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OPENSEQ.org
L1-vs-S10
Genes: A B A+B
Length: 234 103 325
Sequences: 3196 1460 1304
Seq/Len: 13.66 14.17 4.01
MirrorTree (Pazo et al. 2001) 0.88
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 0.09 0.00
2 0.09 0.09 0.00
5 0.09 0.09 0.01
10 0.09 0.09 1.00
20 0.09 0.09 1.49
100 0.09 0.09 2.18
∞ 0.10 0.09 3.87
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
97_M 18_I 1.12 0.84 0.08
189_L 60_D 1.09 0.82 0.08
210_K 71_L 1.07 0.80 0.07
64_V 52_L 1.03 0.77 0.06
212_V 12_A 1.03 0.76 0.06
113_V 82_K 1.03 0.76 0.06
129_Q 65_Y 0.95 0.68 0.05
23_I 60_D 0.94 0.66 0.05
120_A 18_I 0.91 0.63 0.04
164_R 74_V 0.87 0.58 0.04
195_A 18_I 0.87 0.58 0.04
124_V 69_T 0.87 0.58 0.04
142_V 93_A 0.87 0.57 0.04
160_Q 46_K 0.86 0.56 0.04
124_V 75_D 0.86 0.56 0.04
142_V 16_R 0.84 0.54 0.03
18_T 45_R 0.83 0.53 0.03
162_R 63_D 0.83 0.52 0.03
199_A 31_R 0.83 0.52 0.03
167_K 92_L 0.83 0.52 0.03
160_Q 48_R 0.81 0.50 0.03
129_Q 18_I 0.80 0.49 0.03
218_M 14_D 0.80 0.49 0.03
175_I 89_R 0.80 0.49 0.03
184_K 45_R 0.78 0.46 0.03
215_S 58_N 0.78 0.46 0.03
83_N 9_R 0.77 0.45 0.03
107_G 57_V 0.77 0.44 0.03
219_G 79_P 0.77 0.43 0.03
86_A 18_I 0.76 0.43 0.03
11_I 82_K 0.76 0.42 0.03
169_G 49_F 0.75 0.42 0.02
170_I 89_R 0.75 0.41 0.02
166_D 93_A 0.74 0.41 0.02
187_E 51_V 0.74 0.40 0.02
41_S 94_A 0.73 0.39 0.02
195_A 67_I 0.73 0.39 0.02
40_E 94_A 0.72 0.38 0.02
193_L 100_I 0.72 0.38 0.02
67_H 14_D 0.72 0.38 0.02
11_I 12_A 0.72 0.38 0.02
63_T 99_Q 0.71 0.37 0.02
209_I 84_V 0.71 0.37 0.02
219_G 58_N 0.70 0.35 0.02
134_R 37_R 0.69 0.34 0.02
43_D 15_H 0.69 0.34 0.02
62_A 55_P 0.68 0.33 0.02
162_R 61_A 0.68 0.33 0.02
113_V 22_T 0.68 0.33 0.02
44_V 16_R 0.68 0.33 0.02
30_L 99_Q 0.68 0.32 0.02
221_G 79_P 0.67 0.32 0.02
12_R 78_E 0.67 0.32 0.02
86_A 81_E 0.66 0.31 0.02
59_V 100_I 0.66 0.30 0.02
31_K 3_N 0.66 0.30 0.02
225_D 49_F 0.66 0.30 0.02
107_G 49_F 0.65 0.30 0.02
114_V 52_L 0.65 0.30 0.02
77_V 4_Q 0.65 0.30 0.02
118_P 87_L 0.65 0.29 0.02
59_V 48_R 0.65 0.29 0.02
78_F 94_A 0.65 0.29 0.02
187_E 76_I 0.65 0.29 0.02
114_V 78_E 0.64 0.29 0.02
162_R 65_Y 0.64 0.29 0.02
43_D 17_L 0.64 0.29 0.02
98_E 29_A 0.64 0.28 0.01
128_G 44_T 0.64 0.28 0.01
43_D 40_I 0.63 0.27 0.01
124_V 31_R 0.63 0.27 0.01
212_V 55_P 0.63 0.27 0.01
179_D 65_Y 0.63 0.27 0.01
41_S 4_Q 0.63 0.27 0.01
7_R 47_E 0.62 0.27 0.01
127_L 55_P 0.62 0.26 0.01
85_E 9_R 0.62 0.26 0.01
5_T 20_Q 0.62 0.26 0.01
219_G 10_L 0.62 0.26 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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