May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
du
Genes: A B A+B
Length: 158 153 311
Sequences: 734 5080 209
Seq/Len: 4.65 33.2 0.67
MirrorTree (Pazo et al. 2001) 0.52
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 0.00 0.01 0.67
2 0.00 0.01 0.68
5 0.00 0.01 0.68
10 0.00 0.02 0.69
20 0.00 0.02 0.71
100 0.00 0.05 0.78
∞ 0.00 0.14 1.23
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
73_T 1_P 1.42 0.59 0.00
78_P 144_P 1.27 0.46 0.00
88_N 109_M 1.26 0.46 0.00
62_Y 109_M 1.25 0.45 0.00
27_D 80_A 1.20 0.41 0.00
74_E 96_V 1.20 0.41 0.00
98_V 63_L 1.15 0.37 0.00
8_R 40_L 1.14 0.36 0.00
24_A 78_V 1.14 0.36 0.00
23_P 98_V 1.13 0.36 0.00
73_T 72_T 1.09 0.32 0.00
154_R 95_T 1.07 0.31 0.00
36_K 66_K 1.07 0.31 0.00
151_R 144_P 1.06 0.30 0.00
150_K 83_W 1.06 0.30 0.00
125_L 81_C 1.05 0.30 0.00
85_S 105_A 1.05 0.29 0.00
33_D 108_V 1.04 0.29 0.00
128_T 103_T 1.04 0.29 0.00
121_A 122_P 1.03 0.28 0.00
35_A 95_T 1.02 0.28 0.00
11_W 1_P 1.02 0.27 0.00
115_D 82_R 1.00 0.26 0.00
77_A 5_A 1.00 0.26 0.00
125_L 115_V 1.00 0.26 0.00
117_P 98_V 0.98 0.25 0.00
124_A 38_R 0.98 0.25 0.00
84_F 119_R 0.98 0.25 0.00
29_A 11_M 0.97 0.24 0.00
3_F 11_M 0.96 0.24 0.00
46_K 100_L 0.96 0.24 0.00
31_A 24_A 0.94 0.23 0.00
53_R 23_L 0.94 0.23 0.00
59_K 109_M 0.94 0.22 0.00
144_M 120_G 0.94 0.22 0.00
79_F 119_R 0.94 0.22 0.00
62_Y 71_K 0.93 0.22 0.00
8_R 36_F 0.93 0.22 0.00
141_P 126_P 0.93 0.22 0.00
87_M 22_D 0.92 0.21 0.00
55_E 1_P 0.91 0.21 0.00
62_Y 118_T 0.91 0.21 0.00
139_L 109_M 0.91 0.21 0.00
41_A 61_H 0.91 0.21 0.00
151_R 80_A 0.90 0.20 0.00
107_V 132_L 0.90 0.20 0.00
52_R 61_H 0.90 0.20 0.00
33_D 48_E 0.90 0.20 0.00
23_P 36_F 0.89 0.20 0.00
101_N 123_L 0.89 0.20 0.00
10_L 81_C 0.89 0.20 0.00
41_A 72_T 0.89 0.20 0.00
156_L 9_P 0.88 0.19 0.00
100_W 118_T 0.88 0.19 0.00
42_A 100_L 0.88 0.19 0.00
145_R 100_L 0.87 0.19 0.00
150_K 106_F 0.87 0.19 0.00
38_V 149_R 0.86 0.18 0.00
121_A 62_E 0.85 0.18 0.00
115_D 105_A 0.85 0.18 0.00
20_I 1_P 0.85 0.18 0.00
77_A 51_Y 0.84 0.17 0.00
121_A 35_I 0.84 0.17 0.00
37_A 100_L 0.84 0.17 0.00
105_L 93_R 0.84 0.17 0.00
74_E 132_L 0.83 0.17 0.00
104_R 97_I 0.83 0.17 0.00
122_Q 108_V 0.83 0.17 0.00
140_N 152_A 0.83 0.17 0.00
60_E 96_V 0.83 0.17 0.00
30_R 152_A 0.82 0.16 0.00
81_A 35_I 0.82 0.16 0.00
73_T 42_E 0.82 0.16 0.00
127_R 97_I 0.82 0.16 0.00
10_L 7_S 0.82 0.16 0.00
88_N 80_A 0.82 0.16 0.00
14_E 112_P 0.82 0.16 0.00
3_F 81_C 0.81 0.16 0.00
116_A 96_V 0.81 0.16 0.00
17_P 134_T 0.81 0.16 0.00
108_S 149_R 0.81 0.16 0.00
146_Q 150_E 0.81 0.16 0.00
74_E 7_S 0.81 0.16 0.00
111_A 82_R 0.81 0.16 0.00
96_V 126_P 0.81 0.16 0.00
156_L 93_R 0.81 0.16 0.00
147_E 75_Q 0.80 0.15 0.00
74_E 122_P 0.80 0.15 0.00
111_A 24_A 0.80 0.15 0.00
146_Q 140_L 0.80 0.15 0.00
23_P 12_F 0.79 0.15 0.00
142_R 95_T 0.79 0.15 0.00
106_W 35_I 0.79 0.15 0.00
45_M 54_N 0.79 0.15 0.00
21_E 126_P 0.79 0.15 0.00
92_L 109_M 0.79 0.15 0.00
27_D 93_R 0.79 0.15 0.00
141_P 72_T 0.79 0.15 0.00
10_L 8_A 0.79 0.15 0.00
15_R 86_D 0.79 0.15 0.00
36_K 60_K 0.79 0.15 0.00
30_R 50_T 0.79 0.15 0.00
117_P 10_L 0.79 0.15 0.00
77_A 47_R 0.78 0.15 0.00
88_N 105_A 0.78 0.15 0.00
84_F 61_H 0.78 0.14 0.00
125_L 85_L 0.78 0.14 0.00
56_D 146_A 0.78 0.14 0.00
34_M 9_P 0.78 0.14 0.00
45_M 66_K 0.78 0.14 0.00
110_G 105_A 0.77 0.14 0.00
100_W 123_L 0.77 0.14 0.00
57_A 24_A 0.77 0.14 0.00
4_A 92_V 0.77 0.14 0.00
109_E 116_R 0.77 0.14 0.00
50_R 59_F 0.76 0.14 0.00
76_T 91_L 0.76 0.14 0.00
101_N 146_A 0.76 0.14 0.00
124_A 103_T 0.76 0.14 0.00
35_A 121_R 0.76 0.14 0.00
49_V 87_A 0.76 0.14 0.00
100_W 39_A 0.76 0.14 0.00
136_P 59_F 0.76 0.14 0.00
117_P 110_G 0.76 0.14 0.00
66_F 83_W 0.76 0.14 0.00
145_R 38_R 0.76 0.14 0.00
44_K 83_W 0.75 0.14 0.00
2_R 149_R 0.75 0.13 0.00
109_E 36_F 0.75 0.13 0.00
81_A 74_T 0.75 0.13 0.00
37_A 138_S 0.75 0.13 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)
ID Seq/Len Name Options I_Prob Status
7836 1.23 du Δgene:(0, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.01 Done
7832 0.67 du Δgene:(0, 0) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done
7831 0 DUF Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) Killed - Shared
7829 0.02 DUF Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
Page generated in 0.0721 seconds.