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OPENSEQ.org
H0993
Genes: A B A+B
Length: 269 109 342
Sequences: 75042 4382 1075
Seq/Len: 278.97 40.2 3.14
MirrorTree (Pazo et al. 2001) 0.31
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 0.10 0.01 0.16
2 0.10 0.02 0.26
5 0.14 0.02 1.34
10 0.18 0.03 1.90
20 0.23 0.04 2.84
100 0.34 0.06 6.66
∞ 0.37 0.16 8.89
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
158_A 105_D 0.90 0.54 0.00
27_I 26_L 0.85 0.48 0.00
211_I 65_G 0.84 0.47 0.00
42_P 30_G 0.81 0.43 0.00
153_A 64_T 0.75 0.36 0.00
218_L 54_I 0.71 0.32 0.00
199_V 79_K 0.71 0.31 0.00
165_L 29_S 0.70 0.30 0.00
28_S 86_L 0.70 0.30 0.00
244_L 66_G 0.69 0.29 0.00
158_A 81_G 0.69 0.29 0.00
14_V 29_S 0.68 0.28 0.00
193_A 77_A 0.67 0.26 0.00
151_R 100_Y 0.67 0.26 0.00
218_L 106_V 0.65 0.25 0.00
123_S 54_I 0.64 0.24 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
8980 3.14 H0993 Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8973 0.8 mla Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.44 Done - Shared
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