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OPENSEQ.org
L4-vs-L20
Genes: A B A+B
Length: 201 118 316
Sequences: 3177 1984 1100
Seq/Len: 15.81 16.81 3.48
MirrorTree (Pazo et al. 2001) 0.67
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 0.08 0.10 0.00
2 0.08 0.10 0.00
5 0.08 0.10 0.01
10 0.09 0.10 0.03
20 0.09 0.10 0.08
100 0.09 0.10 0.50
∞ 0.09 0.10 3.45
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
92_H 32_Y 1.04 0.73 0.02
86_A 14_H 0.99 0.68 0.02
183_F 14_H 0.95 0.64 0.02
172_A 96_A 0.94 0.63 0.01
105_L 33_R 0.92 0.60 0.01
46_Q 4_V 0.92 0.59 0.01
175_I 109_L 0.84 0.50 0.01
79_R 6_R 0.84 0.49 0.01
44_R 2_A 0.83 0.49 0.01
92_H 2_A 0.82 0.47 0.01
50_A 52_Q 0.79 0.43 0.01
98_K 101_F 0.79 0.43 0.01
172_A 100_V 0.78 0.42 0.01
130_K 15_K 0.78 0.41 0.01
27_L 33_R 0.78 0.41 0.01
196_V 27_A 0.77 0.40 0.01
159_L 52_Q 0.75 0.39 0.01
175_I 47_Y 0.74 0.37 0.01
84_T 22_K 0.74 0.37 0.01
97_N 31_V 0.73 0.35 0.01
195_Q 59_Q 0.73 0.35 0.01
169_V 49_D 0.72 0.34 0.01
22_D 21_A 0.71 0.34 0.01
116_D 78_K 0.71 0.34 0.01
110_S 24_Y 0.71 0.33 0.01
164_L 81_N 0.71 0.33 0.01
57_K 84_K 0.71 0.33 0.01
160_A 91_D 0.70 0.32 0.01
125_S 53_R 0.70 0.32 0.01
116_D 87_S 0.69 0.32 0.01
54_G 27_A 0.69 0.31 0.01
41_Q 91_D 0.69 0.30 0.01
139_K 114_K 0.69 0.30 0.01
64_G 39_V 0.68 0.30 0.01
86_A 75_S 0.68 0.30 0.01
83_V 4_V 0.68 0.30 0.01
157_L 91_D 0.68 0.30 0.01
76_P 51_R 0.68 0.29 0.01
35_Y 22_K 0.68 0.29 0.01
166_K 88_V 0.67 0.29 0.01
28_V 87_S 0.67 0.28 0.01
70_S 10_A 0.67 0.28 0.01
29_H 6_R 0.66 0.28 0.01
105_L 73_G 0.66 0.28 0.01
136_Q 78_K 0.66 0.28 0.01
52_V 102_D 0.66 0.28 0.01
192_A 73_G 0.66 0.28 0.01
57_K 17_I 0.65 0.27 0.01
189_T 27_A 0.65 0.27 0.01
87_A 14_H 0.65 0.26 0.01
39_A 42_A 0.64 0.26 0.01
107_S 90_I 0.63 0.25 0.01
91_D 86_A 0.63 0.25 0.01
39_A 53_R 0.63 0.25 0.01
84_T 80_I 0.63 0.25 0.01
199_M 40_I 0.63 0.24 0.01
83_V 2_A 0.63 0.24 0.01
160_A 70_R 0.62 0.24 0.01
138_L 102_D 0.62 0.24 0.01
36_A 30_R 0.62 0.24 0.01
45_A 69_A 0.62 0.24 0.01
9_Q 87_S 0.62 0.24 0.01
24_N 8_V 0.62 0.24 0.01
61_R 98_I 0.62 0.24 0.01
196_V 75_S 0.62 0.23 0.01
102_R 51_R 0.61 0.23 0.01
27_L 25_Y 0.61 0.23 0.01
178_V 103_K 0.61 0.23 0.01
64_G 1_M 0.61 0.23 0.01
84_T 83_L 0.61 0.23 0.01
199_M 28_R 0.60 0.22 0.01
134_L 98_I 0.60 0.22 0.01
121_V 36_F 0.60 0.22 0.01
180_L 109_L 0.60 0.22 0.01
30_Q 28_R 0.60 0.22 0.01
100_M 43_G 0.59 0.21 0.01
41_Q 9_I 0.59 0.21 0.01
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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