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OPENSEQ.org
GraX-GraS
Genes: A B A+B
Length: 307 346 558
Sequences: 1803 5684 439
Seq/Len: 5.87 16.43 0.79
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 0.03 0.00 0.00
2 0.03 0.00 0.03
5 0.03 0.01 0.04
10 0.03 0.01 0.06
20 0.03 0.01 0.08
100 0.03 0.04 0.16
∞ 0.08 0.15 0.67
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
11_T 56_I 1.10 0.37 0.00
172_N 188_L 1.08 0.35 0.00
109_V 135_V 1.07 0.35 0.00
62_M 324_V 1.02 0.30 0.00
254_Y 318_V 1.01 0.30 0.00
23_E 235_L 0.98 0.27 0.00
231_L 235_L 0.97 0.27 0.00
68_A 224_T 0.93 0.24 0.00
68_A 90_P 0.92 0.24 0.00
5_V 269_I 0.89 0.22 0.00
9_G 129_H 0.89 0.22 0.00
9_G 237_N 0.89 0.22 0.00
9_G 297_G 0.89 0.22 0.00
113_P 262_I 0.87 0.21 0.00
240_G 66_V 0.87 0.20 0.00
174_V 90_P 0.86 0.20 0.00
18_L 247_I 0.86 0.20 0.00
68_A 270_S 0.85 0.20 0.00
9_G 295_G 0.85 0.20 0.00
252_V 190_R 0.85 0.20 0.00
252_V 53_L 0.85 0.20 0.00
240_G 328_F 0.85 0.19 0.00
12_G 129_H 0.85 0.19 0.00
12_G 237_N 0.85 0.19 0.00
12_G 297_G 0.85 0.19 0.00
18_L 269_I 0.84 0.19 0.00
102_A 161_I 0.83 0.19 0.00
98_G 250_G 0.83 0.18 0.00
7_L 275_P 0.82 0.18 0.00
192_E 65_E 0.82 0.18 0.00
123_E 124_I 0.82 0.18 0.00
9_G 298_L 0.82 0.18 0.00
196_D 231_I 0.82 0.18 0.00
28_L 299_Y 0.82 0.18 0.00
15_G 295_G 0.81 0.17 0.00
181_M 300_L 0.81 0.17 0.00
26_A 208_I 0.81 0.17 0.00
191_T 220_V 0.80 0.17 0.00
257_L 249_I 0.80 0.17 0.00
97_F 159_S 0.80 0.17 0.00
169_T 326_L 0.80 0.17 0.00
54_H 326_L 0.80 0.17 0.00
45_M 208_I 0.79 0.17 0.00
12_G 295_G 0.79 0.17 0.00
29_F 247_I 0.79 0.16 0.00
120_E 142_I 0.79 0.16 0.00
209_L 247_I 0.78 0.16 0.00
184_T 166_D 0.78 0.16 0.00
197_Q 301_V 0.78 0.16 0.00
70_F 247_I 0.78 0.16 0.00
15_G 129_H 0.78 0.16 0.00
15_G 237_N 0.78 0.16 0.00
15_G 297_G 0.78 0.16 0.00
66_D 252_E 0.77 0.16 0.00
12_G 298_L 0.77 0.15 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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