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OPENSEQ.org
3u43
Genes: A B A+B
Length: 134 95 214
Sequences: 138 208 106
Seq/Len: 1.03 2.19 0.5
MirrorTree (Pazo et al. 2001) 0.54
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 0.45
2 0.02 0.32 0.46
5 0.03 0.34 0.46
10 0.03 0.34 0.46
20 0.03 0.34 0.46
100 0.03 0.34 0.46
∞ 0.05 0.36 0.46
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
89_E 52_D 2.11 0.90 0.41
75_N 56_Y 1.71 0.71 0.17
128_I 64_S 1.59 0.63 0.12
74_A 23_F 1.53 0.59 0.11
18_V 83_G 1.53 0.58 0.10
89_E 42_K 1.43 0.51 0.08
97_T 39_L 1.41 0.49 0.07
78_N 31_N 1.36 0.45 0.06
86_F 38_V 1.29 0.40 0.05
120_R 53_L 1.25 0.37 0.04
78_N 38_V 1.24 0.36 0.04
98_T 38_V 1.22 0.35 0.04
60_E 78_A 1.22 0.35 0.04
72_S 63_D 1.19 0.33 0.03
98_T 37_L 1.17 0.32 0.03
132_R 8_S 1.15 0.30 0.03
79_I 42_K 1.12 0.29 0.03
98_T 35_I 1.12 0.28 0.03
99_Y 45_T 1.12 0.28 0.03
88_R 52_D 1.12 0.28 0.03
4_K 81_K 1.11 0.28 0.03
109_Q 55_Y 1.08 0.26 0.02
95_G 36_K 1.04 0.24 0.02
11_A 62_E 1.04 0.24 0.02
4_K 72_I 1.01 0.22 0.02
101_L 51_S 0.99 0.21 0.01
119_I 4_K 0.99 0.21 0.01
75_N 68_I 0.99 0.21 0.01
116_M 64_S 0.96 0.20 0.01
100_E 64_S 0.96 0.20 0.01
92_Q 51_S 0.96 0.20 0.01
93_V 64_S 0.96 0.20 0.01
56_K 72_I 0.94 0.19 0.01
119_I 55_Y 0.92 0.17 0.01
14_K 69_V 0.91 0.17 0.01
121_V 13_A 0.91 0.17 0.01
113_V 67_G 0.91 0.17 0.01
80_K 49_D 0.90 0.17 0.01
51_D 62_E 0.89 0.16 0.01
112_G 53_L 0.89 0.16 0.01
45_K 5_H 0.89 0.16 0.01
99_Y 22_I 0.88 0.16 0.01
100_E 67_G 0.88 0.16 0.01
83_N 28_P 0.88 0.16 0.01
18_V 77_A 0.87 0.15 0.01
40_D 10_Y 0.86 0.15 0.01
98_T 31_N 0.86 0.15 0.01
12_T 81_K 0.85 0.15 0.01
24_D 74_E 0.85 0.15 0.01
66_D 72_I 0.85 0.15 0.01
88_R 54_I 0.85 0.15 0.01
64_D 46_E 0.85 0.15 0.01
114_Y 57_P 0.84 0.14 0.01
4_K 79_N 0.84 0.14 0.01
38_I 83_G 0.83 0.14 0.01
69_K 53_L 0.82 0.14 0.01
117_N 35_I 0.82 0.14 0.01
99_Y 54_I 0.82 0.14 0.01
43_R 73_K 0.81 0.13 0.01
74_A 54_I 0.81 0.13 0.01
64_D 83_G 0.81 0.13 0.01
43_R 12_E 0.80 0.13 0.01
105_K 81_K 0.80 0.13 0.01
89_E 53_L 0.80 0.13 0.01
92_Q 67_G 0.80 0.13 0.01
4_K 58_R 0.80 0.13 0.01
102_H 12_E 0.80 0.13 0.01
107_I 55_Y 0.79 0.13 0.01
18_V 79_N 0.79 0.13 0.01
86_F 42_K 0.79 0.13 0.01
62_A 53_L 0.79 0.12 0.01
54_R 76_R 0.79 0.12 0.01
56_K 66_E 0.78 0.12 0.01
62_A 8_S 0.78 0.12 0.01
12_T 40_E 0.78 0.12 0.01
124_P 82_S 0.78 0.12 0.01
79_I 52_D 0.77 0.12 0.01
17_P 78_A 0.77 0.12 0.01
44_D 82_S 0.77 0.12 0.01
89_E 22_I 0.77 0.12 0.01
49_N 71_E 0.77 0.12 0.01
44_D 60_D 0.77 0.12 0.01
132_R 69_V 0.77 0.12 0.01
41_K 72_I 0.76 0.12 0.01
93_V 26_S 0.76 0.12 0.01
84_A 23_F 0.76 0.11 0.01
64_D 79_N 0.75 0.11 0.01
134_K 81_K 0.75 0.11 0.01
95_G 39_L 0.75 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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