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pred_2G77_l_u_ApdbAfas_2G77_r_u_ApdbAfastable_PRtxt
Genes: A B A+B
Length: 165 223 372
Sequences: 11306 2669 310
Seq/Len: 68.52 11.97 0.83
MirrorTree (Pazo et al. 2001) 0.10
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 0.05 0.04 0.06
2 0.06 0.04 0.09
5 0.08 0.04 0.26
10 0.10 0.04 0.47
20 0.13 0.04 0.80
100 0.23 0.06 2.05
∞ 0.28 0.14 3.19
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
9_G 38_R 1.07 0.36 0.00
91_F 183_L 0.91 0.24 0.00
116_G 128_Y 0.86 0.21 0.00
127_V 69_D 0.85 0.20 0.00
130_D 205_L 0.83 0.19 0.00
143_L 26_R 0.83 0.19 0.00
83_Y 208_L 0.83 0.19 0.00
133_Q 41_V 0.79 0.17 0.00
132_A 29_S 0.79 0.17 0.00
55_L 36_I 0.79 0.17 0.00
16_T 17_K 0.79 0.17 0.00
45_D 6_R 0.78 0.16 0.00
18_L 85_T 0.77 0.16 0.00
5_I 137_T 0.76 0.15 0.00
121_L 93_I 0.76 0.15 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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