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OPENSEQ.org
METI - METQ
Genes: A B A+B
Length: 217 271 474
Sequences: 14593 1605 1145
Seq/Len: 67.25 5.92 2.42
MirrorTree (Pazo et al. 2001) 0.33
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 0.32 0.05 1.53
2 0.38 0.06 2.11
5 0.39 0.06 2.23
10 0.39 0.07 2.28
20 0.40 0.07 2.35
100 0.43 0.10 2.57
∞ 0.46 0.59 2.81
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
80_R 193_D 2.38 1.00 0.99
80_R 192_D 1.38 0.89 0.80
87_I 66_F 1.11 0.70 0.54
87_I 182_L 1.05 0.64 0.48
174_Q 67_N 1.03 0.61 0.45
115_I 115_A 1.02 0.61 0.45
178_Q 183_E 0.99 0.57 0.40
117_T 172_E 0.95 0.52 0.36
87_I 75_A 0.87 0.43 0.27
83_V 81_I 0.83 0.39 0.23
167_V 170_V 0.82 0.37 0.22
80_R 78_K 0.79 0.34 0.20
179_Y 181_E 0.79 0.34 0.20
129_T 163_L 0.78 0.33 0.19
72_L 71_L 0.77 0.32 0.18
134_V 108_N 0.74 0.29 0.16
17_L 33_I 0.74 0.29 0.15
192_V 183_E 0.73 0.28 0.15
137_V 186_Q 0.71 0.27 0.14
210_I 232_V 0.70 0.26 0.13
116_P 259_A 0.70 0.26 0.13
161_S 143_G 0.70 0.25 0.12
66_I 247_V 0.69 0.24 0.12
178_Q 65_T 0.69 0.24 0.12
158_V 143_G 0.68 0.23 0.11
125_A 92_L 0.67 0.23 0.11
184_Y 189_R 0.67 0.23 0.11
94_V 186_Q 0.67 0.23 0.11
177_Y 189_R 0.67 0.22 0.11
169_A 92_L 0.66 0.22 0.10
147_V 126_E 0.65 0.21 0.10
181_Y 71_L 0.65 0.21 0.10
197_V 50_Q 0.65 0.21 0.10
115_I 121_I 0.64 0.21 0.10
185_N 35_V 0.64 0.20 0.09
86_S 186_Q 0.64 0.20 0.09
11_R 158_K 0.64 0.20 0.09
137_V 36_G 0.64 0.20 0.09
199_L 181_E 0.64 0.20 0.09
161_S 65_T 0.64 0.20 0.09
160_Y 152_V 0.63 0.20 0.09
100_A 69_Y 0.63 0.20 0.09
97_T 33_I 0.63 0.19 0.09
190_N 189_R 0.62 0.19 0.08
160_Y 211_L 0.62 0.19 0.08
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
0072 2.42 METI - METQ Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) (2013_03) 0.99 Done
0071 2.26 METI - METQ Δgene:(1, 20) A:(1E-40, 8) B:(1E-20, 8) (2013_03) 0.99 Done - Shared
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