27_I 1.13 0.32 0.02
87_W 14_F 1.12 0.32 0.02
91_A 23_M 1.12 0.32 0.02
91_A 14_F 1.11 0.31 0.02
7_P 13_V 1.11 0.31 0.02
120_A 117_V 1.10 0.30 0.02
92_P 26_A 1.10 0.30 0.02
87_W 23_M 1.09 0.30 0.02
6_K 117_V 1.09 0.29 0.02
82_L 68_L 1.08 0.29 0.01
54_P 53_E 1.07 0.29 0.01
124_I 31_V 1.06 0.28 0.01
17_W 9_S 1.06 0.28 0.01
95_A 68_L 1.05 0.27 0.01
91_A 78_C 1.05 0.27 0.01
13_T 105_A 1.04 0.27 0.01
70_V 99_W 1.04 0.27 0.01
76_T 78_C 1.04 0.26 0.01
113_L 27_I 1.03 0.26 0.01
73_N 35_L 1.02 0.25 0.01
29_R 11_E 1.02 0.25 0.01
87_W 86_A 1.02 0.25 0.01
123_V 100_V 1.02 0.25 0.01
68_V 34_L 1.01 0.25 0.01
119_V 57_A 1.01 0.24 0.01
6_K 16_G 1.01 0.24 0.01
35_P 91_K 1.01 0.24 0.01
34_V 62_F 1.00 0.24 0.01
5_R 84_H 1.00 0.24 0.01
122_I 113_L 1.00 0.24 0.01
31_G 107_I 0.99 0.24 0.01
23_Y 66_V 0.99 0.24 0.01
40_S 29_A 0.99 0.23 0.01
114_W 91_K 0.99 0.23 0.01
49_A 36_V 0.98 0.23 0.01
35_P 84_H 0.98 0.23 0.01
40_S 23_M 0.98 0.23 0.01
9_V 7_K 0.98 0.23 0.01
83_H 22_G 0.98 0.23 0.01
12_M 119_I 0.98 0.23 0.01
46_G 64_G 0.98 0.23 0.01
62_D 42_L 0.97 0.23 0.01
87_W 72_I 0.96 0.22 0.01
39_F 36_V 0.96 0.22 0.01
75_I 54_R 0.96 0.22 0.01
123_V 44_L 0.95 0.21 0.01
78_A 113_L 0.95 0.21 0.01
88_F 105_A 0.95 0.21 0.01
50_L 89_D 0.95 0.21 0.01
11_P 106_A 0.94 0.21 0.01
94_A 29_A 0.94 0.21 0.01
32_T 79_G 0.94 0.21 0.01
3_T 19_G 0.94 0.21 0.01
90_L 11_E 0.94 0.21 0.01
87_W 25_S 0.94 0.21 0.01
39_F 91_K 0.94 0.20 0.01
49_A 106_A 0.92 0.20 0.01
40_S 14_F 0.92 0.20 0.01
18_K 119_I 0.92 0.20 0.01
10_R 77_W 0.92 0.20 0.01
104_M 68_L 0.92 0.20 0.01
31_G 23_M 0.92 0.20 0.01
59_G 109_T 0.92 0.19 0.01
99_V 51_S 0.92 0.19 0.01
113_L 78_C 0.91 0.19 0.01
53_G 57_A 0.91 0.19 0.01
60_F 118_T 0.91 0.19 0.01
83_H 74_L 0.91 0.19 0.01
14_S 59_A 0.91 0.19 0.01
57_W 16_G 0.91 0.19 0.01
13_T 5_N 0.90 0.19 0.01
76_T 17_L 0.90 0.18 0.01
57_W 52_Y 0.90 0.18 0.01
63_F 116_V 0.89 0.18 0.01
64_L 9_S 0.89 0.18 0.01
17_W 75_P 0.88 0.18 0.01
2_T 95_P 0.88 0.18 0.01
39_F 116_V 0.88 0.18 0.01
125_L 88_H 0.88 0.18 0.01
