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OPENSEQ.org
NusB_nusE_test
Genes: A B A+B
Length: 103 139 236
Sequences: 705 2477 1015
Seq/Len: 6.84 17.82 4.3
MirrorTree (Pazo et al. 2001) 0.62
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 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.02
20 0.00 0.00 0.04
100 0.00 0.00 0.38
∞ 0.00 0.00 4.19
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
98_V 128_D 1.83 1.00 0.97
8_I 91_E 1.32 0.94 0.81
64_Q 15_Q 1.19 0.89 0.71
16_R 81_E 1.05 0.80 0.57
18_I 20_W 1.05 0.80 0.56
52_L 115_G 1.03 0.78 0.54
13_F 24_Q 1.01 0.76 0.52
13_F 43_V 0.97 0.72 0.47
20_Q 84_V 0.95 0.70 0.45
29_A 15_Q 0.93 0.67 0.42
11_K 88_A 0.92 0.66 0.41
12_A 6_R 0.91 0.65 0.40
60_D 47_Y 0.91 0.65 0.40
73_L 127_L 0.91 0.65 0.40
30_K 25_N 0.91 0.65 0.40
78_E 131_A 0.91 0.64 0.39
14_D 89_L 0.90 0.63 0.38
54_S 128_D 0.89 0.62 0.38
8_I 99_P 0.87 0.60 0.36
13_F 82_K 0.86 0.59 0.34
97_D 51_L 0.85 0.56 0.33
60_D 71_S 0.84 0.55 0.32
4_Q 44_D 0.83 0.54 0.30
93_A 78_G 0.81 0.52 0.29
3_N 62_L 0.81 0.52 0.28
77_V 121_K 0.80 0.51 0.28
14_D 9_A 0.80 0.50 0.27
49_F 112_K 0.79 0.49 0.27
24_E 18_Y 0.79 0.48 0.26
3_N 105_N 0.79 0.48 0.26
12_A 98_V 0.78 0.48 0.26
81_E 110_L 0.77 0.46 0.24
14_D 62_L 0.76 0.45 0.23
67_I 44_D 0.75 0.44 0.23
45_R 53_A 0.75 0.44 0.23
40_I 57_T 0.75 0.43 0.22
74_V 66_M 0.75 0.43 0.22
8_I 88_A 0.75 0.43 0.22
80_T 85_L 0.74 0.42 0.22
53_I 76_E 0.74 0.42 0.21
84_V 83_A 0.74 0.42 0.21
14_D 7_R 0.73 0.41 0.21
16_R 77_L 0.73 0.41 0.20
70_H 117_E 0.72 0.40 0.20
66_E 63_D 0.72 0.39 0.20
52_L 11_E 0.72 0.39 0.20
59_K 105_N 0.72 0.39 0.19
65_Y 66_M 0.72 0.39 0.19
29_A 9_A 0.72 0.39 0.19
4_Q 14_V 0.72 0.39 0.19
20_Q 98_V 0.71 0.39 0.19
17_L 104_I 0.71 0.38 0.19
63_D 76_E 0.71 0.38 0.18
60_D 117_E 0.70 0.37 0.18
12_A 70_L 0.70 0.37 0.18
34_A 92_L 0.70 0.37 0.18
54_S 101_K 0.69 0.36 0.17
60_D 66_M 0.69 0.36 0.17
23_A 22_L 0.69 0.36 0.17
13_F 91_E 0.68 0.34 0.16
74_V 43_V 0.68 0.34 0.16
61_A 116_A 0.68 0.34 0.16
29_A 20_W 0.68 0.34 0.16
18_I 59_T 0.67 0.33 0.16
26_V 80_V 0.67 0.33 0.16
81_E 72_R 0.67 0.33 0.16
36_V 71_S 0.67 0.33 0.15
56_H 76_E 0.67 0.33 0.15
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
2504 4.3 NusB_nusE_test Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.97 Done
2503 0.04 NusB_nusE_test Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) Killed - Shared
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