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OPENSEQ.org
PpSiaQPpSiaQ
Genes: A B A+B
Length: 170 299 443
Sequences: 5610 6487 5018
Seq/Len: 33 21.7 11.33
MirrorTree (Pazo et al. 2001) 0.66
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 0.00 0.02 8.85
2 0.00 0.03 10.39
5 0.02 0.06 10.61
10 0.04 0.08 10.67
20 0.06 0.11 10.70
100 0.12 0.16 10.77
∞ 0.20 0.23 10.86
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
38_P 162_S 1.57 1.00 0.91
110_R 57_M 0.71 0.63 0.18
110_R 56_S 0.69 0.59 0.16
40_L 163_P 0.66 0.55 0.14
110_R 219_D 0.62 0.47 0.12
43_E 143_K 0.61 0.46 0.11
114_F 53_Q 0.61 0.45 0.11
36_D 143_K 0.58 0.40 0.09
112_A 56_S 0.56 0.37 0.08
36_D 162_S 0.56 0.37 0.08
114_F 73_W 0.55 0.35 0.08
33_W 181_D 0.52 0.31 0.07
40_L 157_K 0.51 0.29 0.06
120_G 150_K 0.49 0.27 0.06
38_P 164_T 0.49 0.27 0.06
31_S 164_T 0.48 0.26 0.05
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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