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OPENSEQ.org
3DBO
Genes: A B A+B
Length: 86 135 204
Sequences: 2579 9210 622
Seq/Len: 29.99 68.22 3.05
MirrorTree (Pazo et al. 2001) 0.68
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 0.04 2.81
2 0.02 0.05 2.94
5 0.03 0.08 3.22
10 0.03 0.09 3.43
20 0.04 0.11 3.69
100 0.06 0.15 4.54
∞ 0.12 0.20 6.18
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
52_T 22_R 1.26 0.87 0.21
36_A 104_A 1.01 0.66 0.10
54_F 79_A 0.98 0.63 0.09
12_D 108_A 0.97 0.62 0.09
28_I 26_E 0.97 0.62 0.09
52_T 18_T 0.97 0.62 0.09
31_S 15_F 0.97 0.61 0.08
4_V 113_P 0.95 0.59 0.08
9_L 82_W 0.92 0.55 0.07
28_I 74_V 0.91 0.54 0.07
31_S 96_V 0.90 0.53 0.07
70_D 85_L 0.89 0.52 0.06
28_I 48_L 0.89 0.51 0.06
10_R 8_G 0.88 0.50 0.06
5_A 14_V 0.88 0.50 0.06
68_R 108_A 0.87 0.50 0.06
52_T 28_L 0.86 0.48 0.06
26_V 126_G 0.86 0.48 0.06
5_A 78_A 0.85 0.47 0.05
33_R 50_A 0.85 0.47 0.05
42_R 24_L 0.85 0.47 0.05
22_A 30_P 0.84 0.46 0.05
16_V 82_W 0.84 0.45 0.05
54_F 15_F 0.83 0.45 0.05
73_V 28_L 0.83 0.44 0.05
41_V 28_L 0.83 0.44 0.05
15_G 32_R 0.82 0.44 0.05
12_D 33_V 0.82 0.43 0.05
21_R 54_D 0.82 0.43 0.05
56_S 25_D 0.82 0.43 0.05
10_R 124_L 0.82 0.43 0.05
7_R 97_R 0.81 0.42 0.05
20_V 19_E 0.81 0.42 0.05
60_G 70_E 0.81 0.42 0.05
20_V 62_T 0.80 0.40 0.04
14_A 9_V 0.80 0.40 0.04
33_R 85_L 0.80 0.40 0.04
17_L 75_D 0.80 0.40 0.04
55_L 35_T 0.79 0.40 0.04
67_L 19_E 0.78 0.38 0.04
56_S 21_G 0.78 0.38 0.04
8_E 43_L 0.78 0.38 0.04
36_A 108_A 0.78 0.38 0.04
20_V 39_T 0.77 0.38 0.04
19_R 32_R 0.77 0.38 0.04
35_V 44_R 0.76 0.36 0.04
16_V 38_V 0.76 0.36 0.04
8_E 63_L 0.76 0.35 0.04
28_I 51_A 0.76 0.35 0.04
47_R 77_D 0.75 0.35 0.04
35_V 13_S 0.75 0.34 0.04
3_E 86_R 0.75 0.34 0.04
51_K 67_A 0.74 0.34 0.04
28_I 79_A 0.74 0.34 0.04
7_R 41_A 0.74 0.34 0.04
55_L 98_I 0.74 0.34 0.04
24_E 114_V 0.74 0.33 0.03
42_R 34_A 0.73 0.33 0.03
27_T 31_D 0.73 0.33 0.03
40_P 119_D 0.73 0.33 0.03
69_N 109_S 0.73 0.33 0.03
25_D 16_I 0.73 0.32 0.03
22_A 10_L 0.72 0.32 0.03
13_T 97_R 0.72 0.32 0.03
49_L 29_I 0.72 0.32 0.03
49_L 63_L 0.72 0.31 0.03
33_R 15_F 0.72 0.31 0.03
43_P 73_P 0.71 0.31 0.03
73_V 22_R 0.71 0.31 0.03
4_V 40_L 0.71 0.31 0.03
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
4850 3.05 3DBO Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.21 Done - Shared
0728 2.04 3DBO_Jackhmmer Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.18 Done
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