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OPENSEQ.org
Joel
Genes: A B A+B
Length: 286 291 561
Sequences: 35010 6861 889
Seq/Len: 122.41 23.58 1.58
MirrorTree (Pazo et al. 2001) 0.22
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 0.05 0.10
2 0.11 0.05 0.21
5 0.13 0.06 0.46
10 0.16 0.06 0.86
20 0.19 0.07 1.54
100 0.28 0.10 3.67
∞ 0.31 0.15 4.82
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
150_I 216_V 1.20 0.66 0.01
150_I 97_V 1.08 0.54 0.00
192_W 36_Q 1.05 0.50 0.00
198_A 104_A 0.99 0.44 0.00
270_H 94_G 0.99 0.44 0.00
196_T 21_A 0.95 0.40 0.00
118_A 112_I 0.95 0.40 0.00
198_A 151_A 0.93 0.38 0.00
79_L 73_Y 0.85 0.31 0.00
32_C 218_T 0.82 0.28 0.00
7_L 156_D 0.81 0.28 0.00
150_I 70_L 0.80 0.26 0.00
111_L 114_H 0.79 0.26 0.00
191_Y 233_A 0.79 0.25 0.00
118_A 115_N 0.78 0.25 0.00
150_I 218_T 0.78 0.25 0.00
116_A 150_Y 0.78 0.25 0.00
118_A 28_T 0.78 0.24 0.00
193_S 116_S 0.77 0.24 0.00
196_T 33_A 0.77 0.24 0.00
139_L 240_Q 0.75 0.23 0.00
59_V 224_V 0.75 0.23 0.00
57_P 161_L 0.75 0.23 0.00
133_K 43_A 0.75 0.23 0.00
201_C 149_L 0.74 0.22 0.00
179_L 48_G 0.73 0.21 0.00
118_A 263_P 0.73 0.21 0.00
192_W 135_T 0.72 0.21 0.00
219_S 27_G 0.72 0.20 0.00
107_A 150_Y 0.72 0.20 0.00
104_R 245_V 0.72 0.20 0.00
207_P 86_M 0.71 0.20 0.00
33_R 102_I 0.71 0.20 0.00
52_R 120_Y 0.71 0.20 0.00
113_S 171_R 0.71 0.20 0.00
137_I 151_A 0.70 0.19 0.00
121_Y 73_Y 0.70 0.19 0.00
190_D 247_G 0.70 0.19 0.00
57_P 219_E 0.70 0.19 0.00
90_L 180_M 0.69 0.19 0.00
132_L 249_Y 0.69 0.19 0.00
115_I 116_S 0.69 0.19 0.00
129_H 248_G 0.69 0.19 0.00
125_N 277_G 0.69 0.18 0.00
56_H 139_G 0.69 0.18 0.00
59_V 238_V 0.69 0.18 0.00
31_Q 215_D 0.69 0.18 0.00
127_I 192_L 0.69 0.18 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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