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OPENSEQ.org
N3toN5b
Genes: A B A+B
Length: 73 97 163
Sequences: 1026 9385 172
Seq/Len: 14.05 96.75 1.06
MirrorTree (Pazo et al. 2001) 0.14
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 0.07 0.07 0.06
2 0.08 0.08 0.12
5 0.08 0.09 0.15
10 0.08 0.10 0.24
20 0.09 0.11 0.38
100 0.12 0.13 0.68
∞ 0.14 0.16 1.01
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
45_W 59_S 1.24 0.57 0.00
5_P 17_I 1.20 0.54 0.00
54_P 40_W 1.03 0.38 0.00
54_P 59_S 0.96 0.32 0.00
47_F 75_V 0.95 0.31 0.00
63_P 11_S 0.95 0.31 0.00
24_G 2_P 0.94 0.30 0.00
63_P 18_T 0.92 0.28 0.00
47_F 11_S 0.91 0.28 0.00
39_R 7_A 0.89 0.27 0.00
26_C 71_Y 0.89 0.26 0.00
28_C 71_Y 0.89 0.26 0.00
37_C 71_Y 0.89 0.26 0.00
40_C 71_Y 0.89 0.26 0.00
56_D 55_A 0.87 0.25 0.00
59_G 37_T 0.85 0.24 0.00
17_T 10_L 0.85 0.23 0.00
29_K 87_S 0.83 0.22 0.00
23_N 76_M 0.83 0.22 0.00
5_P 40_W 0.83 0.22 0.00
57_C 69_T 0.82 0.22 0.00
50_Y 67_P 0.82 0.22 0.00
61_C 62_V 0.81 0.21 0.00
31_G 57_T 0.81 0.21 0.00
32_V 87_S 0.80 0.21 0.00
25_D 36_Y 0.80 0.20 0.00
70_S 69_T 0.79 0.20 0.00
43_G 24_L 0.79 0.20 0.00
45_W 37_T 0.78 0.19 0.00
20_D 15_I 0.77 0.19 0.00
55_C 71_Y 0.77 0.19 0.00
26_C 19_W 0.77 0.18 0.00
28_C 19_W 0.77 0.18 0.00
37_C 19_W 0.77 0.18 0.00
40_C 19_W 0.77 0.18 0.00
47_F 90_A 0.76 0.18 0.00
23_N 67_P 0.75 0.18 0.00
55_C 69_T 0.75 0.17 0.00
42_V 92_G 0.74 0.17 0.00
20_D 5_V 0.74 0.17 0.00
66_G 69_T 0.74 0.17 0.00
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
6303 1.12 N3toN5c Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
6300 1.06 N3toN5b Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
6299 0.62 N3toN5 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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