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OPENSEQ.org
4uhp_A_B
Genes: A B A+B
Length: 136 98 214
Sequences: 135 206 103
Seq/Len: 0.99 2.1 0.48
MirrorTree (Pazo et al. 2001) 0.49
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 0.42
2 0.02 0.32 0.44
5 0.02 0.34 0.44
10 0.02 0.34 0.44
20 0.02 0.34 0.44
100 0.03 0.34 0.44
∞ 0.05 0.36 0.44
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
84_P 56_G 2.10 0.89 0.37
70_N 60_H 1.87 0.79 0.23
92_E 43_K 1.56 0.59 0.10
123_S 67_T 1.54 0.58 0.10
13_V 86_G 1.54 0.58 0.10
84_P 46_E 1.45 0.51 0.07
69_S 23_F 1.42 0.49 0.07
73_F 35_E 1.29 0.39 0.04
93_K 41_L 1.24 0.36 0.04
81_Y 42_V 1.21 0.34 0.03
55_A 81_A 1.20 0.33 0.03
104_S 59_F 1.19 0.32 0.03
115_V 57_V 1.17 0.31 0.03
114_L 4_K 1.17 0.31 0.03
94_F 49_T 1.15 0.30 0.03
88_L 67_T 1.13 0.29 0.02
73_F 42_V 1.13 0.29 0.02
127_K 8_S 1.11 0.27 0.02
74_V 46_E 1.08 0.26 0.02
93_K 39_D 1.06 0.24 0.02
44_S 81_A 1.05 0.24 0.02
93_K 42_V 1.05 0.24 0.02
46_R 66_E 1.02 0.22 0.02
111_I 67_T 1.01 0.22 0.01
83_V 56_G 1.01 0.21 0.01
19_A 77_E 1.00 0.21 0.01
107_A 57_V 1.00 0.21 0.01
61_S 75_V 0.99 0.20 0.01
6_A 66_E 0.97 0.20 0.01
35_D 10_Y 0.97 0.19 0.01
51_Q 75_V 0.96 0.19 0.01
40_K 5_N 0.94 0.18 0.01
90_S 40_K 0.94 0.18 0.01
109_Y 61_P 0.93 0.18 0.01
64_E 57_V 0.93 0.18 0.01
94_F 58_I 0.92 0.17 0.01
108_L 70_G 0.92 0.17 0.01
33_I 86_G 0.92 0.17 0.01
70_N 71_I 0.92 0.17 0.01
9_N 72_V 0.91 0.17 0.01
39_G 64_G 0.91 0.17 0.01
59_D 86_G 0.91 0.17 0.01
87_H 55_S 0.90 0.16 0.01
116_I 13_S 0.89 0.16 0.01
81_Y 46_E 0.89 0.16 0.01
72_Y 71_I 0.88 0.16 0.01
57_S 8_S 0.86 0.15 0.01
49_R 79_R 0.86 0.15 0.01
100_V 84_L 0.85 0.15 0.01
83_V 58_I 0.85 0.14 0.01
24_G 84_L 0.85 0.14 0.01
33_I 34_L 0.84 0.14 0.01
59_D 82_N 0.84 0.14 0.01
13_V 82_N 0.84 0.14 0.01
70_N 59_F 0.84 0.14 0.01
87_H 70_G 0.83 0.14 0.01
94_F 18_I 0.83 0.14 0.01
59_D 50_S 0.82 0.13 0.01
57_S 57_V 0.82 0.13 0.01
7_T 41_L 0.82 0.13 0.01
95_E 70_G 0.82 0.13 0.01
7_T 84_L 0.81 0.13 0.01
104_S 18_I 0.81 0.13 0.01
12_P 81_A 0.80 0.13 0.01
102_L 59_F 0.80 0.13 0.01
116_I 17_E 0.80 0.13 0.01
74_V 56_G 0.80 0.13 0.01
28_P 14_E 0.80 0.13 0.01
116_I 85_P 0.80 0.12 0.01
107_A 55_S 0.79 0.12 0.01
57_S 83_G 0.79 0.12 0.01
85_E 46_E 0.79 0.12 0.01
110_N 11_T 0.78 0.12 0.01
36_Q 75_V 0.78 0.12 0.01
94_F 22_F 0.78 0.12 0.01
79_A 23_F 0.78 0.12 0.01
88_L 26_K 0.78 0.12 0.01
112_D 39_D 0.77 0.12 0.01
42_F 76_K 0.77 0.12 0.01
114_L 59_F 0.77 0.12 0.01
84_P 57_V 0.76 0.11 0.01
7_T 48_V 0.76 0.11 0.01
79_A 25_N 0.76 0.11 0.01
61_S 57_V 0.76 0.11 0.01
80_P 70_G 0.76 0.11 0.01
95_E 67_T 0.75 0.11 0.01
82_A 57_V 0.75 0.11 0.01
59_D 84_L 0.75 0.11 0.01
3_P 66_E 0.75 0.11 0.01
64_E 84_L 0.74 0.11 0.01
46_R 83_G 0.74 0.11 0.01
108_L 10_Y 0.74 0.11 0.01
44_S 74_E 0.74 0.11 0.01
88_L 28_G 0.74 0.11 0.01
108_L 50_S 0.74 0.11 0.01
13_V 64_G 0.74 0.11 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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