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OPENSEQ.org
pengfei
Genes: A B A+B
Length: 99 132 231
Sequences: 10854 1687 835
Seq/Len: 109.64 12.78 3.61
MirrorTree (Pazo et al. 2001) 0.77
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 3.63
2 0.01 0.01 3.61
5 0.02 0.01 3.61
10 0.03 0.01 3.61
20 0.03 0.01 3.61
100 0.04 0.01 3.61
∞ 0.06 0.01 3.61
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 2.44 1.00 1.00
15_I 85_L 1.51 0.97 0.91
38_L 80_N 1.35 0.94 0.85
11_V 51_L 1.35 0.94 0.85
32_V 45_A 1.33 0.93 0.83
15_I 95_K 1.29 0.92 0.81
50_I 24_G 1.29 0.91 0.81
32_V 76_K 1.28 0.91 0.80
50_I 87_C 1.27 0.91 0.79
61_Q 117_Q 1.24 0.89 0.78
16_G 86_Y 1.24 0.89 0.77
82_V 32_K 1.24 0.89 0.77
76_L 13_L 1.23 0.88 0.76
64_I 22_R 1.20 0.87 0.74
17_G 104_I 1.20 0.87 0.74
57_R 61_I 1.16 0.84 0.70
12_T 99_E 1.13 0.82 0.68
18_Q 34_L 1.12 0.82 0.67
71_A 59_Q 1.11 0.81 0.66
62_I 59_Q 1.08 0.78 0.62
69_H 99_E 1.06 0.77 0.61
83_N 77_S 1.05 0.76 0.59
15_I 20_R 1.05 0.75 0.58
77_V 88_V 1.03 0.73 0.56
77_V 65_Q 1.01 0.71 0.54
4_T 116_Q 1.01 0.71 0.54
83_N 79_F 1.01 0.71 0.54
32_V 68_I 1.01 0.71 0.54
57_R 77_S 1.00 0.70 0.53
15_I 74_E 1.00 0.70 0.53
67_C 99_E 1.00 0.70 0.53
65_E 104_I 1.00 0.70 0.53
89_L 86_Y 1.00 0.70 0.53
56_V 13_L 0.99 0.69 0.52
77_V 13_L 0.99 0.69 0.52
83_N 64_I 0.98 0.68 0.50
16_G 79_F 0.97 0.67 0.49
10_L 105_E 0.97 0.66 0.49
21_E 114_K 0.95 0.65 0.47
69_H 46_L 0.94 0.63 0.46
82_V 41_L 0.94 0.63 0.45
2_Q 94_V 0.93 0.62 0.44
40_G 11_G 0.93 0.62 0.44
67_C 74_E 0.93 0.62 0.44
35_E 4_R 0.92 0.60 0.43
10_L 15_A 0.91 0.60 0.42
60_D 34_L 0.91 0.59 0.42
47_I 45_A 0.91 0.59 0.41
82_V 103_K 0.91 0.59 0.41
92_Q 99_E 0.90 0.59 0.41
62_I 117_Q 0.90 0.59 0.41
68_G 31_L 0.90 0.58 0.40
89_L 105_E 0.89 0.57 0.40
22_A 77_S 0.89 0.57 0.39
89_L 58_L 0.89 0.57 0.39
68_G 11_G 0.89 0.57 0.39
20_K 22_R 0.89 0.57 0.39
34_E 19_I 0.88 0.56 0.39
16_G 122_K 0.88 0.56 0.38
93_I 90_R 0.88 0.55 0.38
71_A 113_Q 0.88 0.55 0.38
7_Q 16_W 0.87 0.55 0.37
67_C 102_D 0.87 0.54 0.37
33_L 22_R 0.87 0.54 0.36
32_V 82_V 0.87 0.54 0.36
97_L 87_C 0.86 0.54 0.36
72_I 61_I 0.86 0.53 0.36
38_L 76_K 0.86 0.53 0.36
46_M 91_K 0.86 0.53 0.35
65_E 19_I 0.85 0.52 0.35
64_I 30_R 0.85 0.52 0.35
57_R 91_K 0.85 0.52 0.35
1_P 113_Q 0.85 0.52 0.35
57_R 129_S 0.85 0.52 0.34
73_G 19_I 0.84 0.51 0.34
97_L 7_V 0.84 0.51 0.34
94_G 27_K 0.84 0.51 0.33
1_P 111_S 0.84 0.51 0.33
89_L 22_R 0.84 0.50 0.33
73_G 12_K 0.84 0.50 0.33
46_M 94_V 0.83 0.49 0.33
11_V 105_E 0.83 0.49 0.32
45_K 86_Y 0.83 0.49 0.32
54_I 86_Y 0.82 0.48 0.32
11_V 82_V 0.82 0.48 0.31
95_C 88_V 0.82 0.48 0.31
47_I 30_R 0.82 0.48 0.31
6_W 37_A 0.82 0.47 0.31
20_K 67_A 0.82 0.47 0.31
33_L 73_E 0.81 0.47 0.30
32_V 57_C 0.81 0.47 0.30
93_I 116_Q 0.81 0.46 0.29
7_Q 83_A 0.80 0.46 0.29
74_T 85_L 0.80 0.45 0.29
73_G 106_E 0.80 0.45 0.28
3_I 83_A 0.79 0.44 0.28
66_I 31_L 0.79 0.44 0.28
34_E 88_V 0.79 0.44 0.27
77_V 18_K 0.79 0.44 0.27
92_Q 25_G 0.79 0.43 0.27
70_K 30_R 0.79 0.43 0.27
69_H 58_L 0.79 0.43 0.27
55_K 99_E 0.78 0.43 0.27
22_A 90_R 0.78 0.43 0.27
93_I 11_G 0.78 0.43 0.27
54_I 75_L 0.78 0.42 0.26
68_G 53_T 0.78 0.42 0.26
53_F 47_N 0.78 0.42 0.26
60_D 101_L 0.78 0.42 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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