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OPENSEQ.org
ExbD-ExbB
Genes: A B A+B
Length: 141 244 356
Sequences: 4093 3392 2723
Seq/Len: 29.03 13.9 7.65
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 0.10 0.00 7.07
2 0.10 0.00 7.74
5 0.10 0.00 7.76
10 0.10 0.01 7.76
20 0.10 0.01 7.78
100 0.14 0.05 7.79
∞ 0.24 0.18 7.87
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 1.70 1.00 0.95
29_V 180_A 1.59 1.00 0.93
20_V 180_A 1.41 0.99 0.87
21_T 142_F 1.41 0.99 0.87
29_V 152_I 1.33 0.98 0.82
27_M 180_A 1.27 0.98 0.79
29_V 170_V 1.25 0.97 0.77
28_L 182_A 1.23 0.97 0.76
26_V 182_A 1.23 0.97 0.76
33_I 152_I 1.15 0.95 0.69
22_P 145_L 1.13 0.95 0.67
21_T 180_A 1.12 0.94 0.66
29_V 142_F 1.10 0.93 0.64
32_I 174_I 1.10 0.93 0.64
18_I 142_F 1.06 0.92 0.60
21_T 159_I 1.05 0.91 0.58
26_V 178_L 1.04 0.91 0.58
29_V 171_A 1.04 0.91 0.57
21_T 137_G 1.04 0.91 0.57
39_P 134_A 1.02 0.89 0.55
35_M 155_S 1.01 0.89 0.54
36_V 167_L 1.01 0.89 0.54
16_H 134_A 0.99 0.88 0.52
27_M 149_V 0.97 0.86 0.49
33_I 142_F 0.96 0.86 0.48
24_I 145_L 0.96 0.85 0.48
19_N 138_A 0.94 0.84 0.46
19_N 171_A 0.93 0.82 0.44
32_I 175_A 0.93 0.82 0.44
28_L 152_I 0.92 0.82 0.43
62_K 159_I 0.91 0.81 0.42
29_V 155_S 0.91 0.81 0.42
70_A 56_K 0.90 0.80 0.41
17_D 134_A 0.90 0.80 0.41
36_V 174_I 0.90 0.80 0.40
103_F 129_G 0.89 0.79 0.39
29_V 182_A 0.88 0.78 0.39
54_S 194_I 0.88 0.77 0.38
21_T 145_L 0.87 0.77 0.38
21_T 170_V 0.87 0.77 0.37
112_Y 178_L 0.87 0.76 0.37
37_A 170_V 0.86 0.76 0.36
20_V 145_L 0.86 0.76 0.36
32_I 134_A 0.84 0.73 0.34
20_V 153_M 0.84 0.73 0.34
18_I 192_V 0.84 0.73 0.33
26_V 166_N 0.83 0.72 0.33
27_M 152_I 0.83 0.72 0.33
24_I 142_F 0.83 0.71 0.32
28_L 142_F 0.82 0.70 0.31
32_I 118_R 0.81 0.69 0.30
21_T 190_P 0.80 0.68 0.29
19_N 167_L 0.80 0.68 0.29
29_V 138_A 0.80 0.67 0.29
34_F 176_E 0.80 0.67 0.29
29_V 190_P 0.79 0.66 0.28
39_P 170_V 0.79 0.66 0.28
40_L 190_P 0.78 0.65 0.27
130_I 160_A 0.78 0.64 0.27
27_M 115_L 0.77 0.64 0.26
33_I 135_T 0.77 0.63 0.26
36_V 165_T 0.77 0.63 0.26
72_N 189_I 0.76 0.62 0.25
19_N 190_P 0.76 0.62 0.25
39_P 190_P 0.76 0.61 0.24
81_V 140_S 0.75 0.60 0.24
128_L 87_L 0.75 0.60 0.24
22_P 178_L 0.75 0.60 0.24
66_L 99_E 0.75 0.60 0.24
39_P 171_A 0.74 0.59 0.23
19_N 152_I 0.74 0.59 0.23
44_D 156_F 0.74 0.59 0.23
124_Q 56_K 0.74 0.59 0.23
31_L 141_P 0.73 0.58 0.22
21_T 188_A 0.73 0.57 0.22
130_I 60_Q 0.73 0.57 0.22
29_V 174_I 0.73 0.57 0.22
15_M 134_A 0.73 0.57 0.22
21_T 174_I 0.72 0.56 0.21
113_E 53_R 0.72 0.56 0.21
27_M 155_S 0.72 0.56 0.21
39_P 137_G 0.72 0.56 0.21
35_M 173_G 0.72 0.56 0.21
104_F 54_R 0.72 0.56 0.21
103_F 156_F 0.72 0.56 0.21
127_Y 165_T 0.71 0.55 0.21
32_I 196_N 0.71 0.54 0.20
74_M 85_L 0.71 0.54 0.20
20_V 19_A 0.70 0.53 0.19
19_N 170_V 0.70 0.53 0.19
23_F 20_D 0.70 0.53 0.19
73_S 220_Q 0.70 0.52 0.19
30_L 152_I 0.70 0.52 0.19
35_M 36_V 0.70 0.52 0.19
21_T 138_A 0.70 0.52 0.19
32_I 149_V 0.70 0.52 0.19
104_F 76_A 0.70 0.52 0.19
41_A 198_F 0.70 0.52 0.19
53_T 96_E 0.69 0.52 0.19
131_G 170_V 0.69 0.52 0.19
29_V 134_A 0.69 0.51 0.18
116_M 37_T 0.69 0.51 0.18
132_L 173_G 0.69 0.50 0.18
49_L 133_L 0.68 0.50 0.18
39_P 152_I 0.68 0.49 0.17
30_L 179_L 0.67 0.48 0.17
76_I 174_I 0.67 0.48 0.17
102_I 51_Q 0.67 0.48 0.17
86_M 42_F 0.67 0.48 0.17
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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