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OPENSEQ.org
MFD_SALTY_ 472-603-RPOB_ SALTY_19-142
Genes: A B A+B
Length: 132 123 250
Sequences: 2085 1300 872
Seq/Len: 15.8 10.57 3.49
MirrorTree (Pazo et al. 2001) 0.65
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 0.00 0.09 0.01
2 0.00 0.09 0.01
5 0.00 0.09 0.01
10 0.00 0.09 0.01
20 0.00 0.09 0.07
100 0.00 0.09 0.55
∞ 0.01 0.09 3.42
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
46_A 101_Q 1.99 1.00 0.98
28_L 82_R 1.73 0.99 0.95
102_A 105_M 1.53 0.97 0.91
40_L 72_T 1.37 0.94 0.84
59_S 16_F 1.37 0.94 0.83
28_L 52_V 1.34 0.93 0.81
49_Y 100_E 1.13 0.82 0.64
81_R 10_S 1.11 0.80 0.61
97_L 115_G 1.09 0.78 0.60
90_V 103_V 1.07 0.77 0.58
43_A 104_Y 1.06 0.75 0.56
28_L 98_I 1.05 0.75 0.56
8_V 4_D 1.03 0.73 0.53
119_Y 122_T 1.00 0.69 0.50
22_Y 17_Q 1.00 0.69 0.49
59_S 56_L 1.00 0.69 0.49
105_A 11_I 0.99 0.68 0.48
16_E 47_S 0.97 0.66 0.46
89_K 81_L 0.96 0.65 0.45
72_H 80_K 0.94 0.63 0.42
103_Q 41_Q 0.94 0.62 0.42
27_T 103_V 0.92 0.60 0.40
22_Y 72_T 0.92 0.59 0.39
38_L 10_S 0.92 0.59 0.39
98_L 74_S 0.90 0.58 0.38
19_V 51_Y 0.90 0.57 0.37
84_Q 17_Q 0.89 0.56 0.36
52_V 38_F 0.89 0.56 0.36
34_K 78_R 0.89 0.56 0.36
55_L 9_L 0.89 0.56 0.36
13_V 116_T 0.87 0.54 0.34
24_G 83_L 0.87 0.54 0.34
122_F 36_S 0.86 0.53 0.33
59_S 81_L 0.86 0.53 0.33
129_E 87_E 0.86 0.52 0.33
42_Y 112_T 0.86 0.52 0.32
22_Y 32_A 0.85 0.51 0.32
50_V 108_I 0.85 0.51 0.32
8_V 87_E 0.85 0.51 0.32
92_D 7_Y 0.85 0.51 0.32
101_Y 30_L 0.85 0.51 0.32
36_E 16_F 0.85 0.50 0.31
122_F 105_M 0.84 0.50 0.31
49_Y 66_C 0.84 0.50 0.31
122_F 16_F 0.84 0.50 0.30
76_G 34_F 0.84 0.49 0.30
97_L 106_G 0.83 0.48 0.29
127_P 107_E 0.83 0.48 0.29
19_V 31_E 0.83 0.48 0.29
15_L 11_I 0.82 0.47 0.29
27_T 58_E 0.82 0.47 0.28
98_L 54_Y 0.82 0.47 0.28
82_A 78_R 0.82 0.47 0.28
62_A 108_I 0.82 0.47 0.28
40_L 45_G 0.81 0.46 0.27
52_V 108_I 0.81 0.46 0.27
31_G 118_V 0.81 0.46 0.27
24_G 80_K 0.81 0.45 0.27
128_F 37_V 0.81 0.45 0.27
56_H 73_Y 0.80 0.45 0.27
126_F 106_G 0.80 0.44 0.26
71_L 66_C 0.79 0.43 0.25
10_Q 16_F 0.79 0.43 0.25
57_L 30_L 0.79 0.43 0.25
82_A 52_V 0.79 0.42 0.24
60_R 61_F 0.79 0.42 0.24
50_V 98_I 0.78 0.42 0.24
99_D 16_F 0.78 0.41 0.24
46_A 59_P 0.78 0.41 0.24
73_K 99_K 0.78 0.41 0.24
71_L 110_L 0.77 0.41 0.23
21_R 16_F 0.77 0.41 0.23
108_E 56_L 0.77 0.41 0.23
10_Q 50_Q 0.77 0.41 0.23
91_R 7_Y 0.77 0.40 0.23
50_V 80_K 0.77 0.40 0.23
83_R 33_A 0.76 0.39 0.22
83_R 52_V 0.76 0.39 0.22
127_P 79_V 0.75 0.38 0.21
17_H 76_P 0.75 0.38 0.21
109_G 104_Y 0.75 0.38 0.21
129_E 46_N 0.75 0.38 0.21
86_A 61_F 0.75 0.38 0.21
39_M 56_L 0.75 0.38 0.21
75_G 66_C 0.74 0.37 0.21
49_Y 81_L 0.74 0.37 0.21
55_L 70_G 0.74 0.37 0.20
34_K 51_Y 0.74 0.37 0.20
122_F 51_Y 0.74 0.37 0.20
91_R 103_V 0.74 0.37 0.20
19_V 34_F 0.74 0.37 0.20
24_G 105_M 0.74 0.37 0.20
94_A 83_L 0.74 0.37 0.20
48_L 69_R 0.74 0.37 0.20
71_L 8_L 0.74 0.36 0.20
57_L 8_L 0.73 0.36 0.20
16_E 84_V 0.73 0.36 0.20
51_P 99_K 0.73 0.36 0.20
42_Y 80_K 0.73 0.36 0.19
126_F 115_G 0.73 0.35 0.19
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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