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OPENSEQ.org
3OAA_H_G
Genes: A B A+B
Length: 138 286 418
Sequences: 2587 3024 1747
Seq/Len: 18.75 10.57 4.18
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 0.08
2 0.09 0.09 3.93
5 0.09 0.09 4.04
10 0.09 0.09 4.06
20 0.09 0.09 4.12
100 0.09 0.09 4.18
∞ 0.09 0.10 4.37
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 206_L 1.28 0.93 0.40
68_I 220_R 1.16 0.88 0.30
42_L 55_L 1.16 0.88 0.30
40_P 64_H 1.12 0.84 0.26
81_D 167_L 1.09 0.83 0.25
29_E 214_L 1.07 0.81 0.23
29_E 208_E 1.04 0.78 0.21
70_E 47_T 1.02 0.77 0.20
41_L 259_E 1.02 0.77 0.20
11_A 5_E 0.99 0.73 0.18
42_L 51_V 0.98 0.72 0.17
81_D 221_R 0.96 0.70 0.16
48_G 30_K 0.95 0.69 0.16
48_G 4_K 0.93 0.67 0.15
8_V 214_L 0.93 0.67 0.15
33_G 222_Y 0.90 0.63 0.13
40_P 203_W 0.89 0.62 0.13
11_A 145_L 0.88 0.61 0.12
77_T 145_L 0.87 0.59 0.12
78_V 227_V 0.87 0.59 0.12
70_E 243_M 0.87 0.59 0.12
70_E 205_Y 0.86 0.57 0.11
7_D 47_T 0.86 0.57 0.11
73_P 203_W 0.85 0.56 0.11
22_K 241_A 0.85 0.56 0.11
4_Y 45_A 0.84 0.55 0.10
68_I 52_I 0.84 0.55 0.10
79_L 51_V 0.83 0.54 0.10
71_V 169_I 0.82 0.53 0.10
78_V 219_L 0.82 0.52 0.10
51_R 89_G 0.82 0.52 0.10
70_E 25_M 0.82 0.52 0.10
85_R 25_M 0.81 0.51 0.09
57_G 80_V 0.81 0.51 0.09
11_A 29_S 0.81 0.50 0.09
42_L 205_Y 0.78 0.47 0.08
130_V 171_S 0.78 0.47 0.08
26_T 1_A 0.77 0.45 0.08
72_Q 54_H 0.77 0.45 0.08
23_I 1_A 0.76 0.44 0.08
69_L 38_M 0.76 0.44 0.07
76_V 34_S 0.75 0.42 0.07
94_A 188_L 0.75 0.42 0.07
24_Q 241_A 0.75 0.42 0.07
65_S 271_S 0.74 0.41 0.07
80_A 51_V 0.74 0.41 0.07
78_V 159_Y 0.73 0.41 0.07
83_A 51_V 0.73 0.40 0.07
25_V 281_S 0.73 0.40 0.07
83_A 143_P 0.72 0.39 0.06
37_G 54_H 0.72 0.39 0.06
44_A 214_L 0.72 0.39 0.06
64_L 178_M 0.72 0.38 0.06
27_G 208_E 0.71 0.38 0.06
78_V 263_V 0.71 0.37 0.06
8_V 284_A 0.71 0.37 0.06
83_A 243_M 0.71 0.37 0.06
45_I 276_L 0.70 0.37 0.06
128_L 92_I 0.70 0.36 0.06
24_Q 281_S 0.70 0.36 0.06
103_E 87_C 0.69 0.36 0.06
128_L 99_L 0.69 0.35 0.06
38_H 236_A 0.69 0.35 0.06
74_G 55_L 0.69 0.35 0.05
31_E 89_G 0.69 0.35 0.05
21_E 104_T 0.68 0.34 0.05
40_P 205_Y 0.68 0.34 0.05
66_G 44_Y 0.68 0.34 0.05
134_T 27_A 0.68 0.34 0.05
106_S 114_L 0.68 0.33 0.05
52_I 24_E 0.67 0.32 0.05
128_L 52_I 0.67 0.32 0.05
32_L 244_V 0.66 0.32 0.05
111_D 250_T 0.66 0.31 0.05
64_L 247_K 0.66 0.31 0.05
56_H 199_K 0.66 0.31 0.05
83_A 231_V 0.66 0.31 0.05
82_T 276_L 0.66 0.31 0.05
17_S 163_R 0.65 0.30 0.05
48_G 91_N 0.65 0.30 0.05
35_Y 276_L 0.65 0.30 0.04
125_I 48_M 0.65 0.30 0.04
60_E 191_P 0.65 0.30 0.04
18_G 143_P 0.64 0.29 0.04
21_E 102_M 0.64 0.29 0.04
15_M 219_L 0.64 0.29 0.04
22_K 281_S 0.64 0.29 0.04
95_M 254_G 0.64 0.29 0.04
80_A 164_L 0.64 0.29 0.04
9_V 232_V 0.64 0.29 0.04
78_V 210_D 0.64 0.29 0.04
95_M 259_E 0.64 0.29 0.04
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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