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OPENSEQ.org
pengfei
Genes: A B A+B
Length: 99 132 231
Sequences: 9838 1785 845
Seq/Len: 99.37 13.52 3.66
MirrorTree (Pazo et al. 2001) 0.78
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.01 3.68
2 0.01 0.01 3.66
5 0.01 0.01 3.66
10 0.02 0.01 3.66
20 0.02 0.01 3.66
100 0.03 0.01 3.66
∞ 0.05 0.01 3.66
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
15_I 28_K 2.14 1.00 0.99
32_V 45_A 1.39 0.95 0.86
38_L 80_N 1.38 0.95 0.85
57_R 61_I 1.32 0.93 0.82
50_I 24_G 1.31 0.92 0.81
69_H 99_E 1.29 0.92 0.80
11_V 51_L 1.29 0.92 0.80
17_G 104_I 1.28 0.91 0.80
50_I 87_C 1.27 0.91 0.79
61_Q 117_Q 1.26 0.91 0.78
76_L 13_L 1.24 0.90 0.77
77_V 88_V 1.24 0.90 0.77
64_I 22_R 1.22 0.88 0.75
16_G 86_Y 1.21 0.88 0.74
15_I 95_K 1.20 0.87 0.73
82_V 32_K 1.18 0.86 0.71
32_V 76_K 1.18 0.86 0.71
60_D 34_L 1.15 0.84 0.68
71_A 59_Q 1.14 0.84 0.68
12_T 99_E 1.10 0.80 0.63
15_I 20_R 1.09 0.79 0.62
65_E 104_I 1.09 0.79 0.62
67_C 74_E 1.07 0.78 0.60
44_P 41_L 1.07 0.77 0.60
38_L 68_I 1.06 0.77 0.59
83_N 77_S 1.05 0.76 0.58
89_L 86_Y 1.05 0.76 0.58
83_N 79_F 1.02 0.73 0.54
77_V 13_L 1.02 0.73 0.54
56_V 13_L 1.01 0.71 0.53
10_L 15_A 1.00 0.71 0.52
4_T 116_Q 1.00 0.70 0.52
82_V 41_L 1.00 0.70 0.52
39_P 95_K 0.99 0.70 0.51
32_V 68_I 0.99 0.69 0.50
18_Q 34_L 0.98 0.69 0.50
16_G 122_K 0.97 0.67 0.48
21_E 114_K 0.96 0.67 0.48
83_N 64_I 0.96 0.67 0.48
38_L 15_A 0.96 0.66 0.47
77_V 65_Q 0.95 0.65 0.46
64_I 30_R 0.95 0.65 0.46
22_A 77_S 0.94 0.64 0.45
62_I 59_Q 0.94 0.63 0.44
68_G 11_G 0.93 0.63 0.43
62_I 117_Q 0.93 0.62 0.43
15_I 74_E 0.93 0.62 0.43
71_A 113_Q 0.93 0.62 0.43
68_G 31_L 0.92 0.62 0.42
10_L 105_E 0.92 0.61 0.41
45_K 37_A 0.91 0.59 0.40
20_K 22_R 0.91 0.59 0.40
35_E 4_R 0.90 0.59 0.40
47_I 45_A 0.89 0.58 0.39
97_L 87_C 0.88 0.57 0.38
92_Q 99_E 0.88 0.56 0.38
67_C 99_E 0.88 0.56 0.37
38_L 76_K 0.88 0.56 0.37
4_T 74_E 0.88 0.55 0.36
89_L 105_E 0.88 0.55 0.36
62_I 94_V 0.88 0.55 0.36
42_W 39_R 0.87 0.55 0.36
68_G 53_T 0.87 0.54 0.35
32_V 5_A 0.86 0.54 0.35
6_W 37_A 0.86 0.54 0.35
46_M 91_K 0.86 0.54 0.35
57_R 102_D 0.86 0.53 0.35
89_L 22_R 0.86 0.53 0.35
69_H 87_C 0.86 0.53 0.34
33_L 28_K 0.85 0.53 0.34
5_L 116_Q 0.85 0.53 0.34
34_E 19_I 0.85 0.53 0.34
45_K 19_I 0.85 0.52 0.34
54_I 86_Y 0.85 0.52 0.34
40_G 76_K 0.85 0.52 0.34
33_L 73_E 0.84 0.51 0.33
93_I 116_Q 0.84 0.51 0.33
93_I 90_R 0.84 0.51 0.32
73_G 12_K 0.84 0.51 0.32
10_L 34_L 0.84 0.51 0.32
89_L 58_L 0.83 0.50 0.32
33_L 22_R 0.83 0.50 0.32
85_I 101_L 0.83 0.50 0.32
34_E 88_V 0.83 0.50 0.32
97_L 7_V 0.83 0.50 0.32
45_K 18_K 0.83 0.50 0.31
4_T 92_I 0.83 0.50 0.31
13_I 115_T 0.83 0.50 0.31
2_Q 31_L 0.82 0.49 0.30
20_K 67_A 0.82 0.48 0.30
73_G 106_E 0.82 0.48 0.30
61_Q 51_L 0.81 0.48 0.30
40_G 80_N 0.81 0.47 0.29
73_G 69_K 0.81 0.47 0.29
47_I 5_A 0.80 0.46 0.28
92_Q 25_G 0.80 0.46 0.28
16_G 79_F 0.80 0.46 0.28
11_V 82_V 0.80 0.46 0.28
55_K 99_E 0.80 0.46 0.28
32_V 57_C 0.80 0.46 0.28
32_V 63_Q 0.80 0.46 0.28
32_V 82_V 0.80 0.45 0.28
69_H 58_L 0.80 0.45 0.28
1_P 113_Q 0.79 0.45 0.27
47_I 76_K 0.79 0.45 0.27
68_G 39_R 0.79 0.45 0.27
7_Q 16_W 0.79 0.44 0.27
16_G 112_Q 0.79 0.44 0.26
53_F 47_N 0.78 0.44 0.26
73_G 19_I 0.78 0.43 0.26
7_Q 22_R 0.78 0.43 0.26
14_K 53_T 0.78 0.43 0.26
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
5609 3.61 pengfei Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 1.00 Done - Shared
5608 3.66 pengfei Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b) 0.99 Done - Shared
5587 3.18 hivma Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.99 Done - Shared
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