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OPENSEQ.org
MazEF_lower_thresholds
Genes: A B A+B
Length: 111 82 193
Sequences: 2052 717 505
Seq/Len: 18.49 8.74 2.62
MirrorTree (Pazo et al. 2001) 0.68
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 0.00 2.60
2 0.01 0.00 2.59
5 0.01 0.01 2.61
10 0.01 0.01 2.61
20 0.02 0.02 2.62
100 0.04 0.02 2.63
∞ 0.10 0.06 2.82
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
38_M 56_A 1.77 0.98 0.92
104_A 53_F 1.54 0.95 0.84
79_K 73_W 1.47 0.94 0.80
105_K 58_L 1.24 0.83 0.61
49_V 2_I 1.17 0.77 0.53
10_G 58_L 1.12 0.73 0.48
105_K 53_F 1.08 0.69 0.43
4_R 25_L 1.07 0.68 0.43
16_D 5_S 1.04 0.65 0.40
108_V 54_T 1.03 0.64 0.38
59_P 62_I 1.02 0.62 0.37
45_M 54_T 1.02 0.62 0.37
39_Y 23_Q 0.99 0.59 0.34
101_L 53_F 0.98 0.58 0.33
73_A 38_V 0.97 0.57 0.32
6_V 43_I 0.94 0.53 0.28
27_G 12_S 0.92 0.51 0.27
60_F 62_I 0.92 0.51 0.27
83_W 68_H 0.91 0.50 0.26
38_M 59_V 0.90 0.48 0.25
45_M 32_E 0.89 0.48 0.24
16_D 17_I 0.88 0.46 0.23
58_Y 62_I 0.87 0.45 0.23
82_A 78_D 0.87 0.45 0.23
73_A 32_E 0.87 0.45 0.22
111_G 49_K 0.85 0.43 0.21
39_Y 68_H 0.85 0.43 0.21
32_V 33_V 0.85 0.43 0.21
48_C 73_W 0.85 0.43 0.21
76_D 66_N 0.84 0.42 0.20
42_K 62_I 0.84 0.41 0.20
108_V 53_F 0.84 0.41 0.20
107_N 52_V 0.84 0.41 0.20
106_I 31_D 0.83 0.40 0.19
62_V 58_L 0.82 0.39 0.18
12_L 26_N 0.81 0.38 0.18
102_I 61_D 0.80 0.37 0.17
93_T 45_E 0.79 0.36 0.16
90_K 57_E 0.79 0.36 0.16
80_S 15_V 0.79 0.35 0.16
41_N 38_V 0.79 0.35 0.16
18_D 41_K 0.78 0.35 0.16
13_I 11_N 0.78 0.35 0.15
72_V 57_E 0.78 0.34 0.15
12_L 20_T 0.77 0.34 0.15
22_G 80_E 0.77 0.34 0.15
90_K 37_L 0.76 0.33 0.14
14_W 49_K 0.76 0.32 0.14
108_V 58_L 0.76 0.32 0.14
81_I 5_S 0.74 0.31 0.13
61_E 66_N 0.74 0.31 0.13
43_T 7_K 0.74 0.31 0.13
59_P 59_V 0.74 0.31 0.13
42_K 40_G 0.74 0.30 0.13
100_Q 3_H 0.74 0.30 0.13
54_Q 14_A 0.73 0.29 0.12
54_Q 30_D 0.72 0.29 0.12
106_I 69_E 0.72 0.29 0.12
62_V 39_D 0.72 0.29 0.12
109_L 39_D 0.72 0.29 0.12
57_G 6_V 0.72 0.28 0.12
71_G 31_D 0.72 0.28 0.12
61_E 68_H 0.72 0.28 0.11
58_Y 66_N 0.71 0.28 0.11
5_Y 27_L 0.71 0.28 0.11
101_L 5_S 0.71 0.28 0.11
12_L 49_K 0.71 0.28 0.11
1_M 21_L 0.71 0.28 0.11
3_S 72_D 0.71 0.27 0.11
69_R 22_M 0.71 0.27 0.11
33_V 14_A 0.71 0.27 0.11
93_T 27_L 0.70 0.27 0.11
35_S 21_L 0.70 0.27 0.11
24_E 80_E 0.70 0.27 0.11
25_Q 9_W 0.70 0.27 0.11
76_D 8_R 0.70 0.27 0.11
15_V 24_A 0.70 0.27 0.11
25_Q 12_S 0.70 0.27 0.11
94_V 14_A 0.70 0.27 0.11
75_A 22_M 0.70 0.27 0.10
6_V 20_T 0.70 0.26 0.10
21_K 77_K 0.70 0.26 0.10
101_L 24_A 0.69 0.26 0.10
46_C 14_A 0.69 0.26 0.10
74_L 9_W 0.69 0.26 0.10
26_A 58_L 0.69 0.25 0.10
52_T 24_A 0.69 0.25 0.10
76_D 9_W 0.68 0.25 0.10
9_M 79_K 0.68 0.24 0.09
74_L 6_V 0.68 0.24 0.09
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
13058 2.68 idr Δgene:(1, 20) A:(1E-06, 4) B:(1E-06, 8) msa: HHblits (2015_06) 0.93 Done - Shared
6413 2.62 MazEF_lower_thresholds Δgene:(1, 20) A:(1E-20, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.92 Done - Shared
3423 0.67 MAZF_ECOLI_MAZE_ECOLI Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.06 Done
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