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OPENSEQ.org
1fs0_1_E_G
Genes: A B A+B
Length: 138 230 363
Sequences: 2587 3213 1839
Seq/Len: 18.75 13.97 5.07
MirrorTree (Pazo et al. 2001) 0.76
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 0.09
2 0.09 0.09 4.78
5 0.09 0.09 4.92
10 0.09 0.09 4.92
20 0.09 0.09 5.00
100 0.09 0.09 5.06
∞ 0.09 0.10 5.29
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
39_A 189_L 1.33 0.96 0.58
42_L 38_L 1.21 0.93 0.46
81_D 150_L 1.17 0.91 0.43
68_I 203_R 1.16 0.91 0.41
40_P 47_H 1.11 0.88 0.38
70_E 30_T 1.05 0.84 0.31
29_E 197_L 1.02 0.81 0.29
42_L 34_V 1.01 0.80 0.28
81_D 204_R 0.99 0.79 0.27
29_E 191_E 0.98 0.78 0.26
48_G 13_K 0.98 0.78 0.26
22_K 224_A 0.95 0.74 0.23
7_D 30_T 0.92 0.71 0.21
11_A 128_L 0.91 0.69 0.20
40_P 186_W 0.89 0.67 0.19
77_T 128_L 0.87 0.65 0.18
11_A 12_S 0.87 0.65 0.17
33_G 205_Y 0.87 0.65 0.17
70_E 226_M 0.87 0.65 0.17
79_L 34_V 0.86 0.64 0.17
73_P 186_W 0.85 0.62 0.16
68_I 35_I 0.85 0.62 0.16
70_E 188_Y 0.84 0.61 0.16
78_V 202_L 0.83 0.60 0.15
4_Y 28_A 0.82 0.58 0.15
70_E 8_M 0.82 0.58 0.14
71_V 152_I 0.82 0.57 0.14
42_L 188_Y 0.81 0.57 0.14
37_G 37_H 0.81 0.56 0.14
85_R 8_M 0.81 0.56 0.14
78_V 210_V 0.80 0.55 0.13
72_Q 37_H 0.80 0.54 0.13
94_A 171_L 0.78 0.53 0.12
51_R 72_G 0.77 0.51 0.12
130_V 154_S 0.77 0.50 0.12
57_G 63_V 0.77 0.50 0.12
125_I 193_D 0.76 0.49 0.11
27_G 191_E 0.76 0.49 0.11
40_P 188_Y 0.75 0.48 0.11
69_L 21_M 0.74 0.46 0.10
8_V 197_L 0.73 0.46 0.10
78_V 38_L 0.73 0.45 0.10
24_Q 224_A 0.72 0.45 0.10
128_L 129_S 0.72 0.44 0.10
66_G 27_Y 0.72 0.43 0.09
21_E 85_M 0.72 0.43 0.09
102_E 114_N 0.72 0.43 0.09
44_A 197_L 0.72 0.43 0.09
31_E 72_G 0.70 0.41 0.09
78_V 142_Y 0.70 0.41 0.09
83_A 34_V 0.69 0.40 0.08
16_F 159_N 0.69 0.40 0.08
83_A 214_V 0.69 0.40 0.08
83_A 126_P 0.69 0.39 0.08
80_A 147_L 0.69 0.39 0.08
48_G 74_N 0.68 0.39 0.08
125_I 31_M 0.68 0.39 0.08
21_E 87_T 0.68 0.38 0.08
80_A 34_V 0.68 0.38 0.08
38_H 219_A 0.68 0.38 0.08
6_L 15_R 0.68 0.38 0.08
106_S 97_L 0.68 0.38 0.08
76_V 17_S 0.68 0.38 0.08
10_S 1_K 0.67 0.37 0.08
32_L 227_V 0.67 0.37 0.07
23_I 161_M 0.67 0.37 0.07
88_D 145_G 0.67 0.36 0.07
114_Y 77_L 0.66 0.36 0.07
18_G 126_P 0.66 0.36 0.07
52_I 7_E 0.66 0.35 0.07
71_V 189_L 0.66 0.35 0.07
13_Q 197_L 0.66 0.35 0.07
129_R 77_L 0.65 0.35 0.07
26_T 226_M 0.65 0.34 0.07
118_S 210_V 0.65 0.34 0.07
79_L 11_A 0.65 0.34 0.07
83_A 226_M 0.65 0.34 0.07
14_Q 29_E 0.65 0.34 0.07
64_L 230_K 0.64 0.33 0.07
26_T 60_Y 0.64 0.33 0.07
9_V 188_Y 0.64 0.33 0.06
9_V 215_V 0.64 0.32 0.06
70_E 58_V 0.63 0.32 0.06
50_I 199_D 0.63 0.32 0.06
60_E 174_P 0.63 0.32 0.06
82_T 12_S 0.63 0.32 0.06
132_E 137_V 0.63 0.32 0.06
94_A 76_N 0.63 0.32 0.06
15_M 202_L 0.63 0.32 0.06
79_L 129_S 0.63 0.31 0.06
98_K 125_N 0.63 0.31 0.06
85_R 202_L 0.63 0.31 0.06
70_E 37_H 0.62 0.31 0.06
56_H 176_S 0.62 0.31 0.06
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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