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OPENSEQ.org
N3toN5
Genes: A B A+B
Length: 73 97 162
Sequences: 850 4655 100
Seq/Len: 11.64 47.99 0.62
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 0.08 0.05
2 0.08 0.09 0.10
5 0.08 0.10 0.12
10 0.08 0.10 0.15
20 0.08 0.12 0.17
100 0.11 0.14 0.34
∞ 0.14 0.17 0.59
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
4_H 2_P 1.16 0.36 0.00
5_P 2_P 0.98 0.24 0.00
62_D 87_S 0.91 0.20 0.00
8_S 17_I 0.91 0.20 0.00
65_T 38_V 0.90 0.19 0.00
45_W 15_I 0.89 0.19 0.00
21_P 11_S 0.88 0.18 0.00
41_M 38_V 0.87 0.18 0.00
8_S 88_M 0.85 0.17 0.00
7_G 71_Y 0.85 0.17 0.00
26_C 71_Y 0.85 0.17 0.00
28_C 71_Y 0.85 0.17 0.00
37_C 71_Y 0.85 0.17 0.00
40_C 71_Y 0.85 0.17 0.00
29_K 96_E 0.84 0.16 0.00
7_G 19_W 0.84 0.16 0.00
26_C 19_W 0.84 0.16 0.00
28_C 19_W 0.84 0.16 0.00
37_C 19_W 0.84 0.16 0.00
40_C 19_W 0.84 0.16 0.00
30_P 14_T 0.83 0.16 0.00
20_D 70_L 0.83 0.16 0.00
61_C 2_P 0.83 0.16 0.00
55_C 22_N 0.83 0.16 0.00
5_P 63_T 0.82 0.16 0.00
39_R 8_S 0.82 0.16 0.00
44_Y 49_K 0.82 0.15 0.00
53_R 28_Q 0.81 0.15 0.00
24_G 87_S 0.80 0.15 0.00
31_G 51_K 0.80 0.15 0.00
32_V 35_Y 0.80 0.14 0.00
25_D 62_V 0.79 0.14 0.00
56_D 53_A 0.79 0.14 0.00
53_R 44_I 0.79 0.14 0.00
46_G 40_W 0.78 0.14 0.00
19_C 22_N 0.78 0.14 0.00
32_V 75_V 0.78 0.14 0.00
23_N 66_K 0.78 0.14 0.00
48_G 58_L 0.78 0.14 0.00
44_Y 38_V 0.77 0.14 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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