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OPENSEQ.org
RUVX_YQGE
Genes: A B A+B
Length: 138 187 311
Sequences: 2702 1466 864
Seq/Len: 19.58 7.84 2.78
MirrorTree (Pazo et al. 2001) 0.72
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 0.08 1.63
2 0.07 0.08 1.66
5 0.07 0.08 1.65
10 0.07 0.08 1.64
20 0.07 0.08 1.66
100 0.07 0.08 1.74
∞ 0.07 0.08 2.66
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
10_F 38_I 1.32 0.89 0.28
121_V 41_K 1.32 0.89 0.28
70_Q 4_Q 1.30 0.88 0.26
29_P 39_V 1.11 0.74 0.16
56_E 157_L 1.10 0.73 0.15
65_M 35_M 1.09 0.72 0.14
125_S 22_S 1.08 0.70 0.14
17_V 17_P 1.07 0.70 0.14
48_L 109_R 1.06 0.69 0.13
131_E 105_M 1.03 0.66 0.12
7_A 177_I 1.00 0.63 0.11
100_T 182_G 0.98 0.60 0.10
99_S 47_K 0.97 0.59 0.10
5_L 81_D 0.97 0.58 0.10
106_G 166_W 0.94 0.56 0.09
100_T 11_M 0.93 0.54 0.09
124_A 26_I 0.93 0.54 0.08
134_F 1_M 0.92 0.53 0.08
98_L 151_P 0.92 0.52 0.08
70_Q 176_D 0.91 0.52 0.08
94_H 23_V 0.91 0.52 0.08
133_Y 153_D 0.91 0.51 0.08
42_W 170_A 0.91 0.51 0.08
69_E 172_L 0.89 0.49 0.07
5_L 125_L 0.89 0.49 0.07
66_D 110_D 0.88 0.48 0.07
99_S 148_L 0.86 0.46 0.07
50_K 56_K 0.86 0.45 0.06
127_V 38_I 0.85 0.44 0.06
67_G 34_A 0.84 0.43 0.06
107_L 166_W 0.84 0.43 0.06
8_F 108_S 0.83 0.42 0.06
130_L 5_H 0.83 0.42 0.06
134_F 37_I 0.83 0.42 0.06
74_A 13_A 0.83 0.42 0.06
7_A 173_I 0.83 0.42 0.06
5_L 144_D 0.83 0.42 0.06
12_T 14_L 0.83 0.41 0.06
32_A 117_T 0.82 0.41 0.06
13_K 51_I 0.82 0.41 0.06
58_I 140_Q 0.82 0.41 0.06
58_I 153_D 0.81 0.40 0.05
67_G 135_K 0.80 0.39 0.05
34_K 142_I 0.80 0.38 0.05
114_R 21_R 0.80 0.38 0.05
47_R 142_I 0.79 0.38 0.05
5_L 124_V 0.79 0.37 0.05
72_L 146_A 0.79 0.37 0.05
121_V 35_M 0.78 0.36 0.05
43_N 115_L 0.78 0.36 0.05
70_Q 139_E 0.78 0.36 0.05
101_V 24_V 0.77 0.35 0.05
47_R 101_D 0.77 0.35 0.05
21_Q 130_Y 0.77 0.35 0.04
34_K 80_E 0.77 0.35 0.04
133_Y 51_I 0.77 0.35 0.04
57_I 169_A 0.77 0.35 0.04
6_L 159_K 0.77 0.35 0.04
42_W 150_A 0.77 0.35 0.04
33_I 34_A 0.76 0.34 0.04
6_L 102_N 0.76 0.34 0.04
127_V 52_L 0.76 0.34 0.04
22_R 38_I 0.76 0.34 0.04
45_I 37_I 0.76 0.34 0.04
100_T 166_W 0.76 0.34 0.04
20_G 81_D 0.75 0.33 0.04
110_Q 174_G 0.75 0.33 0.04
51_E 156_I 0.75 0.33 0.04
77_R 148_L 0.75 0.32 0.04
28_R 80_E 0.74 0.32 0.04
31_P 5_H 0.74 0.32 0.04
7_A 54_K 0.74 0.32 0.04
100_T 2_N 0.74 0.32 0.04
61_L 37_I 0.74 0.32 0.04
92_K 51_I 0.73 0.31 0.04
123_S 48_I 0.73 0.31 0.04
115_A 166_W 0.73 0.31 0.04
45_I 49_E 0.73 0.31 0.04
46_E 142_I 0.73 0.31 0.04
41_D 166_W 0.73 0.31 0.04
33_I 135_K 0.73 0.31 0.04
32_A 166_W 0.73 0.31 0.04
14_S 127_A 0.73 0.31 0.04
40_P 39_V 0.73 0.30 0.04
54_P 96_S 0.73 0.30 0.04
49_L 172_L 0.73 0.30 0.04
15_I 157_L 0.72 0.30 0.04
99_S 174_G 0.72 0.30 0.04
57_I 178_L 0.72 0.30 0.04
4_T 184_A 0.72 0.30 0.04
133_Y 170_A 0.72 0.30 0.04
41_D 114_T 0.72 0.30 0.04
116_L 24_V 0.72 0.30 0.04
133_Y 110_D 0.72 0.30 0.04
91_V 166_W 0.72 0.29 0.04
58_I 73_M 0.72 0.29 0.04
99_S 85_I 0.72 0.29 0.04
30_L 11_M 0.72 0.29 0.04
41_D 184_A 0.72 0.29 0.04
93_L 143_L 0.72 0.29 0.04
45_I 167_R 0.72 0.29 0.04
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
2568 2.78 RUVX_YQGE Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.28 Done - Shared
2567 1.84 RUVX_YQGE Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.06 Done - Shared
2485 1.62 RUVX - YQGE Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.17 Done - Shared
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