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OPENSEQ.org
hivma
Genes: A B A+B
Length: 99 132 231
Sequences: 10221 3128 735
Seq/Len: 103.24 23.7 3.18
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 0.01 0.03 3.25
2 0.01 0.03 3.18
5 0.02 0.03 3.18
10 0.02 0.03 3.18
20 0.02 0.03 3.18
100 0.02 0.03 3.18
∞ 0.04 0.03 3.18
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 2.31 1.00 0.99
69_H 58_L 1.52 0.96 0.90
15_I 126_N 1.41 0.94 0.86
69_H 46_L 1.37 0.93 0.84
50_I 87_C 1.37 0.93 0.83
11_V 51_L 1.35 0.92 0.83
50_I 24_G 1.22 0.85 0.73
56_V 13_L 1.20 0.84 0.71
18_Q 60_I 1.19 0.84 0.71
71_A 59_Q 1.17 0.82 0.69
76_L 13_L 1.14 0.80 0.66
64_I 22_R 1.12 0.78 0.63
62_I 123_E 1.11 0.78 0.63
32_V 45_A 1.10 0.77 0.61
67_C 99_E 1.10 0.77 0.61
12_T 70_T 1.09 0.76 0.61
15_I 95_K 1.08 0.75 0.59
93_I 11_G 1.07 0.74 0.58
10_L 15_A 1.06 0.73 0.57
73_G 110_K 1.06 0.73 0.57
77_V 88_V 1.05 0.71 0.55
62_I 128_V 1.03 0.70 0.53
96_T 38_S 1.03 0.70 0.53
12_T 99_E 1.03 0.69 0.53
11_V 82_V 1.02 0.68 0.52
77_V 59_Q 0.98 0.64 0.47
89_L 58_L 0.98 0.64 0.47
56_V 96_D 0.96 0.62 0.45
34_E 19_I 0.94 0.60 0.43
99_F 68_I 0.94 0.59 0.42
85_I 85_L 0.93 0.58 0.41
93_I 116_Q 0.93 0.58 0.41
15_I 127_K 0.92 0.57 0.40
61_Q 84_V 0.91 0.56 0.39
46_M 91_K 0.91 0.56 0.39
69_H 67_A 0.91 0.55 0.38
84_I 89_H 0.90 0.55 0.38
61_Q 51_L 0.90 0.55 0.38
55_K 99_E 0.89 0.53 0.36
21_E 83_A 0.89 0.53 0.36
39_P 128_V 0.89 0.53 0.36
67_C 105_E 0.89 0.53 0.36
69_H 99_E 0.89 0.53 0.36
89_L 96_D 0.88 0.52 0.35
69_H 87_C 0.86 0.49 0.33
32_V 5_A 0.86 0.49 0.32
62_I 61_I 0.86 0.49 0.32
7_Q 83_A 0.86 0.49 0.32
10_L 34_L 0.85 0.48 0.31
98_N 35_V 0.85 0.48 0.31
83_N 77_S 0.84 0.47 0.31
6_W 17_E 0.84 0.47 0.31
47_I 45_A 0.84 0.47 0.31
19_L 104_I 0.84 0.47 0.30
33_L 105_E 0.84 0.46 0.30
32_V 68_I 0.83 0.46 0.30
44_P 6_S 0.83 0.46 0.30
69_H 53_T 0.83 0.46 0.29
15_I 22_R 0.83 0.45 0.29
91_T 19_I 0.83 0.45 0.29
57_R 104_I 0.82 0.45 0.29
62_I 73_E 0.82 0.45 0.29
11_V 105_E 0.82 0.45 0.29
21_E 19_I 0.82 0.45 0.29
82_V 41_L 0.82 0.44 0.28
77_V 94_V 0.82 0.44 0.28
85_I 95_K 0.82 0.44 0.28
15_I 123_E 0.82 0.44 0.28
42_W 39_R 0.82 0.44 0.28
62_I 59_Q 0.81 0.44 0.28
77_V 15_A 0.81 0.43 0.27
84_I 50_L 0.80 0.42 0.27
64_I 30_R 0.80 0.42 0.26
18_Q 51_L 0.80 0.42 0.26
88_N 33_H 0.80 0.41 0.26
32_V 16_W 0.80 0.41 0.26
70_K 117_Q 0.80 0.41 0.26
48_G 6_S 0.79 0.41 0.25
77_V 13_L 0.79 0.41 0.25
20_K 67_A 0.79 0.41 0.25
32_V 63_Q 0.79 0.40 0.25
93_I 90_R 0.78 0.40 0.24
30_D 66_P 0.78 0.40 0.24
69_H 94_V 0.78 0.40 0.24
2_Q 4_R 0.78 0.39 0.24
57_R 102_D 0.78 0.39 0.24
22_A 11_G 0.78 0.39 0.23
89_L 22_R 0.77 0.38 0.23
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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