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OPENSEQ.org
Ecoli NusG-S10
Genes: A B A+B
Length: 87 40 119
Sequences: 1110 2296 299
Seq/Len: 12.76 57.4 2.51
MirrorTree (Pazo et al. 2001) 0.42
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 0.09 0.01 0.01
2 0.09 0.01 0.02
5 0.09 0.01 0.05
10 0.09 0.01 0.48
20 0.09 0.02 2.35
100 0.09 0.02 3.36
∞ 0.09 0.06 5.52
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
26_A 38_E 1.63 0.97 0.81
82_V 27_A 1.51 0.94 0.74
26_A 13_E 1.44 0.92 0.69
50_R 27_A 1.35 0.88 0.61
66_K 1_A 1.34 0.88 0.60
64_T 11_D 1.17 0.77 0.44
62_E 21_V 1.12 0.72 0.39
17_A 33_D 1.09 0.69 0.35
78_A 14_K 1.04 0.63 0.30
76_L 3_F 1.03 0.63 0.30
42_R 5_G 1.01 0.60 0.28
19_D 23_I 1.00 0.60 0.27
66_K 2_D 1.00 0.59 0.27
58_V 10_V 0.98 0.56 0.25
35_K 14_K 0.97 0.56 0.24
79_G 5_G 0.96 0.55 0.24
29_E 23_I 0.96 0.55 0.24
82_V 1_A 0.96 0.54 0.23
65_E 2_D 0.95 0.53 0.23
36_R 17_L 0.91 0.49 0.20
20_H 7_V 0.90 0.47 0.19
31_V 36_Q 0.90 0.47 0.19
22_L 18_K 0.88 0.45 0.17
35_K 8_E 0.87 0.43 0.17
67_T 32_L 0.86 0.43 0.16
28_A 23_I 0.86 0.43 0.16
33_T 9_E 0.85 0.42 0.16
73_R 27_A 0.84 0.40 0.15
34_A 33_D 0.84 0.40 0.15
73_R 8_E 0.84 0.40 0.15
31_V 19_V 0.84 0.40 0.15
37_T 32_L 0.83 0.39 0.14
33_T 18_K 0.83 0.39 0.14
78_A 11_D 0.83 0.39 0.14
23_I 23_I 0.82 0.39 0.14
27_T 23_I 0.82 0.39 0.14
18_F 18_K 0.81 0.37 0.13
68_V 7_V 0.80 0.36 0.12
29_E 27_A 0.78 0.34 0.12
37_T 15_S 0.78 0.33 0.11
23_I 22_S 0.77 0.33 0.11
77_A 27_A 0.76 0.32 0.10
45_I 1_A 0.76 0.32 0.10
24_D 32_L 0.76 0.31 0.10
66_K 12_Y 0.75 0.31 0.10
83_Q 20_S 0.75 0.31 0.10
81_D 30_V 0.75 0.31 0.10
75_D 37_V 0.74 0.30 0.10
31_V 21_V 0.73 0.29 0.09
82_V 23_I 0.73 0.29 0.09
50_R 10_V 0.73 0.28 0.09
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
13970 3.61 Ecoli NusG-S10_delta100 Δgene:(1, 100) A:(1E-20, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.94 Done - Shared
13969 2.51 Ecoli NusG-S10 Δgene:(1, 20) A:(1E-20, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.81 Done - Shared
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