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OPENSEQ.org
2wpt_B_A
Genes: A B A+B
Length: 134 86 215
Sequences: 136 211 105
Seq/Len: 1.01 2.45 0.49
MirrorTree (Pazo et al. 2001) 0.57
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 0.27 0.46
2 0.02 0.31 0.48
5 0.03 0.33 0.48
10 0.03 0.33 0.48
20 0.03 0.33 0.48
100 0.03 0.33 0.48
∞ 0.05 0.36 0.48
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
89_K 51_D 2.09 0.88 0.35
75_N 55_Y 1.70 0.70 0.15
97_K 38_R 1.63 0.65 0.12
74_S 23_A 1.51 0.56 0.09
89_K 41_E 1.49 0.55 0.08
18_V 82_G 1.47 0.54 0.07
128_I 63_S 1.44 0.51 0.07
78_S 30_E 1.36 0.45 0.05
99_Y 44_T 1.27 0.39 0.04
98_V 37_V 1.25 0.37 0.04
86_F 37_V 1.25 0.37 0.04
78_S 37_V 1.24 0.36 0.03
98_V 36_L 1.21 0.34 0.03
72_N 62_D 1.18 0.32 0.03
60_E 77_A 1.17 0.31 0.03
4_K 80_K 1.16 0.30 0.03
120_R 52_L 1.15 0.30 0.03
98_V 34_N 1.14 0.29 0.02
66_E 71_I 1.13 0.28 0.02
132_R 8_S 1.09 0.27 0.02
109_Q 54_Y 1.09 0.26 0.02
95_C 35_K 1.08 0.26 0.02
79_V 41_E 1.08 0.26 0.02
119_I 4_K 1.06 0.25 0.02
88_P 51_D 1.06 0.24 0.02
11_A 61_E 1.03 0.23 0.02
101_L 50_S 1.01 0.22 0.01
45_K 5_H 0.99 0.21 0.01
4_K 71_I 0.97 0.20 0.01
100_E 63_S 0.97 0.20 0.01
112_E 52_L 0.96 0.19 0.01
119_I 54_Y 0.95 0.19 0.01
116_M 63_S 0.95 0.19 0.01
92_Q 50_S 0.95 0.19 0.01
93_V 63_S 0.94 0.18 0.01
86_F 41_E 0.92 0.17 0.01
75_N 67_I 0.92 0.17 0.01
18_V 85_Q 0.92 0.17 0.01
24_D 73_E 0.91 0.17 0.01
100_E 66_G 0.89 0.16 0.01
14_K 68_V 0.88 0.16 0.01
99_Y 22_I 0.88 0.16 0.01
121_V 17_E 0.87 0.15 0.01
40_D 10_Y 0.87 0.15 0.01
43_R 72_K 0.86 0.15 0.01
88_P 53_I 0.85 0.15 0.01
87_T 58_D 0.85 0.15 0.01
43_R 12_E 0.84 0.14 0.01
38_I 82_G 0.84 0.14 0.01
18_V 78_N 0.84 0.14 0.01
114_Y 56_P 0.83 0.14 0.01
64_D 45_E 0.83 0.14 0.01
4_K 78_N 0.83 0.14 0.01
62_S 8_S 0.83 0.14 0.01
134_K 80_K 0.82 0.14 0.01
91_Q 37_V 0.82 0.13 0.01
80_S 48_D 0.82 0.13 0.01
69_K 52_L 0.82 0.13 0.01
49_S 77_A 0.82 0.13 0.01
77_S 67_I 0.81 0.13 0.01
51_D 61_E 0.81 0.13 0.01
79_V 51_D 0.81 0.13 0.01
74_S 53_I 0.81 0.13 0.01
5_R 75_R 0.80 0.13 0.01
12_T 80_K 0.78 0.12 0.01
56_A 65_E 0.78 0.12 0.01
62_S 52_L 0.78 0.12 0.01
99_Y 53_I 0.78 0.12 0.01
92_Q 66_G 0.77 0.12 0.01
17_P 77_A 0.77 0.12 0.01
126_R 80_K 0.77 0.12 0.01
102_H 12_E 0.77 0.12 0.01
85_P 66_G 0.76 0.12 0.01
120_R 79_G 0.76 0.11 0.01
59_E 85_Q 0.75 0.11 0.01
4_K 57_R 0.75 0.11 0.01
64_D 82_G 0.75 0.11 0.01
64_D 78_N 0.75 0.11 0.01
75_N 54_Y 0.75 0.11 0.01
105_K 80_K 0.75 0.11 0.01
124_P 81_S 0.75 0.11 0.01
27_G 9_D 0.74 0.11 0.01
121_V 13_A 0.74 0.11 0.01
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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