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OPENSEQ.org
LexAfun2
Genes: A B A+B
Length: 202 353 529
Sequences: 4735 1819 1316
Seq/Len: 23.44 5.15 2.49
MirrorTree (Pazo et al. 2001) 0.27
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 0.05 0.07 0.02
2 0.05 0.07 0.03
5 0.05 0.07 0.06
10 0.05 0.07 0.21
20 0.05 0.07 0.37
100 0.07 0.07 0.81
∞ 0.13 0.08 2.37
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
163_N 27_I 1.00 0.59 0.00
40_P 196_I 0.79 0.35 0.00
40_P 287_K 0.76 0.32 0.00
195_V 156_I 0.76 0.32 0.00
137_Q 290_A 0.72 0.28 0.00
174_F 41_I 0.72 0.27 0.00
157_R 298_K 0.70 0.26 0.00
100_V 320_I 0.70 0.26 0.00
56_I 153_K 0.69 0.25 0.00
19_I 30_L 0.68 0.24 0.00
166_E 290_A 0.66 0.22 0.00
174_F 269_I 0.65 0.22 0.00
68_L 84_A 0.64 0.21 0.00
36_G 243_T 0.63 0.20 0.00
20_S 42_S 0.63 0.20 0.00
71_E 54_A 0.63 0.20 0.00
94_I 63_V 0.63 0.20 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
14190 2.49 LexAfun2 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9704 0.4 LexAfun Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
3611 2.48 lexA-recA Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done
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