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OPENSEQ.org
L1-vs-L33
Genes: A B A+B
Length: 234 55 278
Sequences: 3196 1895 1429
Seq/Len: 13.66 34.45 5.14
MirrorTree (Pazo et al. 2001) 0.53
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 0.09 0.08 0.01
2 0.09 0.08 0.08
5 0.09 0.08 2.10
10 0.09 0.08 2.38
20 0.09 0.08 2.61
100 0.09 0.10 3.09
∞ 0.10 0.13 4.94
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
128_G 25_K 0.84 0.62 0.00
134_R 53_K 0.79 0.55 0.00
160_Q 33_K 0.77 0.51 0.00
151_E 32_E 0.73 0.45 0.00
202_T 9_I 0.72 0.44 0.00
219_G 52_A 0.71 0.43 0.00
63_T 9_I 0.71 0.42 0.00
169_G 22_T 0.68 0.39 0.00
177_K 12_V 0.67 0.37 0.00
123_V 33_K 0.62 0.31 0.00
40_E 46_H 0.62 0.30 0.00
167_K 28_R 0.59 0.27 0.00
161_V 6_R 0.59 0.27 0.00
114_V 53_K 0.58 0.27 0.00
209_I 30_K 0.58 0.26 0.00
23_I 44_R 0.58 0.26 0.00
216_T 52_A 0.57 0.25 0.00
23_I 30_K 0.56 0.24 0.00
85_E 34_L 0.56 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)
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