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OPENSEQ.org
pap_omp
Genes: A B A+B
Length: 383 485 796
Sequences: 14469 13022 6008
Seq/Len: 37.78 26.85 7.55
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 0.02 0.00 3.09
2 0.02 0.00 5.99
5 0.04 0.02 6.59
10 0.05 0.04 6.76
20 0.07 0.06 6.92
100 0.14 0.14 7.66
∞ 0.21 0.21 8.71
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
126_D 419_K 2.29 1.00 0.99
122_L 423_T 1.81 1.00 0.98
127_Q 220_A 1.61 1.00 0.95
126_D 211_R 1.58 1.00 0.95
127_Q 213_Y 1.41 0.99 0.90
122_L 215_V 1.20 0.96 0.78
126_D 415_Q 1.16 0.95 0.76
128_A 419_K 1.14 0.95 0.74
120_Y 425_V 1.08 0.93 0.68
130_S 219_S 1.07 0.92 0.67
120_Y 217_V 1.05 0.91 0.65
128_A 211_R 0.84 0.73 0.40
128_A 416_L 0.81 0.69 0.36
126_D 207_D 0.76 0.61 0.30
127_Q 422_R 0.72 0.56 0.25
132_Q 217_V 0.64 0.43 0.17
133_Q 420_R 0.62 0.40 0.16
128_A 208_L 0.62 0.39 0.15
131_K 216_G 0.61 0.38 0.15
127_Q 204_K 0.57 0.33 0.12
123_L 217_V 0.54 0.28 0.10
250_V 323_A 0.53 0.27 0.10
190_V 106_G 0.52 0.26 0.09
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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