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OPENSEQ.org
3G5O_A_B
Genes: A B A+B
Length: 108 102 179
Sequences: 950 1107 135
Seq/Len: 8.8 10.85 0.75
MirrorTree (Pazo et al. 2001) 0.70
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 0.00 0.58
2 0.00 0.01 0.58
5 0.01 0.01 0.60
10 0.01 0.01 0.61
20 0.01 0.02 0.64
100 0.03 0.04 0.71
∞ 0.09 0.10 1.05
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
61_W 78_L 1.60 0.76 0.01
87_D 51_R 1.51 0.69 0.01
46_L 99_I 1.43 0.63 0.01
75_D 61_R 1.40 0.60 0.01
52_W 24_T 1.39 0.60 0.01
87_D 87_T 1.30 0.53 0.01
45_V 47_G 1.28 0.51 0.01
75_D 80_R 1.27 0.50 0.01
61_W 57_G 1.25 0.48 0.01
91_A 93_V 1.25 0.48 0.01
87_D 85_H 1.17 0.42 0.01
34_I 24_T 1.17 0.41 0.01
76_A 77_L 1.16 0.41 0.01
57_E 58_K 1.15 0.40 0.00
47_V 84_E 1.15 0.40 0.00
64_Q 78_L 1.14 0.39 0.00
33_Q 57_G 1.13 0.38 0.00
76_A 84_E 1.13 0.38 0.00
49_A 25_T 1.11 0.36 0.00
24_V 91_L 1.07 0.33 0.00
39_N 57_G 1.07 0.33 0.00
45_V 59_P 1.06 0.32 0.00
39_N 54_L 1.05 0.32 0.00
12_P 91_L 1.05 0.32 0.00
59_L 45_A 1.05 0.32 0.00
25_D 66_G 1.04 0.31 0.00
8_M 93_V 1.04 0.31 0.00
22_E 98_D 1.04 0.31 0.00
44_A 31_H 1.03 0.31 0.00
50_D 52_E 1.03 0.30 0.00
19_K 88_V 1.03 0.30 0.00
64_Q 88_V 1.02 0.30 0.00
86_E 46_F 1.01 0.29 0.00
50_D 43_E 1.01 0.29 0.00
84_Y 86_T 1.01 0.28 0.00
33_Q 79_Y 1.00 0.28 0.00
71_I 31_H 1.00 0.28 0.00
9_R 99_I 1.00 0.28 0.00
58_T 47_G 0.99 0.27 0.00
75_D 67_T 0.97 0.26 0.00
32_D 75_Y 0.97 0.26 0.00
51_E 90_I 0.96 0.25 0.00
27_V 57_G 0.95 0.25 0.00
73_E 23_T 0.95 0.25 0.00
44_A 54_L 0.94 0.24 0.00
45_V 57_G 0.94 0.24 0.00
73_E 101_R 0.94 0.24 0.00
31_Q 33_L 0.94 0.24 0.00
57_E 37_I 0.93 0.24 0.00
92_E 27_R 0.93 0.24 0.00
60_Y 67_T 0.93 0.24 0.00
83_T 21_R 0.93 0.24 0.00
41_A 88_V 0.93 0.23 0.00
76_A 20_V 0.92 0.23 0.00
52_W 68_F 0.92 0.23 0.00
39_N 24_T 0.92 0.23 0.00
15_T 93_V 0.92 0.23 0.00
39_N 75_Y 0.92 0.23 0.00
36_I 68_F 0.91 0.22 0.00
36_I 38_L 0.91 0.22 0.00
40_G 90_I 0.90 0.22 0.00
61_W 69_S 0.90 0.22 0.00
18_G 44_F 0.90 0.22 0.00
78_I 86_T 0.90 0.22 0.00
77_D 63_E 0.89 0.21 0.00
82_R 81_I 0.89 0.21 0.00
26_A 91_L 0.89 0.21 0.00
18_G 102_R 0.89 0.21 0.00
24_V 83_D 0.89 0.21 0.00
87_D 30_L 0.88 0.20 0.00
17_K 23_T 0.88 0.20 0.00
46_L 52_E 0.87 0.20 0.00
91_A 30_L 0.87 0.20 0.00
17_K 79_Y 0.87 0.20 0.00
27_V 74_T 0.87 0.20 0.00
84_Y 90_I 0.87 0.20 0.00
21_N 77_L 0.87 0.20 0.00
85_G 62_R 0.86 0.20 0.00
60_Y 79_Y 0.86 0.19 0.00
73_E 51_R 0.86 0.19 0.00
56_Q 22_F 0.86 0.19 0.00
88_E 73_G 0.86 0.19 0.00
46_L 95_H 0.85 0.19 0.00
63_A 93_V 0.85 0.19 0.00
84_Y 26_A 0.85 0.19 0.00
92_E 50_S 0.85 0.19 0.00
85_G 31_H 0.85 0.19 0.00
42_P 64_L 0.84 0.19 0.00
97_R 54_L 0.84 0.18 0.00
10_I 88_V 0.83 0.18 0.00
27_V 52_E 0.83 0.18 0.00
26_A 35_P 0.83 0.18 0.00
63_A 30_L 0.83 0.18 0.00
65_P 90_I 0.83 0.18 0.00
50_D 93_V 0.82 0.18 0.00
50_D 21_R 0.82 0.17 0.00
36_I 47_G 0.82 0.17 0.00
55_L 28_R 0.82 0.17 0.00
38_K 29_D 0.82 0.17 0.00
77_D 25_T 0.81 0.17 0.00
27_V 39_A 0.81 0.17 0.00
38_K 77_L 0.81 0.17 0.00
37_T 38_L 0.81 0.17 0.00
11_L 93_V 0.81 0.17 0.00
68_R 88_V 0.81 0.17 0.00
10_I 98_D 0.81 0.17 0.00
74_A 97_A 0.81 0.17 0.00
19_K 20_V 0.80 0.17 0.00
30_T 40_A 0.80 0.17 0.00
16_I 63_E 0.80 0.16 0.00
80_S 54_L 0.80 0.16 0.00
35_T 27_R 0.80 0.16 0.00
47_V 33_L 0.79 0.16 0.00
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
7270 0.75 3G5O_A_B Δgene:(1, 20) A:(1E-10, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.01 Done - Shared
7262 0.39 3G5O_A_B Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.50 Done - Shared
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