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OPENSEQ.org
3TND
Genes: A B A+B
Length: 75 132 206
Sequences: 985 9084 610
Seq/Len: 13.13 68.82 2.96
MirrorTree (Pazo et al. 2001) 0.72
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 0.00 0.04 2.95
2 0.01 0.05 2.97
5 0.01 0.08 3.05
10 0.02 0.09 3.10
20 0.02 0.10 3.15
100 0.03 0.14 3.41
∞ 0.08 0.20 3.89
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
57_S 56_N 1.48 0.95 0.68
56_V 60_I 1.40 0.93 0.61
69_M 96_P 1.29 0.89 0.52
66_Q 96_P 1.20 0.83 0.42
9_N 106_R 1.12 0.77 0.35
71_E 88_A 1.11 0.76 0.34
14_V 81_G 1.08 0.73 0.31
47_W 63_F 1.07 0.71 0.30
16_L 34_C 1.05 0.70 0.29
64_R 13_F 1.03 0.68 0.27
66_Q 97_F 1.00 0.65 0.25
50_W 41_M 1.00 0.65 0.25
57_S 52_M 0.97 0.61 0.22
38_R 34_C 0.96 0.60 0.21
40_I 30_Q 0.94 0.57 0.20
51_F 14_T 0.94 0.57 0.20
65_E 88_A 0.93 0.55 0.19
58_T 3_K 0.91 0.54 0.18
31_V 62_G 0.91 0.53 0.18
55_S 62_G 0.91 0.53 0.18
70_Q 96_P 0.90 0.52 0.17
64_R 11_C 0.88 0.50 0.16
51_F 23_R 0.87 0.48 0.15
42_P 15_I 0.86 0.47 0.15
61_M 130_D 0.85 0.46 0.14
63_N 18_K 0.85 0.46 0.14
16_L 35_I 0.85 0.46 0.14
2_E 92_R 0.84 0.44 0.13
5_V 64_V 0.83 0.44 0.13
49_E 66_R 0.83 0.44 0.13
8_S 39_T 0.83 0.43 0.13
35_G 119_E 0.82 0.43 0.13
68_G 96_P 0.82 0.43 0.13
70_Q 3_K 0.82 0.42 0.12
41_T 72_Y 0.81 0.41 0.12
74_S 51_Q 0.80 0.40 0.12
37_T 100_M 0.78 0.38 0.11
35_G 116_N 0.78 0.38 0.11
20_V 107_S 0.78 0.38 0.11
7_L 70_L 0.77 0.37 0.10
61_M 39_T 0.77 0.36 0.10
30_E 103_G 0.77 0.36 0.10
63_N 111_I 0.77 0.36 0.10
50_W 58_A 0.76 0.36 0.10
46_T 53_P 0.76 0.35 0.10
19_A 106_R 0.76 0.35 0.10
57_S 15_I 0.76 0.35 0.09
14_V 108_R 0.75 0.34 0.09
58_T 90_Q 0.75 0.34 0.09
36_R 67_I 0.75 0.34 0.09
52_D 20_A 0.75 0.34 0.09
18_K 11_C 0.74 0.34 0.09
3_T 123_V 0.74 0.33 0.09
53_G 59_V 0.74 0.33 0.09
16_L 108_R 0.73 0.32 0.08
5_V 73_D 0.73 0.32 0.08
5_V 124_G 0.72 0.32 0.08
19_A 33_M 0.72 0.31 0.08
43_A 20_A 0.72 0.31 0.08
75_F 15_I 0.71 0.30 0.08
16_L 23_R 0.71 0.30 0.08
9_N 2_L 0.71 0.30 0.08
34_V 12_I 0.71 0.30 0.08
58_T 118_R 0.71 0.29 0.07
31_V 13_F 0.71 0.29 0.07
73_E 83_I 0.70 0.29 0.07
39_I 20_A 0.70 0.29 0.07
42_P 119_E 0.70 0.29 0.07
72_R 18_K 0.70 0.28 0.07
23_P 125_G 0.69 0.28 0.07
43_A 24_E 0.69 0.28 0.07
18_K 47_A 0.69 0.28 0.07
6_F 113_V 0.68 0.27 0.07
67_P 96_P 0.68 0.27 0.07
28_R 15_I 0.68 0.27 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
4849 2.96 3TND Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.68 Done - Shared
0739 2.3 3TND_Jackhmmer Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.61 Done
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