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OPENSEQ.org
MFD_THETH_319-398-RPOB_THETH_17_392
Genes: A B A+B
Length: 79 182 240
Sequences: 4463 6630 1166
Seq/Len: 56.49 36.43 4.86
MirrorTree (Pazo et al. 2001) 0.44
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 0.98 0.01
2 0.00 0.98 0.02
5 0.00 0.98 0.03
10 0.00 0.98 0.05
20 0.00 0.98 0.14
100 0.00 0.98 0.90
∞ 0.00 0.98 4.47
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
23_R 79_Q 1.82 1.00 0.97
41_G 91_D 1.79 1.00 0.96
31_D 32_F 1.61 0.99 0.93
54_K 10_Y 1.33 0.96 0.83
44_Y 90_E 1.27 0.94 0.79
23_R 49_L 1.22 0.93 0.75
58_G 137_A 1.19 0.92 0.73
22_T 55_D 1.18 0.91 0.71
23_R 88_I 1.13 0.89 0.67
17_Y 112_A 1.05 0.83 0.59
48_E 120_G 1.03 0.81 0.56
50_L 3_T 1.01 0.80 0.54
32_Y 88_I 0.99 0.77 0.51
44_Y 63_C 0.95 0.73 0.47
69_L 103_E 0.93 0.71 0.44
25_V 81_I 0.92 0.69 0.42
17_Y 11_K 0.91 0.69 0.42
38_K 94_F 0.90 0.68 0.41
22_T 66_K 0.90 0.67 0.40
55_R 58_F 0.89 0.66 0.39
57_P 98_L 0.89 0.65 0.39
42_K 53_I 0.88 0.65 0.38
8_I 106_S 0.88 0.64 0.37
50_L 67_D 0.86 0.63 0.36
16_Q 69_T 0.86 0.62 0.36
50_L 161_V 0.86 0.62 0.35
22_T 93_V 0.86 0.62 0.35
42_K 90_E 0.86 0.62 0.35
71_K 77_R 0.86 0.62 0.35
58_G 66_K 0.85 0.61 0.34
31_D 11_K 0.85 0.61 0.34
77_A 116_I 0.84 0.60 0.34
49_Q 95_L 0.84 0.59 0.33
67_S 77_R 0.83 0.58 0.32
54_K 78_L 0.83 0.58 0.32
47_V 36_F 0.83 0.58 0.32
55_R 130_D 0.82 0.57 0.32
52_L 146_R 0.82 0.56 0.31
46_P 89_K 0.80 0.54 0.29
53_L 61_D 0.80 0.54 0.28
8_I 88_I 0.79 0.52 0.27
75_Q 39_E 0.78 0.51 0.26
17_Y 69_T 0.78 0.51 0.26
50_L 156_T 0.78 0.51 0.26
32_Y 78_L 0.77 0.50 0.26
71_K 33_K 0.77 0.50 0.26
65_E 134_V 0.77 0.50 0.26
32_Y 153_D 0.77 0.49 0.25
22_T 78_L 0.76 0.48 0.24
77_A 105_G 0.75 0.47 0.24
53_L 116_I 0.75 0.47 0.23
14_V 48_F 0.75 0.47 0.23
74_W 127_L 0.75 0.47 0.23
35_L 35_T 0.75 0.46 0.23
16_Q 3_T 0.74 0.46 0.23
10_P 121_G 0.74 0.46 0.23
8_I 79_Q 0.74 0.46 0.23
31_D 140_A 0.74 0.46 0.23
17_Y 104_D 0.74 0.45 0.22
35_L 163_S 0.73 0.44 0.21
7_L 71_Q 0.72 0.43 0.21
31_D 160_L 0.72 0.42 0.20
55_R 152_P 0.72 0.42 0.20
32_Y 82_H 0.72 0.42 0.20
41_G 43_G 0.71 0.42 0.20
48_E 86_G 0.71 0.41 0.20
43_L 66_K 0.70 0.40 0.19
43_L 89_K 0.70 0.40 0.19
3_P 14_L 0.70 0.40 0.19
61_D 44_L 0.70 0.40 0.19
31_D 120_G 0.70 0.40 0.19
55_R 31_A 0.70 0.40 0.19
48_E 50_E 0.70 0.40 0.19
28_V 163_S 0.70 0.39 0.18
21_E 83_K 0.70 0.39 0.18
25_V 59_S 0.69 0.39 0.18
78_K 48_F 0.69 0.39 0.18
67_S 150_G 0.69 0.39 0.18
14_V 29_Q 0.69 0.39 0.18
69_L 89_K 0.69 0.38 0.18
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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.98 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
7859 0.15 MFD_THETH_319-398-RPOB_THETH_17_392 Δgene:(1, 20) A:(1E-06, 8) B:(1E-20, 8) msa: Jackhmmer (r132) Killed - Shared
7857 4.86 MFD_THETH_319-398-RPOB_THETH_17_392 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.97 Done - Shared
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