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OPENSEQ.org
3rko_2_E_F
Genes: A B A+B
Length: 147 184 292
Sequences: 408 2185 297
Seq/Len: 2.78 11.88 1.02
MirrorTree (Pazo et al. 2001) 0.77
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 0.02 0.02 0.02
2 0.02 0.02 0.03
5 0.02 0.02 0.12
10 0.02 0.02 0.85
20 0.02 0.02 0.90
100 0.02 0.03 0.97
∞ 0.03 0.05 1.11
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
94_E 127_K 1.88 0.93 0.59
117_L 145_S 1.75 0.90 0.48
63_R 75_N 1.65 0.86 0.41
73_M 70_V 1.53 0.79 0.31
102_E 145_S 1.50 0.77 0.29
103_A 141_V 1.46 0.75 0.26
57_V 139_L 1.43 0.72 0.24
18_I 7_I 1.37 0.68 0.21
74_F 152_L 1.33 0.64 0.18
88_W 46_L 1.30 0.62 0.17
110_L 148_L 1.29 0.61 0.16
60_A 26_V 1.26 0.58 0.15
31_L 99_L 1.26 0.58 0.14
38_G 64_M 1.24 0.56 0.13
121_G 20_I 1.22 0.55 0.13
31_L 143_L 1.22 0.54 0.13
34_G 28_A 1.22 0.54 0.13
87_A 141_V 1.21 0.53 0.12
16_F 2_E 1.20 0.52 0.12
103_A 125_S 1.19 0.52 0.12
119_R 47_G 1.19 0.51 0.11
113_G 149_L 1.16 0.49 0.10
122_A 20_I 1.15 0.48 0.10
63_R 43_F 1.15 0.47 0.10
94_E 73_M 1.14 0.47 0.10
72_A 142_E 1.13 0.46 0.09
29_L 126_A 1.13 0.46 0.09
74_F 149_L 1.12 0.45 0.09
59_S 45_S 1.12 0.45 0.09
20_L 56_I 1.12 0.45 0.09
65_S 25_P 1.11 0.44 0.09
122_A 15_A 1.10 0.44 0.08
101_V 2_E 1.10 0.43 0.08
77_I 134_F 1.10 0.43 0.08
96_G 142_E 1.08 0.41 0.08
68_F 57_I 1.08 0.41 0.08
87_A 156_F 1.07 0.41 0.07
61_R 33_I 1.07 0.41 0.07
82_A 27_H 1.07 0.41 0.07
110_L 156_F 1.06 0.40 0.07
31_L 137_Y 1.05 0.39 0.07
114_L 51_A 1.05 0.39 0.07
71_V 67_F 1.03 0.37 0.06
71_V 65_V 1.03 0.37 0.06
118_V 49_Y 1.03 0.37 0.06
46_K 151_G 1.02 0.36 0.06
80_V 55_E 1.01 0.36 0.06
20_L 44_F 1.01 0.36 0.06
115_V 100_S 1.01 0.35 0.06
80_V 52_G 1.01 0.35 0.06
93_R 134_F 1.01 0.35 0.06
21_I 123_P 1.00 0.35 0.06
73_M 74_L 1.00 0.34 0.06
82_A 13_I 0.99 0.34 0.06
60_A 25_P 0.99 0.33 0.05
117_L 156_F 0.97 0.32 0.05
66_A 68_V 0.97 0.32 0.05
73_M 45_S 0.97 0.32 0.05
77_I 16_T 0.96 0.31 0.05
86_F 35_S 0.96 0.31 0.05
18_I 52_G 0.96 0.31 0.05
115_V 20_I 0.96 0.31 0.05
24_I 11_I 0.95 0.31 0.05
54_I 31_Y 0.95 0.30 0.05
67_K 49_Y 0.95 0.30 0.04
31_L 30_L 0.94 0.30 0.04
114_L 141_V 0.94 0.30 0.04
37_L 11_I 0.93 0.29 0.04
39_G 16_T 0.93 0.29 0.04
82_A 146_M 0.93 0.29 0.04
105_I 13_I 0.93 0.29 0.04
90_T 24_N 0.93 0.28 0.04
18_I 101_A 0.92 0.28 0.04
117_L 134_F 0.92 0.28 0.04
87_A 51_A 0.92 0.28 0.04
130_S 9_G 0.92 0.28 0.04
64_L 38_A 0.92 0.28 0.04
71_V 70_V 0.92 0.28 0.04
107_I 134_F 0.92 0.28 0.04
40_R 36_L 0.91 0.27 0.04
76_V 48_A 0.91 0.27 0.04
63_R 103_M 0.91 0.27 0.04
83_L 54_L 0.91 0.27 0.04
28_C 56_I 0.90 0.27 0.04
77_I 146_M 0.90 0.27 0.04
33_G 17_L 0.90 0.27 0.04
60_A 64_M 0.90 0.27 0.04
