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OPENSEQ.org
Ecoli NusG-S10_delta100
Genes: A B A+B
Length: 87 40 119
Sequences: 1110 2296 430
Seq/Len: 12.76 57.4 3.61
MirrorTree (Pazo et al. 2001) 0.46
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 0.49
20 0.09 0.02 2.36
100 0.09 0.02 3.39
∞ 0.09 0.06 5.46
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
34_A 33_D 1.74 0.99 0.94
26_A 38_E 1.65 0.99 0.92
36_R 17_L 1.34 0.93 0.78
79_G 5_G 1.33 0.93 0.78
21_R 7_V 1.26 0.90 0.72
82_V 27_A 1.19 0.86 0.65
78_A 11_D 1.16 0.85 0.63
26_A 39_K 1.12 0.81 0.58
27_T 23_I 1.11 0.81 0.57
35_K 8_E 1.03 0.74 0.49
17_A 33_D 1.01 0.71 0.46
66_K 1_A 0.98 0.69 0.43
19_D 30_V 0.98 0.68 0.43
62_E 21_V 0.97 0.67 0.42
26_A 13_E 0.97 0.66 0.41
78_A 1_A 0.96 0.66 0.41
58_V 12_Y 0.96 0.66 0.40
50_R 27_A 0.95 0.64 0.39
29_E 23_I 0.94 0.64 0.38
28_A 23_I 0.93 0.61 0.36
17_A 39_K 0.92 0.60 0.35
55_L 33_D 0.90 0.58 0.33
84_I 32_L 0.89 0.57 0.33
59_D 36_Q 0.89 0.57 0.32
64_T 7_V 0.89 0.57 0.32
28_A 29_P 0.89 0.57 0.32
52_R 33_D 0.88 0.56 0.32
66_K 11_D 0.87 0.54 0.30
19_D 23_I 0.87 0.54 0.30
34_A 23_I 0.87 0.54 0.30
29_E 16_R 0.86 0.53 0.29
42_R 5_G 0.86 0.53 0.29
45_I 15_S 0.84 0.51 0.28
35_K 14_K 0.84 0.51 0.28
31_V 21_V 0.84 0.51 0.27
45_I 4_N 0.84 0.50 0.27
50_R 37_V 0.82 0.48 0.25
73_R 17_L 0.80 0.45 0.23
35_K 11_D 0.80 0.45 0.23
29_E 27_A 0.80 0.45 0.23
18_F 37_V 0.79 0.44 0.23
65_E 40_A 0.78 0.42 0.21
70_A 19_V 0.77 0.42 0.21
27_T 15_S 0.77 0.42 0.21
22_L 18_K 0.77 0.41 0.21
37_T 32_L 0.76 0.41 0.20
32_E 27_A 0.75 0.39 0.19
78_A 30_V 0.75 0.39 0.19
10_R 13_E 0.75 0.39 0.19
66_K 2_D 0.74 0.38 0.18
77_A 15_S 0.74 0.37 0.18
76_L 3_F 0.74 0.37 0.18
33_T 9_E 0.73 0.37 0.17
70_A 30_V 0.73 0.36 0.17
75_D 37_V 0.73 0.36 0.17
33_T 10_V 0.72 0.36 0.17
75_D 39_K 0.72 0.35 0.17
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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