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OPENSEQ.org
TsaD-vs-S4
Genes: A B A+B
Length: 337 206 537
Sequences: 3839 1236 651
Seq/Len: 11.39 6 1.21
MirrorTree (Pazo et al. 2001) 0.28
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 0.09 0.00
2 0.07 0.09 0.00
5 0.08 0.09 0.01
10 0.08 0.09 0.02
20 0.08 0.09 0.04
100 0.08 0.09 0.25
∞ 0.11 0.09 1.20
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
245_D 182_F 1.32 0.69 0.01
184_S 47_R 1.02 0.40 0.00
147_G 146_R 1.01 0.39 0.00
99_A 62_R 0.97 0.36 0.00
80_A 76_Y 0.96 0.35 0.00
297_F 151_K 0.96 0.34 0.00
265_M 156_K 0.95 0.34 0.00
110_H 129_V 0.95 0.34 0.00
61_A 143_V 0.94 0.33 0.00
39_Y 146_R 0.92 0.32 0.00
235_I 107_F 0.91 0.30 0.00
16_A 131_N 0.89 0.29 0.00
265_M 200_I 0.88 0.28 0.00
295_P 119_S 0.87 0.28 0.00
39_Y 130_V 0.86 0.26 0.00
216_T 86_T 0.86 0.26 0.00
76_V 118_V 0.86 0.26 0.00
270_S 187_E 0.85 0.26 0.00
250_K 206_K 0.85 0.26 0.00
177_Y 56_R 0.85 0.26 0.00
212_S 87_G 0.85 0.26 0.00
172_L 189_S 0.84 0.25 0.00
122_E 70_R 0.84 0.25 0.00
147_G 78_E 0.84 0.25 0.00
89_L 144_S 0.84 0.25 0.00
294_R 85_N 0.83 0.25 0.00
253_R 7_P 0.83 0.24 0.00
270_S 29_D 0.79 0.22 0.00
101_A 118_V 0.79 0.21 0.00
52_V 194_D 0.79 0.21 0.00
131_V 110_T 0.79 0.21 0.00
52_V 136_Q 0.78 0.21 0.00
140_T 180_G 0.78 0.21 0.00
162_A 19_L 0.78 0.21 0.00
197_F 206_K 0.77 0.20 0.00
46_L 62_R 0.77 0.20 0.00
35_L 68_L 0.77 0.20 0.00
174_G 179_E 0.77 0.20 0.00
59_I 124_M 0.76 0.20 0.00
57_P 159_L 0.76 0.20 0.00
217_F 178_M 0.75 0.19 0.00
169_T 47_R 0.75 0.19 0.00
59_I 172_E 0.75 0.19 0.00
274_T 146_R 0.75 0.19 0.00
57_P 171_L 0.74 0.19 0.00
106_A 190_D 0.74 0.19 0.00
116_L 20_F 0.74 0.18 0.00
312_R 10_K 0.74 0.18 0.00
112_M 74_N 0.74 0.18 0.00
19_D 105_M 0.73 0.18 0.00
96_R 108_G 0.73 0.18 0.00
143_I 125_V 0.73 0.18 0.00
114_G 73_R 0.73 0.18 0.00
193_G 70_R 0.72 0.18 0.00
265_M 107_F 0.72 0.17 0.00
8_T 118_V 0.72 0.17 0.00
313_F 123_I 0.72 0.17 0.00
238_A 47_R 0.72 0.17 0.00
240_E 198_H 0.72 0.17 0.00
279_L 145_I 0.72 0.17 0.00
251_C 109_A 0.72 0.17 0.00
183_L 167_K 0.71 0.17 0.00
173_L 8_K 0.71 0.17 0.00
218_A 47_R 0.71 0.17 0.00
109_V 101_V 0.71 0.17 0.00
197_F 83_K 0.71 0.17 0.00
275_L 83_K 0.70 0.17 0.00
117_L 8_K 0.70 0.17 0.00
24_L 77_K 0.70 0.17 0.00
18_Y 70_R 0.70 0.16 0.00
57_P 119_S 0.70 0.16 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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