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OPENSEQ.org
3TND_Jackhmmer
Genes: A B A+B
Length: 75 132 206
Sequences: 773 6821 474
Seq/Len: 10.31 51.67 2.3
MirrorTree (Pazo et al. 2001) 0.70
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 0.01 2.29
2 0.00 0.02 2.29
5 0.01 0.05 2.35
10 0.01 0.07 2.41
20 0.01 0.08 2.46
100 0.02 0.13 2.69
∞ 0.05 0.19 3.11
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 1.53 0.94 0.61
9_N 106_R 1.44 0.91 0.54
56_V 60_I 1.37 0.88 0.48
16_L 35_I 1.24 0.80 0.36
64_R 13_F 1.20 0.76 0.32
66_Q 97_F 1.14 0.71 0.27
69_M 96_P 1.12 0.70 0.26
53_G 59_V 1.02 0.59 0.19
71_E 88_A 1.02 0.59 0.19
47_W 63_F 0.99 0.55 0.17
66_Q 96_P 0.98 0.54 0.16
51_F 14_T 0.97 0.53 0.16
35_G 116_N 0.96 0.53 0.15
2_E 92_R 0.96 0.52 0.15
51_F 23_R 0.95 0.50 0.14
31_V 100_M 0.93 0.48 0.14
20_V 45_Y 0.92 0.48 0.13
44_G 127_R 0.92 0.47 0.13
22_L 34_C 0.91 0.46 0.12
64_R 11_C 0.89 0.44 0.12
16_L 34_C 0.88 0.43 0.11
20_V 107_S 0.88 0.43 0.11
61_M 130_D 0.87 0.41 0.11
67_P 96_P 0.86 0.40 0.10
40_I 30_Q 0.86 0.40 0.10
63_N 111_I 0.84 0.38 0.10
67_P 49_K 0.84 0.38 0.09
14_V 4_F 0.84 0.38 0.09
41_T 72_Y 0.83 0.38 0.09
5_V 64_V 0.83 0.38 0.09
19_A 38_V 0.83 0.37 0.09
64_R 36_S 0.83 0.37 0.09
58_T 3_K 0.83 0.37 0.09
37_T 100_M 0.82 0.36 0.09
40_I 41_M 0.82 0.36 0.09
6_F 4_F 0.81 0.35 0.08
22_L 11_C 0.81 0.35 0.08
33_A 89_R 0.81 0.35 0.08
35_G 119_E 0.81 0.35 0.08
50_W 41_M 0.80 0.34 0.08
18_K 11_C 0.79 0.33 0.08
61_M 39_T 0.79 0.33 0.07
8_S 39_T 0.78 0.32 0.07
64_R 26_F 0.78 0.32 0.07
64_R 115_N 0.77 0.31 0.07
33_A 20_A 0.77 0.31 0.07
65_E 88_A 0.77 0.31 0.07
31_V 45_Y 0.77 0.31 0.07
27_K 79_H 0.77 0.30 0.07
23_P 125_G 0.76 0.30 0.07
8_S 41_M 0.76 0.30 0.07
58_T 85_A 0.76 0.30 0.07
31_V 13_F 0.76 0.30 0.07
42_P 116_N 0.75 0.29 0.06
30_E 45_Y 0.75 0.29 0.06
3_T 60_I 0.75 0.29 0.06
14_V 81_G 0.75 0.29 0.06
51_F 26_F 0.75 0.29 0.06
39_I 64_V 0.75 0.29 0.06
38_R 34_C 0.75 0.29 0.06
40_I 71_D 0.74 0.28 0.06
69_M 90_Q 0.74 0.28 0.06
28_R 128_T 0.74 0.28 0.06
6_F 113_V 0.74 0.28 0.06
46_T 128_T 0.74 0.28 0.06
50_W 14_T 0.73 0.27 0.06
62_D 132_S 0.73 0.27 0.06
42_P 56_N 0.73 0.27 0.06
32_I 100_M 0.72 0.27 0.06
47_W 35_I 0.72 0.26 0.06
3_T 77_A 0.72 0.26 0.06
64_R 19_P 0.72 0.26 0.06
65_E 93_P 0.72 0.26 0.05
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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