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OPENSEQ.org
efp-pepq
Genes: A B A+B
Length: 187 372 543
Sequences: 1458 4167 1194
Seq/Len: 7.8 11.2 2.2
MirrorTree (Pazo et al. 2001) 0.42
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 0.00 0.58
2 0.00 0.00 0.60
5 0.00 0.01 0.62
10 0.00 0.01 0.64
20 0.00 0.01 0.67
100 0.00 0.02 0.85
∞ 0.06 0.15 2.14
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
42_K 62_T 1.07 0.62 0.01
175_D 298_V 0.91 0.45 0.00
17_G 319_G 0.91 0.45 0.00
100_D 343_V 0.85 0.38 0.00
143_D 324_V 0.83 0.36 0.00
56_A 216_D 0.75 0.28 0.00
166_I 96_G 0.74 0.28 0.00
87_D 214_V 0.73 0.27 0.00
89_E 289_H 0.71 0.24 0.00
172_L 16_A 0.71 0.24 0.00
42_K 42_A 0.70 0.24 0.00
46_S 110_L 0.69 0.23 0.00
99_G 189_S 0.68 0.22 0.00
158_A 233_M 0.68 0.22 0.00
113_V 242_A 0.67 0.21 0.00
24_E 308_I 0.67 0.21 0.00
8_K 30_V 0.67 0.21 0.00
91_H 369_L 0.67 0.21 0.00
123_I 8_D 0.66 0.21 0.00
8_K 91_G 0.66 0.21 0.00
123_I 185_A 0.66 0.20 0.00
88_Y 321_V 0.66 0.20 0.00
160_I 172_V 0.65 0.20 0.00
13_L 167_R 0.65 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)
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