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OPENSEQ.org
1AHW_l_u_Apdb 1AHW_r_u_Lpdb
Genes: A B A+B
Length: 202 214 383
Sequences: 8616 12011 169
Seq/Len: 42.65 56.13 0.44
MirrorTree (Pazo et al. 2001) 0.25
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 0.14 0.12
2 0.08 0.17 0.17
5 0.09 0.20 0.23
10 0.10 0.21 0.32
20 0.10 0.23 0.41
100 0.12 0.26 0.72
∞ 0.16 0.27 0.90
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
83_P 151_D 1.74 0.69 0.01
116_V 155_R 1.66 0.64 0.01
180_V 134_C 1.57 0.58 0.00
32_V 21_I 1.46 0.49 0.00
57_D 151_D 1.44 0.48 0.00
32_V 78_L 1.36 0.42 0.00
180_V 193_T 1.33 0.40 0.00
146_L 78_L 1.30 0.38 0.00
176_Y 141_P 1.25 0.34 0.00
169_D 128_G 1.23 0.33 0.00
83_P 16_G 1.18 0.30 0.00
110_V 143_D 1.17 0.29 0.00
30_Y 91_H 1.17 0.29 0.00
180_V 194_C 1.15 0.28 0.00
85_Y 16_G 1.15 0.28 0.00
7_N 104_L 1.12 0.26 0.00
169_D 186_Y 1.11 0.26 0.00
57_D 200_T 1.11 0.25 0.00
121_E 35_W 1.11 0.25 0.00
93_P 106_I 1.10 0.25 0.00
168_I 71_Y 1.08 0.24 0.00
121_E 82_D 1.07 0.23 0.00
121_E 73_L 1.06 0.23 0.00
85_Y 41_W 1.06 0.23 0.00
180_V 123_E 1.06 0.23 0.00
21_W 35_W 1.05 0.23 0.00
93_P 88_C 1.04 0.22 0.00
53_C 28_D 1.04 0.22 0.00
19_L 137_N 1.04 0.22 0.00
48_T 21_I 1.04 0.22 0.00
65_Q 21_I 1.01 0.20 0.00
5_A 84_A 1.01 0.20 0.00
75_P 95_P 1.01 0.20 0.00
67_Y 84_A 1.01 0.20 0.00
178_F 153_S 1.00 0.20 0.00
101_Q 28_D 1.00 0.20 0.00
180_V 32_Y 0.99 0.19 0.00
21_W 194_C 0.98 0.19 0.00
19_L 70_D 0.97 0.19 0.00
66_T 144_I 0.97 0.19 0.00
75_P 192_Y 0.96 0.18 0.00
116_V 103_K 0.96 0.18 0.00
144_Y 148_W 0.96 0.18 0.00
144_Y 192_Y 0.96 0.18 0.00
55_L 91_H 0.95 0.18 0.00
32_V 62_F 0.95 0.18 0.00
146_L 100_G 0.95 0.17 0.00
41_W 128_G 0.94 0.17 0.00
19_L 106_I 0.93 0.17 0.00
25_P 86_Y 0.93 0.17 0.00
8_L 76_S 0.92 0.16 0.00
160_K 149_K 0.91 0.16 0.00
109_Q 131_S 0.91 0.16 0.00
19_L 127_S 0.91 0.16 0.00
141_D 159_V 0.91 0.16 0.00
123_T 106_I 0.90 0.15 0.00
83_P 143_D 0.90 0.15 0.00
176_Y 23_C 0.90 0.15 0.00
178_F 185_E 0.89 0.15 0.00
144_Y 82_D 0.89 0.15 0.00
170_V 148_W 0.89 0.15 0.00
32_V 193_T 0.88 0.15 0.00
160_K 179_L 0.88 0.15 0.00
150_K 81_D 0.88 0.15 0.00
116_V 90_Q 0.88 0.15 0.00
71_V 107_N 0.87 0.14 0.00
119_E 130_A 0.87 0.14 0.00
144_Y 73_L 0.87 0.14 0.00
28_Q 33_L 0.87 0.14 0.00
10_W 82_D 0.86 0.14 0.00
183_V 137_N 0.86 0.14 0.00
56_T 104_L 0.86 0.14 0.00
124_L 21_I 0.86 0.14 0.00
171_D 103_K 0.86 0.14 0.00
21_W 134_C 0.86 0.14 0.00
111_G 199_K 0.86 0.14 0.00
169_D 189_H 0.86 0.14 0.00
