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OPENSEQ.org
VapBC_attempt3
Genes: A B A+B
Length: 133 85 190
Sequences: 2950 1636 325
Seq/Len: 22.18 19.25 1.71
MirrorTree (Pazo et al. 2001) 0.85
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 0.00 0.01 1.41
2 0.01 0.01 1.40
5 0.03 0.01 1.41
10 0.03 0.01 1.44
20 0.04 0.02 1.49
100 0.07 0.05 1.61
∞ 0.15 0.09 2.00
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
24_V 51_Q 1.99 0.98 0.94
13_L 57_F 1.62 0.93 0.80
60_S 56_S 1.49 0.88 0.71
49_A 16_L 1.39 0.83 0.62
37_V 52_A 1.37 0.81 0.60
86_N 33_L 1.36 0.81 0.60
59_A 56_S 1.35 0.81 0.59
3_L 64_D 1.21 0.69 0.44
115_P 31_I 1.21 0.69 0.44
63_V 18_K 1.21 0.69 0.44
60_S 57_F 1.19 0.67 0.42
24_V 50_L 1.18 0.66 0.41
42_L 12_Q 1.18 0.66 0.41
12_H 57_F 1.17 0.65 0.40
52_R 42_A 1.16 0.64 0.39
76_D 10_E 1.13 0.62 0.36
52_R 22_Q 1.10 0.58 0.33
89_G 66_P 1.07 0.56 0.30
90_L 33_L 1.04 0.52 0.28
77_M 37_R 1.03 0.51 0.27
87_R 15_S 1.03 0.51 0.27
27_R 40_T 1.03 0.51 0.26
34_I 46_L 1.02 0.50 0.26
74_A 17_D 0.98 0.46 0.23
3_L 61_R 0.98 0.45 0.22
102_Q 8_L 0.98 0.45 0.22
78_M 56_S 0.97 0.45 0.22
58_L 11_E 0.96 0.44 0.21
120_L 30_L 0.95 0.43 0.20
39_T 6_I 0.95 0.42 0.20
2_I 10_E 0.95 0.42 0.20
57_L 12_Q 0.93 0.41 0.19
76_D 37_R 0.93 0.40 0.18
65_P 4_T 0.93 0.40 0.18
62_R 50_L 0.92 0.40 0.18
65_P 51_Q 0.90 0.37 0.16
14_R 31_I 0.89 0.36 0.15
3_L 22_Q 0.89 0.36 0.15
23_L 53_I 0.89 0.36 0.15
99_A 70_S 0.88 0.35 0.15
7_D 34_L 0.88 0.35 0.15
57_L 39_L 0.87 0.35 0.14
24_V 48_S 0.87 0.34 0.14
2_I 34_L 0.86 0.34 0.14
22_W 24_G 0.85 0.33 0.13
58_L 31_I 0.85 0.33 0.13
83_R 66_P 0.85 0.32 0.13
35_S 7_Y 0.85 0.32 0.13
116_M 4_T 0.85 0.32 0.13
63_V 17_D 0.84 0.32 0.13
69_V 55_D 0.84 0.32 0.12
36_V 62_H 0.84 0.31 0.12
88_I 22_Q 0.84 0.31 0.12
56_R 6_I 0.83 0.31 0.12
8_V 20_A 0.83 0.31 0.12
104_L 13_T 0.83 0.30 0.12
44_G 53_I 0.83 0.30 0.12
36_V 68_R 0.82 0.30 0.12
72_R 33_L 0.82 0.29 0.11
57_L 3_R 0.82 0.29 0.11
108_T 62_H 0.82 0.29 0.11
81_Y 13_T 0.81 0.29 0.11
94_L 48_S 0.81 0.29 0.11
8_V 24_G 0.81 0.29 0.11
69_V 25_V 0.81 0.29 0.11
99_A 15_S 0.81 0.28 0.11
53_E 10_E 0.80 0.28 0.10
52_R 37_R 0.80 0.28 0.10
17_V 32_R 0.79 0.27 0.10
80_R 31_I 0.79 0.27 0.10
110_N 17_D 0.79 0.27 0.10
115_P 63_L 0.79 0.27 0.10
113_H 9_D 0.78 0.27 0.10
34_I 14_A 0.78 0.27 0.10
21_D 42_A 0.78 0.27 0.10
91_G 12_Q 0.78 0.26 0.10
51_R 48_S 0.78 0.26 0.10
20_R 50_L 0.78 0.26 0.10
50_E 28_A 0.78 0.26 0.10
55_W 6_I 0.78 0.26 0.10
97_A 21_A 0.78 0.26 0.10
48_T 22_Q 0.78 0.26 0.09
83_R 40_T 0.78 0.26 0.09
9_L 39_L 0.77 0.26 0.09
22_W 20_A 0.76 0.24 0.09
39_T 31_I 0.76 0.24 0.08
88_I 59_T 0.75 0.24 0.08
2_I 25_V 0.75 0.23 0.08
15_G 35_L 0.74 0.23 0.08
1_M 20_A 0.74 0.23 0.08
38_S 65_P 0.74 0.23 0.08
99_A 23_E 0.74 0.23 0.08
107_A 34_L 0.73 0.23 0.08
107_A 10_E 0.73 0.23 0.07
37_V 70_S 0.73 0.23 0.07
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
6407 1.71 VapBC_attempt3 Δgene:(1, 20) A:(1E-20, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.94 Done - Shared
6405 0.02 VapBC_attempt2 Δgene:(1, 20) A:(1E-06, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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