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OPENSEQ.org
L1-vs-L5
Genes: A B A+B
Length: 234 179 404
Sequences: 3196 2042 1267
Seq/Len: 13.66 11.41 3.14
MirrorTree (Pazo et al. 2001) 0.87
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 0.02
10 0.09 0.09 0.03
20 0.09 0.09 0.13
100 0.09 0.09 1.90
∞ 0.10 0.09 3.07
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
130_V 81_Q 1.14 0.80 0.06
56_D 81_Q 0.98 0.64 0.04
85_E 51_D 0.97 0.62 0.04
63_T 12_V 0.92 0.56 0.03
80_Q 111_I 0.89 0.53 0.03
63_T 85_I 0.88 0.51 0.03
161_V 20_F 0.87 0.50 0.03
161_V 143_Y 0.87 0.50 0.03
163_Y 108_V 0.82 0.44 0.02
40_E 143_Y 0.81 0.42 0.02
169_G 136_I 0.80 0.42 0.02
141_K 137_I 0.79 0.40 0.02
128_G 68_T 0.78 0.39 0.02
211_K 175_F 0.78 0.39 0.02
174_T 46_D 0.77 0.38 0.02
113_V 121_S 0.76 0.36 0.02
43_D 26_M 0.75 0.36 0.02
170_I 130_M 0.74 0.35 0.02
59_V 47_K 0.74 0.34 0.02
209_I 144_D 0.73 0.34 0.01
229_L 76_G 0.73 0.33 0.01
52_A 24_S 0.73 0.33 0.01
82_A 104_I 0.73 0.33 0.01
140_P 153_D 0.72 0.32 0.01
22_D 30_R 0.72 0.32 0.01
154_K 64_K 0.71 0.31 0.01
101_A 2_A 0.71 0.31 0.01
163_Y 79_I 0.70 0.30 0.01
52_A 132_V 0.70 0.30 0.01
86_A 146_V 0.70 0.30 0.01
36_A 136_I 0.70 0.30 0.01
28_A 15_K 0.69 0.29 0.01
120_A 68_T 0.69 0.28 0.01
151_E 178_R 0.69 0.28 0.01
200_K 79_I 0.68 0.28 0.01
19_K 19_E 0.68 0.28 0.01
211_K 157_T 0.67 0.27 0.01
115_I 120_K 0.67 0.27 0.01
78_F 38_M 0.66 0.26 0.01
178_V 13_V 0.66 0.26 0.01
108_E 174_D 0.66 0.26 0.01
83_N 42_E 0.66 0.26 0.01
97_M 47_K 0.66 0.26 0.01
12_R 166_G 0.66 0.26 0.01
168_N 166_G 0.66 0.26 0.01
164_R 135_Q 0.65 0.25 0.01
62_A 5_H 0.65 0.25 0.01
58_N 46_D 0.65 0.25 0.01
164_R 143_Y 0.65 0.25 0.01
129_Q 59_A 0.65 0.25 0.01
64_V 154_I 0.65 0.25 0.01
214_I 55_A 0.65 0.24 0.01
128_G 144_D 0.64 0.24 0.01
155_N 174_D 0.64 0.24 0.01
24_N 36_L 0.64 0.24 0.01
109_M 46_D 0.64 0.24 0.01
167_K 78_K 0.64 0.24 0.01
219_G 42_E 0.63 0.23 0.01
130_V 79_I 0.63 0.23 0.01
113_V 149_V 0.63 0.23 0.01
210_K 27_Q 0.63 0.23 0.01
198_K 173_F 0.63 0.23 0.01
89_A 18_T 0.62 0.23 0.01
163_Y 102_R 0.62 0.22 0.01
212_V 16_L 0.62 0.22 0.01
202_T 81_Q 0.62 0.22 0.01
13_E 10_D 0.62 0.22 0.01
229_L 132_V 0.61 0.22 0.01
89_A 13_V 0.61 0.22 0.01
40_E 24_S 0.61 0.22 0.01
220_A 24_S 0.61 0.22 0.01
164_R 144_D 0.61 0.22 0.01
62_A 1_M 0.61 0.21 0.01
136_L 34_I 0.61 0.21 0.01
219_G 133_R 0.61 0.21 0.01
187_E 17_M 0.61 0.21 0.01
67_H 17_M 0.61 0.21 0.01
223_A 111_I 0.61 0.21 0.01
12_R 7_Y 0.61 0.21 0.01
129_Q 157_T 0.61 0.21 0.01
158_A 12_V 0.61 0.21 0.01
45_A 88_K 0.60 0.21 0.01
9_R 17_M 0.60 0.20 0.01
73_V 93_G 0.60 0.20 0.01
199_A 166_G 0.60 0.20 0.01
54_K 68_T 0.60 0.20 0.01
54_K 46_D 0.60 0.20 0.01
191_A 168_A 0.59 0.20 0.01
161_V 117_L 0.59 0.20 0.01
7_R 24_S 0.59 0.20 0.01
134_R 102_R 0.59 0.20 0.01
5_T 47_K 0.59 0.20 0.01
210_K 5_H 0.59 0.20 0.01
161_V 12_V 0.59 0.20 0.01
227_A 27_Q 0.59 0.20 0.01
43_D 136_I 0.59 0.20 0.01
174_T 47_K 0.59 0.20 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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