May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
C_E
Genes: A B A+B
Length: 226 228 439
Sequences: 132 109 93
Seq/Len: 0.58 0.48 0.21
MirrorTree (Pazo et al. 2001) 0.70
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 0.00 0.00 0.00
2 0.00 0.00 0.20
5 0.00 0.00 0.20
10 0.00 0.00 0.20
20 0.00 0.00 0.20
100 0.00 0.00 0.20
∞ 0.00 0.00 0.20
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
59_A 152_S 1.47 0.32 0.00
188_S 152_S 1.37 0.27 0.00
154_S 99_T 1.37 0.26 0.00
141_G 115_I 1.35 0.25 0.00
134_L 186_L 1.28 0.23 0.00
61_S 20_R 1.28 0.23 0.00
179_G 165_H 1.27 0.22 0.00
130_Q 14_L 1.25 0.21 0.00
105_A 21_F 1.25 0.21 0.00
111_A 21_F 1.16 0.18 0.00
148_S 162_I 1.15 0.17 0.00
48_N 121_G 1.15 0.17 0.00
76_G 76_N 1.11 0.16 0.00
71_I 185_V 1.10 0.16 0.00
148_S 45_T 1.09 0.15 0.00
136_I 167_N 1.08 0.15 0.00
186_N 156_G 1.08 0.15 0.00
84_V 54_I 1.07 0.15 0.00
62_G 162_I 1.07 0.15 0.00
48_N 188_G 1.05 0.14 0.00
71_I 221_K 1.05 0.14 0.00
109_N 186_L 1.04 0.14 0.00
66_D 186_L 1.04 0.14 0.00
29_N 89_G 1.04 0.14 0.00
77_D 163_A 1.02 0.13 0.00
12_P 39_T 1.02 0.13 0.00
85_A 150_S 1.02 0.13 0.00
39_N 149_V 1.01 0.13 0.00
16_V 124_P 1.00 0.13 0.00
136_I 92_S 1.00 0.13 0.00
87_I 39_T 1.00 0.13 0.00
26_S 58_T 0.99 0.12 0.00
95_K 45_T 0.99 0.12 0.00
104_N 170_N 0.99 0.12 0.00
89_Q 34_M 0.99 0.12 0.00
186_N 158_V 0.99 0.12 0.00
47_S 153_A 0.98 0.12 0.00
133_N 50_A 0.98 0.12 0.00
18_A 82_G 0.98 0.12 0.00
62_G 115_I 0.98 0.12 0.00
92_K 183_G 0.98 0.12 0.00
203_Q 14_L 0.97 0.12 0.00
123_A 170_N 0.97 0.12 0.00
59_A 51_N 0.97 0.12 0.00
56_N 18_R 0.96 0.12 0.00
41_G 177_G 0.96 0.12 0.00
10_P 39_T 0.96 0.12 0.00
78_A 163_A 0.95 0.12 0.00
61_S 99_T 0.95 0.12 0.00
157_N 66_Q 0.95 0.11 0.00
156_D 32_I 0.95 0.11 0.00
78_A 99_T 0.94 0.11 0.00
114_S 167_N 0.94 0.11 0.00
159_F 162_I 0.94 0.11 0.00
120_V 123_S 0.94 0.11 0.00
49_S 35_S 0.94 0.11 0.00
124_A 52_M 0.94 0.11 0.00
38_N 18_R 0.94 0.11 0.00
8_P 150_S 0.93 0.11 0.00
153_V 150_S 0.92 0.11 0.00
110_S 204_G 0.92 0.11 0.00
57_I 49_S 0.92 0.11 0.00
103_N 4_F 0.92 0.11 0.00
81_V 129_Q 0.91 0.10 0.00
101_T 96_V 0.91 0.10 0.00
70_A 156_G 0.90 0.10 0.00
46_L 14_L 0.90 0.10 0.00
21_T 166_N 0.90 0.10 0.00
39_N 66_Q 0.89 0.10 0.00
181_L 165_H 0.88 0.10 0.00
50_K 9_M 0.88 0.10 0.00
42_A 162_I 0.88 0.10 0.00
100_G 55_D 0.88 0.10 0.00
40_A 82_G 0.88 0.10 0.00
46_L 185_V 0.88 0.10 0.00
66_D 32_I 0.88 0.10 0.00
26_S 97_T 0.87 0.10 0.00
23_T 52_M 0.87 0.10 0.00
177_N 180_V 0.87 0.10 0.00
80_T 198_Q 0.87 0.10 0.00
43_N 166_N 0.87 0.10 0.00
22_D 101_R 0.87 0.10 0.00
53_L 9_M 0.87 0.10 0.00
14_G 214_N 0.86 0.09 0.00
101_T 193_V 0.86 0.09 0.00
39_N 209_N 0.86 0.09 0.00
42_A 106_G 0.86 0.09 0.00
73_S 146_A 0.86 0.09 0.00
139_A 48_V 0.85 0.09 0.00
79_A 39_T 0.85 0.09 0.00
56_N 34_M 0.85 0.09 0.00
139_A 209_N 0.85 0.09 0.00
62_G 32_I 0.84 0.09 0.00
161_N 100_V 0.84 0.09 0.00
66_D 167_N 0.84 0.09 0.00
163_A 9_M 0.84 0.09 0.00
170_K 142_T 0.84 0.09 0.00
111_A 194_N 0.83 0.09 0.00
115_S 99_T 0.83 0.09 0.00
44_G 207_G 0.83 0.09 0.00
138_T 119_E 0.83 0.09 0.00
36_T 17_L 0.83 0.09 0.00
103_N 21_F 0.83 0.09 0.00
123_A 178_G 0.83 0.09 0.00
158_H 15_A 0.83 0.09 0.00
32_D 160_M 0.83 0.09 0.00
74_S 21_F 0.83 0.09 0.00
36_T 24_P 0.83 0.09 0.00
106_L 45_T 0.82 0.09 0.00
13_T 225_T 0.82 0.09 0.00
64_Q 22_V 0.82 0.09 0.00
159_F 187_Q 0.82 0.09 0.00
58_A 14_L 0.82 0.09 0.00
87_I 209_N 0.82 0.09 0.00
65_Q 14_L 0.82 0.09 0.00
196_A 14_L 0.82 0.09 0.00
44_G 27_I 0.82 0.09 0.00
31_F 156_G 0.81 0.09 0.00
98_N 61_P 0.81 0.08 0.00
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 0.0404 seconds.