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OPENSEQ.org
PRDX6GST
Genes: A B A+B
Length: 224 210 384
Sequences: 2664 19207 146
Seq/Len: 11.89 91.46 0.38
MirrorTree (Pazo et al. 2001) 0.13
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 0.01 0.07 0.02
2 0.01 0.08 0.04
5 0.01 0.09 0.09
10 0.01 0.11 0.16
20 0.01 0.13 0.34
100 0.02 0.19 1.33
∞ 0.08 0.25 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
100_F 56_F 1.40 0.41 0.00
137_F 18_L 1.31 0.35 0.00
137_F 128_K 1.29 0.34 0.00
111_A 26_G 1.20 0.28 0.00
23_I 27_Q 1.16 0.26 0.00
102_I 90_V 1.15 0.26 0.00
17_N 146_G 1.04 0.20 0.00
100_F 91_D 1.03 0.20 0.00
172_E 143_F 1.01 0.18 0.00
11_A 186_A 1.00 0.18 0.00
136_V 121_K 0.99 0.18 0.00
140_D 160_L 0.99 0.18 0.00
17_N 184_L 0.98 0.17 0.00
100_F 63_L 0.96 0.17 0.00
24_R 21_L 0.96 0.17 0.00
109_E 150_S 0.94 0.16 0.00
65_N 62_T 0.94 0.16 0.00
65_N 176_L 0.93 0.15 0.00
23_I 179_A 0.93 0.15 0.00
103_I 128_K 0.92 0.15 0.00
27_D 176_L 0.91 0.15 0.00
136_V 43_S 0.91 0.14 0.00
164_V 62_T 0.91 0.14 0.00
170_T 73_L 0.90 0.14 0.00
22_R 190_L 0.90 0.14 0.00
110_L 32_E 0.88 0.14 0.00
8_G 59_G 0.87 0.13 0.00
35_I 62_T 0.86 0.13 0.00
61_F 90_V 0.85 0.13 0.00
13_N 30_K 0.85 0.13 0.00
26_H 150_S 0.84 0.12 0.00
23_I 101_R 0.84 0.12 0.00
40_P 54_P 0.83 0.12 0.00
105_D 54_P 0.83 0.12 0.00
178_P 54_P 0.83 0.12 0.00
107_N 63_L 0.83 0.12 0.00
142_K 24_D 0.83 0.12 0.00
142_K 188_P 0.83 0.12 0.00
192_T 7_V 0.82 0.12 0.00
8_G 36_V 0.81 0.11 0.00
16_A 182_G 0.80 0.11 0.00
78_D 46_A 0.80 0.11 0.00
59_P 21_L 0.79 0.11 0.00
27_D 146_G 0.79 0.11 0.00
174_R 34_V 0.79 0.11 0.00
117_L 80_Y 0.78 0.11 0.00
161_L 147_D 0.78 0.11 0.00
194_P 36_V 0.78 0.11 0.00
182_K 33_V 0.78 0.11 0.00
103_I 97_V 0.77 0.10 0.00
35_I 110_T 0.77 0.10 0.00
30_G 22_L 0.76 0.10 0.00
111_A 28_S 0.76 0.10 0.00
23_I 132_T 0.76 0.10 0.00
190_L 104_Y 0.76 0.10 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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