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OPENSEQ.org
Lys1
Genes: A B A+B
Length: 187 505 675
Sequences: 1458 4526 1190
Seq/Len: 7.8 8.96 1.76
MirrorTree (Pazo et al. 2001) 0.19
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 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.01
10 0.00 0.00 0.04
20 0.00 0.01 0.15
100 0.00 0.03 0.51
∞ 0.06 0.19 1.72
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
118_G 119_V 1.11 0.60 0.00
72_Y 94_I 1.02 0.51 0.00
135_H 483_L 0.98 0.47 0.00
112_Q 390_V 0.93 0.41 0.00
174_V 493_E 0.88 0.36 0.00
13_L 142_A 0.86 0.34 0.00
64_T 465_L 0.86 0.34 0.00
119_V 295_V 0.83 0.31 0.00
168_T 117_V 0.81 0.29 0.00
23_T 62_V 0.80 0.29 0.00
141_Q 272_L 0.80 0.28 0.00
24_E 144_S 0.80 0.28 0.00
128_T 117_V 0.80 0.28 0.00
104_F 350_D 0.79 0.28 0.00
183_G 250_F 0.79 0.28 0.00
166_I 185_V 0.78 0.26 0.00
99_G 294_E 0.77 0.26 0.00
32_K 391_K 0.76 0.25 0.00
132_E 246_F 0.75 0.24 0.00
46_S 488_G 0.74 0.24 0.00
59_K 247_D 0.74 0.24 0.00
113_V 467_Y 0.74 0.23 0.00
69_D 493_E 0.74 0.23 0.00
160_I 190_T 0.74 0.23 0.00
57_G 71_A 0.72 0.22 0.00
65_V 374_E 0.71 0.21 0.00
170_D 50_P 0.71 0.21 0.00
98_V 295_V 0.71 0.21 0.00
132_E 323_Q 0.70 0.21 0.00
172_L 313_Y 0.69 0.20 0.00
132_E 124_I 0.69 0.20 0.00
174_V 248_K 0.69 0.20 0.00
16_D 483_L 0.69 0.20 0.00
174_V 200_V 0.69 0.20 0.00
5_A 272_L 0.68 0.19 0.00
153_T 483_L 0.68 0.19 0.00
138_P 248_K 0.68 0.19 0.00
133_V 290_E 0.68 0.19 0.00
118_G 140_I 0.67 0.18 0.00
133_V 152_H 0.67 0.18 0.00
68_R 64_V 0.66 0.18 0.00
105_L 451_D 0.66 0.18 0.00
49_V 482_L 0.66 0.18 0.00
99_G 301_G 0.66 0.18 0.00
134_T 120_H 0.65 0.17 0.00
104_F 473_T 0.65 0.17 0.00
170_D 156_S 0.65 0.17 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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