43_A 147_L 0.90 0.26 0.04
114_L 58_V 0.90 0.26 0.04
42_R 68_V 0.90 0.26 0.04
76_V 75_N 0.90 0.26 0.04
107_I 12_A 0.89 0.26 0.04
57_V 24_N 0.89 0.26 0.04
15_A 68_V 0.89 0.26 0.04
63_R 37_L 0.89 0.26 0.04
81_E 62_A 0.89 0.26 0.04
84_Y 152_L 0.89 0.26 0.04
49_P 31_Y 0.89 0.26 0.04
69_Y 126_A 0.88 0.25 0.03
43_A 145_S 0.88 0.25 0.03
69_Y 82_E 0.88 0.25 0.03
72_A 146_M 0.88 0.25 0.03
87_A 124_I 0.88 0.25 0.03
38_G 76_L 0.88 0.25 0.03
68_F 158_V 0.88 0.25 0.03
82_A 135_G 0.88 0.25 0.03
22_V 108_V 0.88 0.25 0.03
18_I 34_I 0.88 0.25 0.03
54_I 147_L 0.87 0.25 0.03
89_S 142_E 0.87 0.24 0.03
73_M 67_F 0.87 0.24 0.03
25_G 143_L 0.86 0.24 0.03
64_L 108_V 0.86 0.24 0.03
50_F 21_T 0.86 0.24 0.03
25_G 17_L 0.86 0.24 0.03
115_V 127_K 0.86 0.24 0.03
30_M 75_N 0.86 0.24 0.03
112_A 82_E 0.86 0.23 0.03
73_M 65_V 0.85 0.23 0.03
40_R 86_Q 0.85 0.23 0.03
20_L 117_Q 0.85 0.23 0.03
34_G 43_F 0.85 0.23 0.03
66_A 152_L 0.85 0.23 0.03
16_F 146_M 0.85 0.23 0.03
62_L 74_L 0.85 0.23 0.03
41_A 143_L 0.85 0.23 0.03
87_A 54_L 0.84 0.23 0.03
27_C 98_I 0.84 0.22 0.03
102_E 141_V 0.84 0.22 0.03
15_A 65_V 0.84 0.22 0.03
119_R 140_A 0.84 0.22 0.03
117_L 140_A 0.83 0.22 0.03
57_V 36_L 0.83 0.22 0.03
106_F 148_L 0.83 0.22 0.03
73_M 25_P 0.83 0.22 0.03
122_A 30_L 0.83 0.22 0.03
95_S 154_V 0.83 0.22 0.03
17_A 101_A 0.83 0.22 0.03
35_W 9_G 0.83 0.22 0.03
102_E 142_E 0.83 0.22 0.03
77_I 51_A 0.83 0.21 0.03
115_V 63_I 0.83 0.21 0.03
94_E 102_I 0.82 0.21 0.03
23_A 22_H 0.82 0.21 0.03
86_F 130_G 0.82 0.21 0.03
18_I 79_S 0.82 0.21 0.03
51_E 148_L 0.82 0.21 0.03
69_Y 77_G 0.82 0.21 0.03
102_E 134_F 0.82 0.21 0.03
89_S 48_A 0.82 0.21 0.03
20_L 3_F 0.81 0.21 0.03
120_I 161_E 0.81 0.20 0.03
66_A 122_T 0.81 0.20 0.03
94_E 6_Y 0.81 0.20 0.02
62_L 70_V 0.81 0.20 0.02
71_V 132_T 0.81 0.20 0.02
74_F 134_F 0.80 0.20 0.02
111_L 121_G 0.80 0.20 0.02
22_V 30_L 0.80 0.20 0.02
63_R 27_H 0.80 0.20 0.02
121_G 76_L 0.80 0.20 0.02
73_M 75_N 0.80 0.20 0.02
23_A 43_F 0.80 0.20 0.02
27_C 159_G 0.80 0.20 0.02
82_A 147_L 0.80 0.20 0.02
35_W 31_Y 0.80 0.20 0.02
77_I 85_R 0.80 0.20 0.02
123_L 32_L 0.80 0.20 0.02
32_V 95_G 0.80 0.20 0.02
86_F 62_A 0.79 0.20 0.02
50_F 120_D 0.79 0.20 0.02
86_F 39_I 0.79 0.20 0.02
82_A 9_G 0.79 0.20 0.02
68_F 80_E 0.79 0.19 0.02
78_F 59_Y 0.79 0.19 0.02
86_F 147_L 0.79 0.19 0.02
32_V 34_I 0.79 0.19 0.02
55_D 48_A 0.79 0.19 0.02
21_I 9_G 0.79 0.19 0.02
96_G 57_I 0.79 0.19 0.02
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
7433 1.02 3rko_2_E_F Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.59 Done - Shared
2306 5.49 cI_E_F Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 1.00 Done - Shared
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