87_W 19_G 0.88 0.18 0.01
79_A 38_I 0.88 0.18 0.01
46_G 89_D 0.88 0.18 0.01
32_T 33_I 0.88 0.18 0.01
27_M 86_A 0.88 0.17 0.01
115_A 61_S 0.88 0.17 0.01
49_A 116_V 0.87 0.17 0.01
37_V 97_G 0.87 0.17 0.01
33_A 119_I 0.87 0.17 0.01
82_L 42_L 0.87 0.17 0.01
63_F 36_V 0.87 0.17 0.01
7_P 111_V 0.87 0.17 0.01
24_R 39_L 0.87 0.17 0.01
90_L 16_G 0.87 0.17 0.01
84_T 16_G 0.87 0.17 0.01
81_L 34_L 0.87 0.17 0.01
109_I 107_I 0.86 0.17 0.01
74_L 96_A 0.86 0.17 0.01
49_A 53_E 0.86 0.17 0.01
12_M 93_H 0.86 0.17 0.01
114_W 84_H 0.86 0.17 0.01
42_E 69_F 0.86 0.17 0.01
42_E 37_G 0.86 0.17 0.01
35_P 83_M 0.86 0.17 0.01
126_F 7_K 0.86 0.17 0.01
79_A 95_P 0.86 0.17 0.01
48_F 106_A 0.86 0.17 0.01
96_N 14_F 0.85 0.17 0.01
29_R 39_L 0.85 0.16 0.01
87_W 78_C 0.85 0.16 0.01
114_W 75_P 0.85 0.16 0.01
64_L 14_F 0.84 0.16 0.01
8_Y 8_R 0.84 0.16 0.01
19_K 87_M 0.84 0.16 0.01
49_A 6_P 0.84 0.16 0.01
71_I 112_T 0.84 0.16 0.01
94_A 70_L 0.84 0.16 0.01
42_E 43_G 0.84 0.16 0.01
39_F 84_H 0.84 0.16 0.01
44_I 25_S 0.83 0.16 0.01
58_A 57_A 0.83 0.16 0.01
31_G 86_A 0.83 0.16 0.01
71_I 38_I 0.83 0.16 0.01
99_V 87_M 0.83 0.15 0.01
32_T 68_L 0.83 0.15 0.01
51_K 100_V 0.83 0.15 0.01
31_G 35_L 0.83 0.15 0.01
127_V 68_L 0.83 0.15 0.01
12_M 8_R 0.82 0.15 0.01
115_A 109_T 0.82 0.15 0.01
37_V 61_S 0.82 0.15 0.01
83_H 23_M 0.82 0.15 0.01
6_K 34_L 0.82 0.15 0.01
5_R 8_R 0.82 0.15 0.01
89_E 107_I 0.82 0.15 0.01
36_A 78_C 0.82 0.15 0.01
8_Y 9_S 0.82 0.15 0.01
94_A 23_M 0.81 0.15 0.01
92_P 87_M 0.81 0.15 0.01
46_G 88_H 0.81 0.15 0.01
92_P 17_L 0.81 0.15 0.01
87_W 74_L 0.81 0.15 0.01
49_A 91_K 0.81 0.15 0.01
49_A 42_L 0.81 0.15 0.01
63_F 6_P 0.81 0.15 0.01
122_I 34_L 0.81 0.15 0.01
83_H 30_P 0.81 0.14 0.01
106_P 76_L 0.81 0.14 0.01
12_M 106_A 0.81 0.14 0.01
120_A 112_T 0.80 0.14 0.01
107_E 44_L 0.80 0.14 0.01
22_F 88_H 0.80 0.14 0.01
6_K 72_I 0.80 0.14 0.01
72_I 44_L 0.80 0.14 0.01
94_A 24_W 0.80 0.14 0.01
123_V 86_A 0.79 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 0.2479 seconds.