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OPENSEQ.org
2F9Y(AB)
Genes: A B A+B
Length: 100 106 202
Sequences: 1169 1844 1114
Seq/Len: 11.69 17.4 5.51
MirrorTree (Pazo et al. 2001) 0.60
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 4.50
2 0.00 0.00 5.32
5 0.00 0.00 5.37
10 0.00 0.00 5.42
20 0.00 0.00 5.41
100 0.00 0.00 5.45
∞ 0.01 0.01 5.46
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
75_E 2_I 2.13 1.00 0.99
9_D 93_F 1.30 0.96 0.84
66_R 2_I 1.25 0.95 0.81
61_R 94_R 1.15 0.91 0.73
17_A 75_Q 0.96 0.78 0.53
6_R 75_Q 0.95 0.77 0.52
14_F 75_Q 0.94 0.76 0.50
15_T 64_P 0.88 0.69 0.43
32_Y 8_V 0.87 0.67 0.41
97_N 7_H 0.85 0.65 0.39
9_D 75_Q 0.82 0.60 0.35
85_T 1_M 0.80 0.58 0.33
2_E 62_N 0.80 0.57 0.32
35_S 65_A 0.79 0.56 0.31
24_L 76_K 0.78 0.55 0.31
8_K 93_F 0.78 0.55 0.30
29_K 84_F 0.77 0.53 0.29
91_K 66_G 0.77 0.53 0.29
80_I 85_A 0.77 0.53 0.28
6_R 44_E 0.76 0.52 0.28
4_T 14_A 0.76 0.51 0.28
91_K 5_E 0.74 0.49 0.26
14_F 96_E 0.74 0.49 0.26
70_M 68_A 0.74 0.49 0.26
28_L 76_K 0.73 0.48 0.25
18_L 75_Q 0.72 0.47 0.24
38_L 12_Q 0.72 0.46 0.24
59_E 43_A 0.72 0.46 0.23
32_Y 24_V 0.71 0.45 0.23
95_V 34_I 0.70 0.44 0.22
10_K 93_F 0.70 0.43 0.21
36_V 89_A 0.70 0.43 0.21
65_T 10_P 0.70 0.43 0.21
25_A 7_H 0.69 0.42 0.21
15_T 90_V 0.69 0.42 0.21
95_V 69_V 0.69 0.41 0.20
77_I 91_F 0.68 0.40 0.20
13_L 24_V 0.67 0.39 0.19
61_R 40_Y 0.67 0.38 0.18
55_S 87_H 0.66 0.38 0.18
84_A 93_F 0.66 0.37 0.18
85_T 66_G 0.66 0.37 0.17
61_R 96_E 0.65 0.36 0.17
21_E 93_F 0.65 0.36 0.17
69_V 64_P 0.64 0.35 0.16
73_V 96_E 0.64 0.35 0.16
10_K 6_Y 0.64 0.34 0.16
17_A 36_V 0.64 0.34 0.16
35_S 19_R 0.64 0.34 0.16
40_S 8_V 0.63 0.34 0.16
56_L 5_E 0.63 0.34 0.15
22_R 95_G 0.62 0.33 0.15
6_R 6_Y 0.62 0.33 0.15
51_K 17_T 0.62 0.33 0.15
72_G 81_L 0.62 0.33 0.15
9_D 84_F 0.62 0.33 0.15
82_V 85_A 0.62 0.32 0.15
43_I 43_A 0.62 0.32 0.15
90_S 66_G 0.61 0.31 0.14
6_R 83_A 0.61 0.31 0.14
58_E 9_K 0.61 0.30 0.14
69_V 94_R 0.60 0.30 0.14
37_A 65_A 0.60 0.30 0.13
2_E 98_M 0.60 0.30 0.13
15_T 75_Q 0.60 0.30 0.13
6_R 97_V 0.60 0.30 0.13
8_K 102_E 0.59 0.29 0.13
33_P 65_A 0.59 0.29 0.13
9_D 98_M 0.59 0.28 0.12
15_T 27_E 0.58 0.28 0.12
74_P 78_E 0.58 0.27 0.12
41_A 75_Q 0.58 0.27 0.12
32_Y 62_N 0.58 0.27 0.12
2_E 75_Q 0.57 0.27 0.11
5_P 27_E 0.57 0.26 0.11
42_F 27_E 0.57 0.26 0.11
53_V 32_R 0.57 0.26 0.11
6_R 93_F 0.57 0.26 0.11
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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