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OPENSEQ.org
L1-vs-L20
Genes: A B A+B
Length: 234 118 340
Sequences: 3196 1984 1050
Seq/Len: 13.66 16.81 3.09
MirrorTree (Pazo et al. 2001) 0.66
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 0.09 0.10 0.00
2 0.09 0.10 0.00
5 0.09 0.10 0.01
10 0.09 0.10 0.03
20 0.09 0.10 0.09
100 0.09 0.10 0.50
∞ 0.10 0.10 2.98
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
58_N 91_D 1.00 0.66 0.01
58_N 40_I 1.00 0.65 0.01
45_A 57_F 0.85 0.47 0.01
120_A 91_D 0.82 0.43 0.01
130_V 110_V 0.79 0.40 0.01
189_L 2_A 0.79 0.40 0.01
48_L 21_A 0.79 0.40 0.01
221_G 83_L 0.78 0.39 0.00
228_G 98_I 0.78 0.39 0.00
114_V 25_Y 0.77 0.38 0.00
128_G 51_R 0.76 0.36 0.00
161_V 70_R 0.74 0.34 0.00
52_A 80_I 0.74 0.34 0.00
80_Q 13_R 0.73 0.34 0.00
46_V 86_A 0.73 0.33 0.00
194_V 25_Y 0.73 0.33 0.00
122_R 42_A 0.73 0.33 0.00
124_V 75_S 0.73 0.33 0.00
219_G 37_Q 0.71 0.30 0.00
130_V 39_V 0.69 0.29 0.00
210_K 56_Q 0.68 0.28 0.00
122_R 38_A 0.67 0.27 0.00
42_V 90_I 0.67 0.26 0.00
103_Q 37_Q 0.66 0.26 0.00
219_G 100_V 0.66 0.26 0.00
64_V 63_A 0.66 0.26 0.00
72_S 79_F 0.65 0.25 0.00
115_I 38_A 0.65 0.25 0.00
189_L 24_Y 0.65 0.24 0.00
212_V 53_R 0.65 0.24 0.00
41_S 12_A 0.65 0.24 0.00
48_L 39_V 0.64 0.24 0.00
156_A 90_I 0.64 0.23 0.00
211_K 77_S 0.64 0.23 0.00
103_Q 53_R 0.63 0.23 0.00
39_V 79_F 0.63 0.23 0.00
45_A 48_R 0.63 0.23 0.00
116_A 102_D 0.63 0.23 0.00
140_P 36_F 0.62 0.22 0.00
12_R 80_I 0.62 0.22 0.00
195_A 14_H 0.62 0.22 0.00
113_V 91_D 0.62 0.22 0.00
25_E 56_Q 0.62 0.22 0.00
129_Q 27_A 0.62 0.22 0.00
203_Q 4_V 0.61 0.22 0.00
167_K 35_A 0.61 0.21 0.00
101_A 38_A 0.61 0.21 0.00
158_A 28_R 0.61 0.21 0.00
97_M 48_R 0.61 0.21 0.00
104_I 57_F 0.60 0.21 0.00
11_I 24_Y 0.60 0.21 0.00
173_T 72_N 0.60 0.20 0.00
98_E 91_D 0.60 0.20 0.00
100_L 33_R 0.60 0.20 0.00
155_N 31_V 0.60 0.20 0.00
54_K 30_R 0.60 0.20 0.00
23_I 41_K 0.59 0.20 0.00
175_I 8_V 0.59 0.20 0.00
23_I 38_A 0.59 0.20 0.00
43_D 12_A 0.59 0.20 0.00
173_T 71_Q 0.59 0.20 0.00
100_L 7_G 0.59 0.20 0.00
228_G 110_V 0.59 0.20 0.00
219_G 10_A 0.59 0.20 0.00
45_A 49_D 0.59 0.19 0.00
129_Q 85_K 0.59 0.19 0.00
17_A 88_V 0.58 0.19 0.00
219_G 22_K 0.58 0.19 0.00
24_N 7_G 0.58 0.19 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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