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pred_3BP8_l_u_ApdbAfas_3BP8_r_u_ApdbAfastable_PRtxt
Genes: A B A+B
Length: 74 373 435
Sequences: 4189 5483 249
Seq/Len: 56.61 14.7 0.57
MirrorTree (Pazo et al. 2001) 0.65
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 0.02 0.02
2 0.02 0.02 0.08
5 0.02 0.03 0.31
10 0.02 0.04 0.42
20 0.02 0.05 0.56
100 0.03 0.08 1.30
∞ 0.09 0.18 2.49
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
57_I 228_R 1.52 0.62 0.00
4_L 196_V 1.35 0.48 0.00
39_L 342_V 1.34 0.48 0.00
14_I 253_R 1.27 0.42 0.00
14_I 324_I 1.25 0.41 0.00
17_L 163_V 1.23 0.39 0.00
21_I 155_L 1.18 0.35 0.00
39_L 202_T 1.13 0.32 0.00
5_V 299_V 1.11 0.31 0.00
46_G 204_G 1.11 0.31 0.00
5_V 278_D 1.10 0.29 0.00
38_G 190_V 1.08 0.28 0.00
60_T 212_S 1.03 0.26 0.00
65_L 320_L 1.03 0.25 0.00
43_G 292_V 1.02 0.24 0.00
8_F 89_Q 1.02 0.24 0.00
32_S 147_V 0.99 0.23 0.00
5_V 282_K 0.99 0.23 0.00
57_I 118_L 0.97 0.22 0.00
28_V 108_D 0.96 0.21 0.00
33_K 43_L 0.95 0.21 0.00
63_D 303_N 0.94 0.20 0.00
54_V 126_I 0.94 0.20 0.00
16_N 103_I 0.90 0.18 0.00
34_V 86_E 0.90 0.18 0.00
35_D 109_Q 0.89 0.18 0.00
40_K 304_P 0.88 0.17 0.00
72_I 324_I 0.87 0.17 0.00
37_A 91_L 0.87 0.17 0.00
33_K 163_V 0.86 0.17 0.00
51_G 156_E 0.85 0.16 0.00
14_I 42_E 0.85 0.16 0.00
32_S 321_F 0.85 0.16 0.00
51_G 190_V 0.84 0.15 0.00
61_K 146_D 0.84 0.15 0.00
56_A 272_Q 0.84 0.15 0.00
29_A 248_E 0.84 0.15 0.00
57_I 245_S 0.84 0.15 0.00
57_I 208_H 0.83 0.15 0.00
21_I 270_L 0.83 0.15 0.00
18_D 200_V 0.83 0.15 0.00
38_G 83_L 0.83 0.15 0.00
2_P 342_V 0.82 0.15 0.00
14_I 211_S 0.82 0.15 0.00
8_F 132_I 0.82 0.15 0.00
15_T 342_V 0.81 0.14 0.00
4_L 241_A 0.81 0.14 0.00
37_A 247_L 0.81 0.14 0.00
17_L 100_L 0.81 0.14 0.00
8_F 227_K 0.80 0.14 0.00
56_A 297_A 0.79 0.14 0.00
57_I 182_R 0.79 0.14 0.00
39_L 296_L 0.79 0.14 0.00
57_I 264_P 0.79 0.14 0.00
37_A 174_A 0.79 0.14 0.00
28_V 125_A 0.78 0.13 0.00
34_V 173_T 0.78 0.13 0.00
21_I 199_G 0.78 0.13 0.00
43_G 217_I 0.78 0.13 0.00
32_S 135_E 0.78 0.13 0.00
68_E 328_I 0.78 0.13 0.00
15_T 222_V 0.77 0.13 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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