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OPENSEQ.org
73
Genes: A B A+B
Length: 189 190 367
Sequences: 3931 11310 373
Seq/Len: 20.8 59.53 1.02
MirrorTree (Pazo et al. 2001) 0.21
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 0.05 0.07
2 0.04 0.05 0.15
5 0.04 0.07 0.36
10 0.06 0.09 0.59
20 0.08 0.12 0.98
100 0.12 0.21 2.38
∞ 0.17 0.27 3.59
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
124_V 150_K 1.30 0.61 0.00
139_L 137_I 1.17 0.50 0.00
160_L 165_L 0.91 0.27 0.00
89_F 159_A 0.91 0.27 0.00
53_A 84_V 0.91 0.27 0.00
98_L 117_I 0.90 0.26 0.00
165_G 84_V 0.87 0.24 0.00
113_D 91_E 0.86 0.24 0.00
168_L 8_V 0.86 0.24 0.00
93_L 32_Y 0.84 0.23 0.00
35_V 48_G 0.83 0.22 0.00
125_L 84_V 0.82 0.21 0.00
89_F 76_D 0.81 0.21 0.00
188_L 147_R 0.81 0.21 0.00
177_F 80_V 0.81 0.21 0.00
34_T 9_V 0.80 0.20 0.00
42_A 164_G 0.79 0.20 0.00
151_D 161_T 0.77 0.18 0.00
160_L 44_V 0.77 0.18 0.00
30_V 167_N 0.76 0.18 0.00
169_L 84_V 0.76 0.17 0.00
82_P 82_F 0.75 0.17 0.00
121_T 28_F 0.75 0.17 0.00
38_L 139_P 0.74 0.17 0.00
79_L 84_V 0.74 0.17 0.00
101_D 84_V 0.73 0.16 0.00
96_P 86_S 0.72 0.16 0.00
115_S 8_V 0.72 0.16 0.00
156_T 51_Y 0.72 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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