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OPENSEQ.org
2NZ8_AB
Genes: A B A+B
Length: 177 313 478
Sequences: 11467 3591 333
Seq/Len: 64.79 11.47 0.7
MirrorTree (Pazo et al. 2001) 0.12
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 0.05 0.06
2 0.06 0.05 0.11
5 0.07 0.06 0.26
10 0.09 0.07 0.46
20 0.12 0.09 0.68
100 0.22 0.11 1.75
∞ 0.28 0.14 2.46
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
17_T 70_H 1.29 0.49 0.00
76_D 258_T 0.97 0.25 0.00
160_L 148_I 0.94 0.23 0.00
110_I 15_I 0.94 0.23 0.00
93_V 294_S 0.94 0.23 0.00
111_I 125_D 0.92 0.22 0.00
84_L 158_L 0.91 0.21 0.00
173_I 297_N 0.89 0.20 0.00
53_L 91_C 0.89 0.20 0.00
13_A 272_C 0.89 0.20 0.00
143_L 179_V 0.86 0.19 0.00
114_G 235_L 0.85 0.18 0.00
15_G 23_E 0.85 0.18 0.00
143_L 71_N 0.84 0.18 0.00
36_V 22_T 0.84 0.18 0.00
8_V 66_I 0.84 0.18 0.00
77_V 172_G 0.82 0.17 0.00
79_L 20_I 0.80 0.15 0.00
4_I 139_S 0.79 0.15 0.00
6_C 182_R 0.78 0.15 0.00
172_A 30_L 0.78 0.15 0.00
107_N 177_L 0.78 0.15 0.00
80_I 140_Y 0.78 0.15 0.00
77_V 125_D 0.77 0.15 0.00
82_F 174_E 0.77 0.14 0.00
102_R 258_T 0.76 0.14 0.00
44_V 91_C 0.76 0.14 0.00
101_V 157_E 0.76 0.14 0.00
72_Y 209_E 0.75 0.14 0.00
167_T 250_Y 0.75 0.14 0.00
148_E 33_C 0.75 0.14 0.00
90_F 63_M 0.75 0.14 0.00
48_G 43_S 0.74 0.13 0.00
75_T 155_L 0.73 0.13 0.00
18_C 174_E 0.72 0.13 0.00
167_T 114_Q 0.72 0.13 0.00
90_F 176_M 0.72 0.13 0.00
155_L 184_N 0.72 0.13 0.00
64_Y 72_N 0.72 0.13 0.00
34_P 61_G 0.72 0.12 0.00
17_T 246_G 0.72 0.12 0.00
10_G 23_E 0.72 0.12 0.00
166_K 16_M 0.72 0.12 0.00
64_Y 235_L 0.72 0.12 0.00
23_Y 160_T 0.71 0.12 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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