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OPENSEQ.org
P_huzuo-3
Genes: A B A+B
Length: 272 299 472
Sequences: 4745 3692 69
Seq/Len: 17.44 12.35 0.15
MirrorTree (Pazo et al. 2001) 0.50
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 0.29 0.25 0.01
2 0.29 0.25 0.01
5 0.29 0.25 0.01
10 0.29 0.25 0.01
20 0.29 0.25 0.02
100 0.31 0.27 0.03
∞ 0.33 0.29 0.12
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
163_L 148_F 1.59 0.30 0.00
163_L 33_A 1.38 0.22 0.00
98_P 177_L 1.33 0.20 0.00
224_I 249_I 1.20 0.15 0.00
56_F 162_L 1.18 0.15 0.00
37_V 241_A 1.18 0.15 0.00
83_K 229_E 1.17 0.15 0.00
72_R 148_F 1.16 0.14 0.00
144_E 43_V 1.15 0.14 0.00
220_A 217_A 1.13 0.14 0.00
53_G 157_R 1.13 0.14 0.00
236_I 168_L 1.10 0.13 0.00
32_A 148_F 1.08 0.12 0.00
38_I 43_V 1.07 0.12 0.00
222_E 195_A 1.04 0.11 0.00
244_A 229_E 1.04 0.11 0.00
49_V 223_Q 1.04 0.11 0.00
215_E 244_K 1.03 0.11 0.00
207_K 227_Q 1.02 0.11 0.00
177_K 249_I 1.02 0.11 0.00
204_E 72_I 1.01 0.11 0.00
220_A 107_R 1.01 0.11 0.00
134_F 42_T 1.00 0.11 0.00
22_V 70_F 1.00 0.10 0.00
51_G 97_K 1.00 0.10 0.00
51_G 45_G 0.99 0.10 0.00
55_H 159_Q 0.99 0.10 0.00
159_A 78_P 0.99 0.10 0.00
190_Q 141_L 0.98 0.10 0.00
215_E 70_F 0.98 0.10 0.00
165_L 230_G 0.98 0.10 0.00
90_I 135_S 0.97 0.10 0.00
165_L 60_Q 0.96 0.10 0.00
163_L 196_A 0.95 0.10 0.00
49_V 277_N 0.95 0.10 0.00
43_R 91_S 0.94 0.09 0.00
29_N 153_L 0.94 0.09 0.00
102_Q 234_A 0.94 0.09 0.00
52_E 196_A 0.94 0.09 0.00
88_V 88_R 0.93 0.09 0.00
228_L 269_N 0.93 0.09 0.00
127_L 83_I 0.93 0.09 0.00
220_A 71_R 0.92 0.09 0.00
120_P 151_S 0.92 0.09 0.00
94_I 38_E 0.91 0.09 0.00
239_R 240_E 0.91 0.09 0.00
111_G 229_E 0.91 0.09 0.00
170_L 143_S 0.91 0.09 0.00
222_E 235_A 0.90 0.09 0.00
222_E 266_T 0.90 0.09 0.00
97_R 193_Y 0.89 0.09 0.00
148_R 224_K 0.89 0.08 0.00
97_R 72_I 0.89 0.08 0.00
228_L 232_A 0.89 0.08 0.00
170_L 251_L 0.88 0.08 0.00
205_Q 60_Q 0.88 0.08 0.00
106_I 177_L 0.88 0.08 0.00
83_K 94_T 0.87 0.08 0.00
211_I 60_Q 0.87 0.08 0.00
23_V 40_V 0.87 0.08 0.00
185_A 160_V 0.87 0.08 0.00
53_G 56_G 0.87 0.08 0.00
53_G 73_P 0.87 0.08 0.00
127_L 84_R 0.87 0.08 0.00
45_V 244_K 0.86 0.08 0.00
20_G 52_F 0.86 0.08 0.00
45_V 196_A 0.86 0.08 0.00
60_W 74_W 0.86 0.08 0.00
183_V 143_S 0.85 0.08 0.00
163_L 254_I 0.85 0.08 0.00
219_K 244_K 0.85 0.08 0.00
142_Q 86_R 0.84 0.08 0.00
126_I 148_F 0.84 0.07 0.00
219_K 69_H 0.83 0.07 0.00
173_L 140_V 0.83 0.07 0.00
57_L 36_V 0.83 0.07 0.00
175_F 184_I 0.83 0.07 0.00
80_T 112_P 0.83 0.07 0.00
116_E 225_I 0.82 0.07 0.00
162_G 271_I 0.82 0.07 0.00
45_V 88_R 0.82 0.07 0.00
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
13800 0.01 P_huzuo-5 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) Killed - Shared
13799 0.15 P_huzuo-3 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
13798 0.01 P_huzuo-2 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed - Shared
13797 0 P_huzuo-1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
13795 0 P_huzuo Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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