154_S 184_D 0.86 0.14 0.00
102_P 73_L 0.86 0.14 0.00
87_N 155_R 0.86 0.14 0.00
184_I 82_D 0.85 0.14 0.00
183_V 179_L 0.85 0.14 0.00
91_F 16_G 0.85 0.14 0.00
97_T 30_R 0.85 0.14 0.00
168_I 23_C 0.85 0.14 0.00
71_V 19_V 0.85 0.14 0.00
169_D 83_T 0.85 0.14 0.00
173_G 16_G 0.85 0.14 0.00
121_E 90_Q 0.84 0.14 0.00
168_I 8_P 0.84 0.13 0.00
141_D 187_E 0.84 0.13 0.00
69_A 127_S 0.84 0.13 0.00
141_D 111_A 0.84 0.13 0.00
157_K 149_K 0.84 0.13 0.00
69_A 79_E 0.84 0.13 0.00
194_T 41_W 0.84 0.13 0.00
19_L 187_E 0.83 0.13 0.00
3_V 139_F 0.83 0.13 0.00
67_Y 35_W 0.83 0.13 0.00
168_I 145_N 0.83 0.13 0.00
159_A 10_S 0.83 0.13 0.00
116_V 45_K 0.83 0.13 0.00
71_V 6_Q 0.82 0.13 0.00
178_F 113_P 0.81 0.12 0.00
164_N 38_Q 0.81 0.12 0.00
55_L 87_Y 0.81 0.12 0.00
11_K 20_T 0.81 0.12 0.00
29_V 104_L 0.81 0.12 0.00
43_S 181_L 0.81 0.12 0.00
52_E 199_K 0.81 0.12 0.00
143_I 37_Q 0.81 0.12 0.00
35_S 146_V 0.81 0.12 0.00
196_S 5_T 0.81 0.12 0.00
47_Y 171_S 0.81 0.12 0.00
10_W 104_L 0.81 0.12 0.00
32_V 198_H 0.81 0.12 0.00
58_E 151_D 0.80 0.12 0.00
94_Y 75_I 0.80 0.12 0.00
97_T 195_E 0.80 0.12 0.00
17_T 89_L 0.80 0.12 0.00
36_T 44_P 0.80 0.12 0.00
58_E 190_N 0.80 0.12 0.00
55_L 107_N 0.80 0.12 0.00
140_K 151_D 0.80 0.12 0.00
179_S 33_L 0.80 0.12 0.00
168_I 178_T 0.80 0.12 0.00
54_D 199_K 0.79 0.12 0.00
74_Y 75_I 0.79 0.12 0.00
71_V 61_R 0.79 0.12 0.00
170_V 163_W 0.79 0.12 0.00
174_E 184_D 0.79 0.12 0.00
142_L 75_I 0.79 0.12 0.00
165_E 104_L 0.79 0.12 0.00
124_L 97_T 0.78 0.12 0.00
64_K 155_R 0.78 0.12 0.00
56_T 64_G 0.78 0.12 0.00
2_T 11_M 0.78 0.12 0.00
168_I 104_L 0.78 0.12 0.00
172_K 155_R 0.78 0.12 0.00
69_A 24_K 0.78 0.12 0.00
102_P 35_W 0.78 0.11 0.00
16_K 195_E 0.78 0.11 0.00
164_N 75_I 0.78 0.11 0.00
144_Y 187_E 0.78 0.11 0.00
38_S 130_A 0.78 0.11 0.00
94_Y 22_T 0.77 0.11 0.00
47_Y 32_Y 0.77 0.11 0.00
71_V 4_M 0.77 0.11 0.00
49_T 94_S 0.77 0.11 0.00
82_E 62_F 0.77 0.11 0.00
170_V 35_W 0.77 0.11 0.00
176_Y 31_K 0.77 0.11 0.00
21_W 23_C 0.77 0.11 0.00
100_G 20_T 0.77 0.11 0.00
118_V 141_P 0.77 0.11 0.00
29_V 26_S 0.76 0.11 0.00
115_N 25_A 0.76 0.11 0.00
32_V 131_S 0.76 0.11 0.00
144_Y 35_W 0.76 0.11 0.00
17_T 76_S 0.76 0.11 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
6946 0.44 1AHW_l_u_Apdb 1AHW_r_u_Lpdb Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.01 Done - Shared
6937 0 1AHW_l_u_Apdb 1AHW_r_u_Lpdb Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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