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OPENSEQ.org
1I7Q_CB_DMPmodel
Genes: A B A+B
Length: 192 255 435
Sequences: 16224 6148 2078
Seq/Len: 84.5 24.11 4.78
MirrorTree (Pazo et al. 2001) 0.34
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 0.03 0.01 3.68
2 0.03 0.01 3.91
5 0.03 0.01 4.12
10 0.04 0.01 4.40
20 0.05 0.01 4.65
100 0.12 0.04 5.69
∞ 0.20 0.17 8.33
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
99_Q 18_K 3.31 1.00 1.00
18_D 127_G 2.42 1.00 1.00
21_R 132_Y 2.21 1.00 0.99
103_I 241_A 2.02 1.00 0.99
99_Q 14_D 1.79 1.00 0.97
129_A 116_V 1.59 0.99 0.95
99_Q 17_H 1.53 0.99 0.93
174_L 116_V 1.38 0.97 0.88
107_K 242_D 1.25 0.94 0.81
58_G 15_Y 0.99 0.77 0.56
17_V 132_Y 0.92 0.69 0.48
58_G 20_D 0.84 0.59 0.38
108_A 116_V 0.79 0.52 0.32
129_A 141_M 0.77 0.49 0.29
62_E 20_D 0.74 0.45 0.26
129_A 179_V 0.69 0.38 0.21
173_I 116_V 0.65 0.33 0.17
68_E 162_A 0.63 0.31 0.16
40_I 228_G 0.63 0.30 0.15
31_R 185_V 0.62 0.30 0.15
107_K 13_K 0.62 0.29 0.14
27_V 132_Y 0.60 0.28 0.14
127_P 112_R 0.60 0.27 0.13
14_Y 24_V 0.60 0.27 0.13
173_I 182_A 0.58 0.25 0.12
156_V 57_L 0.58 0.25 0.12
180_R 4_E 0.57 0.24 0.12
50_V 122_G 0.57 0.24 0.11
21_R 161_R 0.57 0.24 0.11
183_E 143_V 0.57 0.24 0.11
173_I 140_Q 0.57 0.23 0.11
27_V 203_A 0.56 0.23 0.11
96_Q 11_K 0.56 0.23 0.11
59_T 18_K 0.56 0.23 0.10
120_A 161_R 0.56 0.23 0.10
172_S 126_L 0.56 0.23 0.10
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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