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OPENSEQ.org
METI - METQ
Genes: A B A+B
Length: 217 271 474
Sequences: 1152 1605 1069
Seq/Len: 5.31 5.92 2.26
MirrorTree (Pazo et al. 2001) 0.60
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 0.00 0.05 1.51
2 0.00 0.06 2.07
5 0.00 0.06 2.18
10 0.01 0.07 2.19
20 0.01 0.07 2.19
100 0.02 0.10 2.22
∞ 0.09 0.59 2.25
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 2.49 1.00 0.99
80_R 192_D 1.46 0.91 0.83
87_I 66_F 1.32 0.85 0.74
174_Q 67_N 1.20 0.76 0.62
178_Q 183_E 1.12 0.69 0.54
87_I 182_L 1.11 0.68 0.52
115_I 115_A 1.08 0.65 0.49
117_T 172_E 1.00 0.56 0.40
87_I 75_A 0.97 0.53 0.36
80_R 78_K 0.89 0.43 0.27
72_L 71_L 0.88 0.42 0.27
179_Y 181_E 0.86 0.40 0.24
177_Y 189_R 0.84 0.38 0.23
83_V 81_I 0.82 0.36 0.21
129_T 163_L 0.82 0.35 0.20
161_S 65_T 0.81 0.35 0.20
192_V 183_E 0.81 0.35 0.20
181_Y 71_L 0.80 0.34 0.19
167_V 170_V 0.80 0.34 0.19
134_V 108_N 0.78 0.31 0.17
65_S 91_Y 0.77 0.31 0.17
116_P 259_A 0.77 0.30 0.17
94_V 186_Q 0.76 0.29 0.16
161_S 143_G 0.76 0.29 0.16
137_V 186_Q 0.76 0.29 0.16
66_I 247_V 0.75 0.28 0.15
100_A 69_Y 0.74 0.28 0.14
160_Y 211_L 0.74 0.28 0.14
178_Q 65_T 0.72 0.26 0.13
147_V 70_V 0.72 0.26 0.13
69_I 36_G 0.72 0.26 0.13
160_Y 152_V 0.70 0.25 0.12
137_V 36_G 0.70 0.24 0.12
86_S 186_Q 0.70 0.24 0.12
158_V 143_G 0.69 0.23 0.11
183_G 65_T 0.69 0.23 0.11
94_V 193_D 0.69 0.23 0.11
197_V 50_Q 0.69 0.23 0.11
162_A 66_F 0.69 0.23 0.11
147_V 126_E 0.69 0.23 0.11
30_I 132_Q 0.69 0.23 0.11
184_Y 189_R 0.68 0.23 0.11
69_I 188_P 0.68 0.23 0.11
125_A 92_L 0.68 0.22 0.11
210_I 232_V 0.68 0.22 0.10
199_L 181_E 0.68 0.22 0.10
17_L 33_I 0.68 0.22 0.10
196_L 189_R 0.66 0.21 0.10
63_F 135_V 0.65 0.20 0.09
129_T 232_V 0.65 0.20 0.09
100_A 72_P 0.65 0.20 0.09
115_I 121_I 0.65 0.20 0.09
136_K 90_P 0.64 0.20 0.09
193_L 232_V 0.64 0.20 0.09
184_Y 209_I 0.64 0.19 0.09
158_V 127_L 0.64 0.19 0.09
91_A 193_D 0.64 0.19 0.09
123_S 154_L 0.63 0.19 0.08
134_V 170_V 0.63 0.19 0.08
15_E 81_I 0.62 0.18 0.08
42_R 133_V 0.62 0.18 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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