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OPENSEQ.org
3i1o_M_S
Genes: A B A+B
Length: 118 92 203
Sequences: 2218 2140 984
Seq/Len: 18.8 23.26 4.85
MirrorTree (Pazo et al. 2001) 0.75
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 0.09 0.09 0.01
2 0.09 0.09 0.09
5 0.09 0.09 0.14
10 0.09 0.09 0.30
20 0.09 0.09 4.69
100 0.09 0.09 6.38
∞ 0.09 0.09 7.15
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
79_R 69_H 1.53 0.99 0.87
89_L 76_P 1.38 0.97 0.78
64_V 56_Q 1.16 0.90 0.60
82_D 65_E 1.14 0.89 0.57
85_C 45_I 1.13 0.88 0.56
81_M 60_V 1.13 0.88 0.56
68_D 14_H 1.06 0.84 0.49
101_R 55_R 1.04 0.82 0.47
103_K 56_Q 1.04 0.82 0.47
83_L 40_I 0.96 0.75 0.38
12_H 40_I 0.92 0.70 0.34
30_S 87_K 0.90 0.67 0.31
89_L 12_D 0.90 0.67 0.31
104_T 55_R 0.89 0.66 0.31
104_T 44_M 0.89 0.66 0.30
11_D 30_P 0.88 0.64 0.29
42_D 91_K 0.87 0.63 0.28
97_V 49_I 0.87 0.63 0.28
8_N 61_F 0.87 0.63 0.28
71_R 57_H 0.86 0.62 0.27
49_S 52_H 0.84 0.60 0.26
110_K 76_P 0.83 0.58 0.24
52_Q 11_I 0.83 0.58 0.24
44_K 87_K 0.83 0.57 0.24
61_A 39_T 0.83 0.57 0.24
57_R 59_P 0.82 0.56 0.23
83_L 30_P 0.81 0.56 0.23
56_L 22_A 0.81 0.56 0.23
47_E 6_K 0.81 0.56 0.23
97_V 45_I 0.81 0.55 0.23
103_K 53_N 0.80 0.53 0.21
85_C 63_T 0.80 0.53 0.21
46_S 57_H 0.79 0.53 0.21
12_H 47_L 0.79 0.52 0.21
71_R 65_E 0.77 0.50 0.20
2_A 32_R 0.76 0.48 0.19
44_K 76_P 0.76 0.48 0.18
76_S 14_H 0.76 0.47 0.18
21_S 76_P 0.75 0.47 0.18
6_G 81_R 0.75 0.47 0.18
104_T 81_R 0.75 0.47 0.18
74_S 41_F 0.75 0.46 0.17
103_K 65_E 0.74 0.46 0.17
71_R 55_R 0.74 0.45 0.17
112_P 80_Y 0.73 0.44 0.17
34_L 51_V 0.72 0.42 0.15
34_L 47_L 0.71 0.42 0.15
81_M 2_P 0.71 0.42 0.15
93_R 37_R 0.71 0.41 0.15
50_E 29_K 0.71 0.41 0.15
47_E 64_D 0.70 0.41 0.14
85_C 65_E 0.70 0.40 0.14
12_H 53_N 0.70 0.40 0.14
84_G 50_A 0.70 0.40 0.14
9_I 66_M 0.70 0.40 0.14
51_G 63_T 0.70 0.40 0.14
53_I 44_M 0.69 0.39 0.14
71_R 34_W 0.69 0.39 0.14
43_V 55_R 0.68 0.37 0.13
55_T 44_M 0.67 0.36 0.12
14_H 76_P 0.67 0.36 0.12
44_K 86_D 0.67 0.36 0.12
61_A 56_Q 0.67 0.36 0.12
49_S 11_I 0.67 0.35 0.12
75_M 91_K 0.67 0.35 0.12
3_R 80_Y 0.66 0.35 0.12
14_H 49_I 0.66 0.34 0.12
71_R 20_E 0.66 0.34 0.12
42_D 63_T 0.66 0.34 0.12
2_A 59_P 0.66 0.34 0.12
56_L 55_R 0.65 0.34 0.11
45_I 49_I 0.65 0.34 0.11
30_S 15_L 0.65 0.34 0.11
41_E 27_D 0.65 0.34 0.11
60_V 21_K 0.65 0.33 0.11
60_V 75_A 0.65 0.33 0.11
104_T 16_L 0.64 0.32 0.11
85_C 2_P 0.64 0.32 0.11
18_A 46_G 0.64 0.32 0.11
58_D 27_D 0.64 0.32 0.10
73_I 64_D 0.64 0.31 0.10
68_D 10_F 0.63 0.31 0.10
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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