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OPENSEQ.org
lexA-recA
Genes: A B A+B
Length: 202 353 528
Sequences: 4937 1812 1312
Seq/Len: 24.44 5.13 2.48
MirrorTree (Pazo et al. 2001) 0.22
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 0.04 0.07 0.02
2 0.04 0.07 0.03
5 0.05 0.07 0.06
10 0.05 0.07 0.21
20 0.05 0.07 0.38
100 0.06 0.07 0.82
∞ 0.13 0.08 2.36
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
174_F 41_I 0.92 0.49 0.00
40_P 287_K 0.78 0.34 0.00
40_P 196_I 0.73 0.28 0.00
164_K 151_T 0.72 0.28 0.00
15_I 191_I 0.72 0.28 0.00
15_I 45_S 0.71 0.26 0.00
137_Q 290_A 0.70 0.26 0.00
163_N 27_I 0.70 0.26 0.00
91_Q 108_L 0.69 0.25 0.00
52_R 264_L 0.69 0.25 0.00
160_K 142_I 0.69 0.24 0.00
19_I 288_A 0.68 0.24 0.00
90_A 257_K 0.66 0.22 0.00
138_D 62_I 0.66 0.22 0.00
19_I 7_K 0.65 0.21 0.00
33_Q 238_V 0.65 0.21 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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