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OPENSEQ.org
NstoN 1
Genes: A B A+B
Length: 147 314 443
Sequences: 905 5641 114
Seq/Len: 6.16 17.96 0.26
MirrorTree (Pazo et al. 2001) 0.23
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 0.07 0.07 0.02
2 0.08 0.08 0.03
5 0.09 0.08 0.03
10 0.09 0.09 0.05
20 0.09 0.10 0.09
100 0.11 0.11 0.16
∞ 0.13 0.15 0.25
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
82_S 240_P 1.43 0.34 0.00
74_P 137_N 1.19 0.21 0.00
41_D 252_I 1.19 0.21 0.00
12_C 18_W 1.15 0.20 0.00
14_C 18_W 1.15 0.20 0.00
18_A 202_S 1.15 0.20 0.00
75_C 59_L 1.14 0.19 0.00
61_D 285_D 1.10 0.18 0.00
59_Y 155_W 1.10 0.18 0.00
13_K 33_I 1.07 0.17 0.00
39_C 134_W 1.06 0.16 0.00
42_C 134_W 1.06 0.16 0.00
48_G 134_W 1.06 0.16 0.00
51_C 134_W 1.06 0.16 0.00
54_C 134_W 1.06 0.16 0.00
111_C 134_W 1.06 0.16 0.00
114_C 134_W 1.06 0.16 0.00
75_C 294_A 1.05 0.16 0.00
58_F 166_K 1.04 0.16 0.00
77_C 294_A 1.03 0.15 0.00
128_P 223_V 1.03 0.15 0.00
129_C 237_W 1.03 0.15 0.00
58_F 134_W 1.02 0.15 0.00
83_A 190_V 1.02 0.15 0.00
74_P 219_K 1.01 0.15 0.00
104_P 180_L 1.00 0.14 0.00
9_C 237_W 0.99 0.14 0.00
77_C 59_L 0.99 0.14 0.00
77_C 240_P 0.97 0.13 0.00
118_Y 78_G 0.96 0.13 0.00
21_C 237_W 0.96 0.13 0.00
108_G 186_Y 0.95 0.13 0.00
12_C 134_W 0.95 0.13 0.00
14_C 134_W 0.95 0.13 0.00
105_G 242_E 0.94 0.13 0.00
75_C 78_G 0.94 0.13 0.00
56_P 258_V 0.93 0.12 0.00
118_Y 231_K 0.93 0.12 0.00
75_C 214_P 0.92 0.12 0.00
39_C 288_Y 0.92 0.12 0.00
42_C 288_Y 0.92 0.12 0.00
48_G 288_Y 0.92 0.12 0.00
51_C 288_Y 0.92 0.12 0.00
54_C 288_Y 0.92 0.12 0.00
111_C 288_Y 0.92 0.12 0.00
114_C 288_Y 0.92 0.12 0.00
39_C 237_W 0.91 0.12 0.00
42_C 237_W 0.91 0.12 0.00
48_G 237_W 0.91 0.12 0.00
51_C 237_W 0.91 0.12 0.00
54_C 237_W 0.91 0.12 0.00
111_C 237_W 0.91 0.12 0.00
114_C 237_W 0.91 0.12 0.00
102_C 134_W 0.91 0.12 0.00
131_C 237_W 0.90 0.11 0.00
80_V 199_S 0.90 0.11 0.00
99_D 286_T 0.89 0.11 0.00
110_R 35_Y 0.89 0.11 0.00
72_C 134_W 0.89 0.11 0.00
59_Y 147_D 0.89 0.11 0.00
16_G 218_P 0.88 0.11 0.00
52_Q 255_S 0.88 0.11 0.00
18_A 55_T 0.88 0.11 0.00
72_C 59_L 0.85 0.10 0.00
117_G 286_T 0.85 0.10 0.00
59_Y 286_T 0.85 0.10 0.00
46_T 288_Y 0.85 0.10 0.00
75_C 65_Y 0.85 0.10 0.00
30_A 221_V 0.85 0.10 0.00
95_P 179_G 0.84 0.10 0.00
139_T 19_T 0.84 0.10 0.00
13_K 189_S 0.83 0.10 0.00
78_H 235_V 0.83 0.10 0.00
46_T 134_W 0.83 0.10 0.00
77_C 78_G 0.83 0.10 0.00
75_C 250_Y 0.83 0.10 0.00
32_G 33_I 0.82 0.10 0.00
83_A 135_A 0.82 0.10 0.00
39_C 18_W 0.82 0.09 0.00
42_C 18_W 0.82 0.09 0.00
48_G 18_W 0.82 0.09 0.00
51_C 18_W 0.82 0.09 0.00
54_C 18_W 0.82 0.09 0.00
111_C 18_W 0.82 0.09 0.00
114_C 18_W 0.82 0.09 0.00
72_C 294_A 0.81 0.09 0.00
118_Y 208_T 0.81 0.09 0.00
70_D 14_I 0.81 0.09 0.00
22_H 246_K 0.81 0.09 0.00
45_N 40_P 0.81 0.09 0.00
24_D 188_F 0.81 0.09 0.00
82_S 87_T 0.81 0.09 0.00
62_L 42_A 0.80 0.09 0.00
50_Y 130_I 0.80 0.09 0.00
12_C 237_W 0.80 0.09 0.00
14_C 237_W 0.80 0.09 0.00
37_G 237_W 0.80 0.09 0.00
12_C 288_Y 0.80 0.09 0.00
14_C 288_Y 0.80 0.09 0.00
47_E 53_Y 0.80 0.09 0.00
12_C 218_P 0.79 0.09 0.00
14_C 218_P 0.79 0.09 0.00
21_C 134_W 0.79 0.09 0.00
118_Y 277_H 0.79 0.09 0.00
78_H 191_M 0.79 0.09 0.00
39_C 250_Y 0.79 0.09 0.00
42_C 250_Y 0.79 0.09 0.00
48_G 250_Y 0.79 0.09 0.00
51_C 250_Y 0.79 0.09 0.00
54_C 250_Y 0.79 0.09 0.00
111_C 250_Y 0.79 0.09 0.00
114_C 250_Y 0.79 0.09 0.00
91_T 188_F 0.79 0.09 0.00
58_F 162_N 0.79 0.09 0.00
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)
ID Seq/Len Name Options I_Prob Status
6297 0.24 NstoN 2 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
6296 0.26 NstoN 1 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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