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OPENSEQ.org
mla
Genes: A B A+B
Length: 269 109 343
Sequences: 75042 393 274
Seq/Len: 278.97 3.61 0.8
MirrorTree (Pazo et al. 2001) 0.41
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 0.10 0.00 0.06
2 0.10 0.00 0.06
5 0.14 0.00 0.71
10 0.18 0.00 0.72
20 0.23 0.00 0.72
100 0.34 0.00 0.73
∞ 0.37 0.00 0.73
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
88_S 69_L 1.92 0.91 0.44
67_F 73_L 1.71 0.83 0.28
218_L 59_V 1.55 0.74 0.19
153_A 64_T 1.49 0.70 0.16
36_I 74_I 1.39 0.62 0.12
100_M 28_L 1.34 0.58 0.10
100_M 102_L 1.30 0.54 0.09
9_V 71_L 1.26 0.51 0.08
9_V 61_R 1.23 0.48 0.07
30_T 59_V 1.22 0.47 0.07
223_I 54_I 1.22 0.47 0.07
59_A 58_R 1.16 0.42 0.06
215_A 89_V 1.16 0.42 0.06
214_H 102_L 1.14 0.41 0.05
241_R 71_L 1.14 0.41 0.05
183_L 67_L 1.13 0.39 0.05
228_S 23_G 1.12 0.39 0.05
199_V 106_V 1.12 0.39 0.05
179_T 97_A 1.12 0.39 0.05
153_A 62_V 1.12 0.38 0.05
189_E 100_Y 1.11 0.38 0.05
223_I 98_K 1.10 0.37 0.04
102_V 67_L 1.09 0.36 0.04
104_D 106_V 1.07 0.34 0.04
179_T 72_H 1.05 0.33 0.04
215_A 106_V 1.04 0.33 0.04
101_N 59_V 1.04 0.32 0.04
241_R 81_G 1.03 0.32 0.03
228_S 104_A 1.03 0.32 0.03
75_M 64_T 1.03 0.31 0.03
225_A 101_N 1.02 0.31 0.03
78_S 57_S 1.02 0.31 0.03
50_L 64_T 1.02 0.31 0.03
11_M 28_L 1.00 0.29 0.03
70_E 45_E 0.99 0.29 0.03
31_V 62_V 0.98 0.28 0.03
117_P 102_L 0.97 0.27 0.03
123_S 75_D 0.97 0.27 0.03
121_L 81_G 0.97 0.27 0.03
26_N 54_I 0.96 0.27 0.03
239_R 69_L 0.95 0.26 0.03
27_I 96_L 0.95 0.26 0.03
127_M 68_A 0.95 0.26 0.02
127_M 102_L 0.94 0.25 0.02
112_E 63_D 0.94 0.25 0.02
188_S 37_L 0.93 0.25 0.02
97_F 41_W 0.93 0.25 0.02
100_M 40_L 0.92 0.24 0.02
192_S 92_K 0.92 0.24 0.02
124_T 17_L 0.92 0.24 0.02
108_Y 84_V 0.91 0.23 0.02
223_I 84_V 0.91 0.23 0.02
110_L 33_D 0.91 0.23 0.02
31_V 37_L 0.91 0.23 0.02
168_F 106_V 0.90 0.23 0.02
45_I 34_Q 0.90 0.23 0.02
100_M 43_M 0.90 0.23 0.02
222_K 103_P 0.90 0.22 0.02
31_V 38_L 0.90 0.22 0.02
65_I 91_D 0.89 0.22 0.02
192_S 105_D 0.89 0.22 0.02
217_I 61_R 0.89 0.22 0.02
126_M 52_T 0.89 0.22 0.02
30_T 100_Y 0.88 0.21 0.02
72_I 34_Q 0.88 0.21 0.02
183_L 54_I 0.88 0.21 0.02
130_E 101_N 0.88 0.21 0.02
193_A 90_N 0.87 0.21 0.02
237_D 41_W 0.86 0.21 0.02
102_V 54_I 0.86 0.20 0.02
28_S 64_T 0.86 0.20 0.02
27_I 92_K 0.86 0.20 0.02
36_I 59_V 0.86 0.20 0.02
67_F 34_Q 0.85 0.20 0.02
100_M 64_T 0.84 0.19 0.02
214_H 55_D 0.84 0.19 0.01
234_A 74_I 0.84 0.19 0.01
13_D 81_G 0.84 0.19 0.01
48_T 26_L 0.84 0.19 0.01
78_S 50_G 0.84 0.19 0.01
189_E 92_K 0.84 0.19 0.01
179_T 41_W 0.83 0.19 0.01
66_L 64_T 0.83 0.19 0.01
52_R 34_Q 0.83 0.19 0.01
31_V 107_L 0.82 0.18 0.01
100_M 61_R 0.82 0.18 0.01
121_L 36_V 0.82 0.18 0.01
232_L 43_M 0.82 0.18 0.01
173_V 69_L 0.82 0.18 0.01
117_P 43_M 0.82 0.18 0.01
198_C 100_Y 0.82 0.18 0.01
224_V 67_L 0.81 0.18 0.01
102_V 105_D 0.81 0.18 0.01
106_V 69_L 0.81 0.17 0.01
97_F 86_L 0.80 0.17 0.01
248_A 19_W 0.80 0.17 0.01
28_S 63_D 0.80 0.17 0.01
33_R 82_N 0.80 0.17 0.01
11_M 106_V 0.80 0.17 0.01
219_A 93_V 0.80 0.17 0.01
120_L 62_V 0.80 0.17 0.01
202_S 41_W 0.79 0.16 0.01
127_M 52_T 0.78 0.16 0.01
6_A 70_L 0.78 0.16 0.01
225_A 100_Y 0.78 0.16 0.01
167_M 74_I 0.77 0.16 0.01
218_L 56_L 0.77 0.16 0.01
114_T 62_V 0.77 0.16 0.01
244_L 96_L 0.77 0.16 0.01
232_L 45_E 0.77 0.16 0.01
42_P 32_L 0.77 0.16 0.01
74_A 96_L 0.77 0.15 0.01
237_D 19_W 0.76 0.15 0.01
221_K 64_T 0.76 0.15 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)
ID Seq/Len Name Options I_Prob Status
8980 3.14 H0993 Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8973 0.8 mla Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.44 Done - Shared
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