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OPENSEQ.org
6
Genes: A B A+B
Length: 187 282 444
Sequences: 1458 1980 605
Seq/Len: 7.8 7.02 1.36
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 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.01 0.00
20 0.00 0.01 0.04
100 0.00 0.04 0.17
∞ 0.06 0.17 1.29
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
88_Y 48_V 1.04 0.45 0.00
49_V 148_I 1.03 0.44 0.00
89_E 93_I 0.99 0.41 0.00
133_V 263_A 0.97 0.38 0.00
49_V 248_S 0.95 0.36 0.00
166_I 73_A 0.94 0.36 0.00
89_E 75_I 0.93 0.35 0.00
113_V 133_L 0.90 0.32 0.00
143_D 235_G 0.90 0.32 0.00
133_V 46_I 0.90 0.32 0.00
154_L 99_A 0.89 0.31 0.00
174_V 69_A 0.89 0.31 0.00
103_R 48_V 0.87 0.30 0.00
88_Y 153_A 0.87 0.29 0.00
183_G 40_L 0.87 0.29 0.00
174_V 99_A 0.85 0.28 0.00
166_I 262_L 0.84 0.27 0.00
97_L 151_A 0.84 0.27 0.00
92_P 44_F 0.83 0.26 0.00
166_I 109_V 0.82 0.26 0.00
153_T 170_A 0.82 0.26 0.00
178_D 109_V 0.81 0.25 0.00
89_E 140_S 0.81 0.25 0.00
22_I 100_L 0.81 0.24 0.00
166_I 225_T 0.81 0.24 0.00
140_L 38_T 0.79 0.23 0.00
160_I 89_I 0.79 0.23 0.00
41_L 68_A 0.78 0.23 0.00
22_I 152_V 0.78 0.23 0.00
88_Y 131_V 0.78 0.22 0.00
141_Q 40_L 0.77 0.22 0.00
178_D 241_R 0.77 0.22 0.00
72_Y 216_L 0.77 0.22 0.00
96_A 133_L 0.77 0.22 0.00
75_R 183_L 0.76 0.21 0.00
46_S 60_G 0.76 0.21 0.00
89_E 268_A 0.76 0.21 0.00
6_D 38_T 0.76 0.21 0.00
100_D 253_R 0.76 0.21 0.00
113_V 214_R 0.76 0.21 0.00
11_L 189_V 0.76 0.21 0.00
174_V 89_I 0.75 0.21 0.00
72_Y 103_G 0.75 0.20 0.00
125_L 268_A 0.75 0.20 0.00
172_L 257_A 0.74 0.20 0.00
89_E 125_I 0.74 0.20 0.00
140_L 153_A 0.74 0.20 0.00
78_S 266_A 0.73 0.19 0.00
46_S 96_L 0.72 0.19 0.00
24_E 67_L 0.72 0.19 0.00
113_V 235_G 0.71 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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