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OPENSEQ.org
DB
Genes: A B A+B
Length: 141 244 355
Sequences: 4093 3392 3005
Seq/Len: 29.03 13.9 8.46
MirrorTree (Pazo et al. 2001) 0.76
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 0.10 0.00 7.08
2 0.10 0.00 7.74
5 0.10 0.00 7.77
10 0.10 0.01 7.76
20 0.10 0.01 7.81
100 0.14 0.05 7.79
∞ 0.24 0.18 7.85
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
28_L 180_A 1.80 1.00 0.97
29_V 180_A 1.61 1.00 0.94
21_T 142_F 1.30 0.98 0.82
29_V 152_I 1.29 0.98 0.82
20_V 180_A 1.29 0.98 0.82
27_M 180_A 1.21 0.97 0.76
22_P 145_L 1.21 0.97 0.76
28_L 182_A 1.19 0.97 0.75
29_V 170_V 1.19 0.97 0.74
26_V 182_A 1.17 0.96 0.73
32_I 174_I 1.14 0.96 0.70
33_I 152_I 1.10 0.94 0.66
21_T 159_I 1.09 0.94 0.65
21_T 180_A 1.08 0.94 0.65
35_M 155_S 1.08 0.94 0.64
29_V 155_S 1.05 0.93 0.61
24_I 145_L 1.04 0.92 0.60
29_V 142_F 1.04 0.92 0.59
21_T 137_G 1.02 0.91 0.57
27_M 149_V 1.01 0.91 0.57
26_V 178_L 1.01 0.91 0.56
19_N 138_A 1.00 0.90 0.55
29_V 171_A 0.97 0.88 0.52
39_P 134_A 0.95 0.86 0.49
18_I 142_F 0.94 0.86 0.48
36_V 167_L 0.93 0.85 0.47
33_I 142_F 0.93 0.85 0.47
37_A 170_V 0.93 0.85 0.46
29_V 182_A 0.93 0.85 0.46
32_I 175_A 0.91 0.83 0.45
18_I 192_V 0.91 0.83 0.44
16_H 134_A 0.90 0.82 0.43
32_I 134_A 0.90 0.82 0.43
36_V 174_I 0.88 0.81 0.41
28_L 152_I 0.87 0.79 0.39
20_V 145_L 0.86 0.78 0.38
15_M 134_A 0.86 0.78 0.38
17_D 134_A 0.86 0.78 0.38
40_L 190_P 0.83 0.75 0.35
54_S 194_I 0.83 0.75 0.35
116_M 37_T 0.83 0.75 0.34
112_Y 178_L 0.83 0.74 0.34
28_L 142_F 0.82 0.74 0.34
70_A 56_K 0.82 0.74 0.34
21_T 145_L 0.81 0.72 0.32
39_P 170_V 0.81 0.72 0.32
29_V 190_P 0.81 0.72 0.32
19_N 171_A 0.81 0.72 0.32
40_L 30_L 0.80 0.71 0.32
36_V 165_T 0.80 0.71 0.31
26_V 166_N 0.79 0.70 0.30
16_H 196_N 0.79 0.69 0.29
46_K 38_W 0.78 0.68 0.29
27_M 152_I 0.78 0.67 0.28
62_K 159_I 0.77 0.66 0.28
29_V 138_A 0.77 0.66 0.27
21_T 170_V 0.76 0.65 0.27
32_I 118_R 0.76 0.65 0.26
103_F 129_G 0.76 0.65 0.26
39_P 190_P 0.75 0.63 0.25
39_P 171_A 0.75 0.63 0.25
34_F 176_E 0.74 0.62 0.25
32_I 149_V 0.74 0.62 0.24
41_A 198_F 0.74 0.62 0.24
130_I 60_Q 0.73 0.61 0.24
24_I 142_F 0.73 0.60 0.24
49_L 44_K 0.73 0.60 0.23
35_M 182_A 0.73 0.60 0.23
33_I 135_T 0.73 0.60 0.23
44_D 156_F 0.73 0.60 0.23
55_T 36_V 0.73 0.60 0.23
20_V 153_M 0.73 0.60 0.23
19_N 190_P 0.72 0.59 0.23
21_T 174_I 0.72 0.58 0.22
24_I 182_A 0.71 0.58 0.22
103_F 156_F 0.71 0.58 0.22
32_I 159_I 0.71 0.57 0.22
127_Y 165_T 0.71 0.56 0.21
81_V 140_S 0.70 0.56 0.21
30_L 152_I 0.70 0.56 0.21
37_A 116_E 0.70 0.56 0.21
20_V 19_A 0.70 0.56 0.21
24_I 171_A 0.70 0.55 0.20
104_F 54_R 0.70 0.55 0.20
29_V 174_I 0.70 0.55 0.20
36_V 179_L 0.70 0.55 0.20
66_L 99_E 0.69 0.54 0.20
76_I 174_I 0.69 0.53 0.19
119_M 33_A 0.68 0.53 0.19
23_F 20_D 0.68 0.53 0.19
39_P 137_G 0.68 0.52 0.19
35_M 36_V 0.68 0.52 0.19
102_I 90_E 0.67 0.51 0.18
21_T 190_P 0.67 0.51 0.18
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
10527 7.65 ExbD-ExbB Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.95 Done - Shared
7824 8.46 DB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.97 Done - Shared
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