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OPENSEQ.org
wspBwspR
Genes: A B A+B
Length: 171 347 485
Sequences: 3789 3627 196
Seq/Len: 22.16 10.45 0.4
MirrorTree (Pazo et al. 2001) 0.66
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 0.04 0.02 0.03
2 0.07 0.03 0.04
5 0.10 0.04 0.23
10 0.11 0.05 0.29
20 0.11 0.05 0.38
100 0.15 0.08 0.92
∞ 0.22 0.16 2.19
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
144_V 66_V 1.45 0.46 0.00
144_V 274_V 1.34 0.38 0.00
28_A 296_V 1.32 0.37 0.00
65_P 119_Y 1.17 0.28 0.00
106_L 257_M 1.15 0.26 0.00
34_V 31_G 1.14 0.26 0.00
67_L 300_V 1.13 0.25 0.00
119_A 258_V 1.12 0.24 0.00
29_L 86_R 1.10 0.24 0.00
23_E 67_I 1.05 0.21 0.00
109_A 273_K 1.05 0.21 0.00
28_A 69_Q 1.05 0.21 0.00
45_R 133_I 1.04 0.20 0.00
83_S 99_L 1.00 0.19 0.00
150_E 87_G 0.99 0.18 0.00
152_L 100_S 0.98 0.18 0.00
88_L 325_Q 0.97 0.18 0.00
67_L 47_H 0.95 0.17 0.00
46_I 277_T 0.94 0.16 0.00
132_Y 337_M 0.93 0.16 0.00
37_V 65_T 0.93 0.16 0.00
113_L 77_D 0.92 0.16 0.00
36_E 179_L 0.92 0.15 0.00
34_V 205_L 0.91 0.15 0.00
44_K 46_F 0.91 0.15 0.00
103_G 167_L 0.91 0.15 0.00
64_V 296_V 0.91 0.15 0.00
132_Y 185_F 0.91 0.15 0.00
29_L 248_A 0.90 0.15 0.00
87_V 178_G 0.89 0.14 0.00
28_A 120_L 0.88 0.14 0.00
148_R 123_L 0.88 0.14 0.00
12_R 116_A 0.88 0.14 0.00
66_V 258_V 0.88 0.14 0.00
153_L 131_A 0.87 0.14 0.00
133_L 166_V 0.87 0.14 0.00
144_V 309_G 0.87 0.14 0.00
159_A 206_L 0.87 0.14 0.00
143_L 99_L 0.86 0.13 0.00
65_P 79_L 0.86 0.13 0.00
106_L 24_V 0.86 0.13 0.00
136_V 130_V 0.85 0.13 0.00
68_D 55_A 0.84 0.13 0.00
29_L 236_I 0.84 0.13 0.00
135_P 21_V 0.83 0.12 0.00
46_I 305_P 0.83 0.12 0.00
66_V 24_V 0.83 0.12 0.00
49_A 66_V 0.83 0.12 0.00
22_M 257_M 0.83 0.12 0.00
133_L 108_K 0.83 0.12 0.00
29_L 270_L 0.82 0.12 0.00
120_F 27_Q 0.82 0.12 0.00
38_L 206_L 0.82 0.12 0.00
65_P 118_D 0.82 0.12 0.00
106_L 85_Y 0.81 0.12 0.00
120_F 278_V 0.81 0.12 0.00
22_M 233_A 0.81 0.12 0.00
46_I 80_T 0.81 0.12 0.00
47_P 155_E 0.81 0.12 0.00
121_R 182_R 0.81 0.12 0.00
46_I 106_T 0.80 0.12 0.00
27_Y 279_E 0.80 0.11 0.00
152_L 46_F 0.80 0.11 0.00
64_V 86_R 0.80 0.11 0.00
50_P 38_L 0.79 0.11 0.00
56_V 220_F 0.79 0.11 0.00
74_F 274_V 0.79 0.11 0.00
65_P 206_L 0.79 0.11 0.00
25_D 258_V 0.79 0.11 0.00
22_M 316_I 0.79 0.11 0.00
64_V 188_Y 0.79 0.11 0.00
73_A 60_N 0.78 0.11 0.00
31_A 294_L 0.78 0.11 0.00
24_G 199_E 0.78 0.11 0.00
87_V 118_D 0.78 0.11 0.00
66_V 168_Q 0.78 0.11 0.00
146_W 120_L 0.78 0.11 0.00
27_Y 190_E 0.78 0.11 0.00
28_A 171_M 0.77 0.11 0.00
27_Y 130_V 0.77 0.11 0.00
152_L 57_A 0.77 0.10 0.00
112_T 273_K 0.77 0.10 0.00
27_Y 247_A 0.77 0.10 0.00
63_L 205_L 0.76 0.10 0.00
86_I 107_V 0.76 0.10 0.00
31_A 49_C 0.76 0.10 0.00
136_V 332_N 0.76 0.10 0.00
87_V 175_G 0.76 0.10 0.00
37_V 106_T 0.75 0.10 0.00
111_D 114_A 0.75 0.10 0.00
93_A 333_Q 0.75 0.10 0.00
48_E 257_M 0.75 0.10 0.00
17_F 240_C 0.75 0.10 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)
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