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OPENSEQ.org
test
Genes: A B A+B
Length: 317 153 463
Sequences: 2574 2584 103
Seq/Len: 8.12 16.89 0.22
MirrorTree (Pazo et al. 2001) 0.55
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 0.11 0.34 0.08
2 0.13 0.37 0.11
5 0.14 0.41 0.15
10 0.15 0.42 0.19
20 0.16 0.43 0.22
100 0.17 0.44 0.33
∞ 0.21 0.48 0.44
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
18_L 125_I 1.60 0.40 0.00
148_V 107_A 1.37 0.27 0.00
15_Y 22_A 1.36 0.27 0.00
247_E 90_K 1.28 0.23 0.00
99_I 110_D 1.27 0.23 0.00
99_I 74_T 1.26 0.22 0.00
140_R 117_D 1.25 0.22 0.00
87_A 43_D 1.24 0.21 0.00
16_Q 139_L 1.22 0.21 0.00
300_G 86_L 1.21 0.20 0.00
269_A 90_K 1.20 0.20 0.00
133_T 75_C 1.18 0.19 0.00
234_S 107_A 1.17 0.18 0.00
181_V 49_A 1.16 0.18 0.00
181_V 139_L 1.13 0.17 0.00
200_C 116_E 1.13 0.17 0.00
234_S 69_K 1.12 0.17 0.00
48_V 88_Q 1.08 0.16 0.00
85_L 117_D 1.08 0.15 0.00
195_T 42_I 1.07 0.15 0.00
55_L 7_S 1.04 0.14 0.00
152_V 89_A 1.03 0.14 0.00
152_V 87_G 1.02 0.14 0.00
35_I 59_L 1.01 0.13 0.00
213_K 33_D 1.01 0.13 0.00
289_A 86_L 1.01 0.13 0.00
4_N 35_K 1.00 0.13 0.00
134_L 19_C 1.00 0.13 0.00
62_M 59_L 1.00 0.13 0.00
184_Q 86_L 1.00 0.13 0.00
230_V 102_N 1.00 0.13 0.00
118_D 117_D 0.99 0.13 0.00
251_D 59_L 0.98 0.13 0.00
121_V 72_Y 0.98 0.12 0.00
218_Y 38_G 0.98 0.12 0.00
58_V 3_N 0.97 0.12 0.00
9_Q 94_T 0.97 0.12 0.00
43_K 138_D 0.97 0.12 0.00
181_V 82_A 0.97 0.12 0.00
17_T 91_Q 0.96 0.12 0.00
127_I 83_I 0.96 0.12 0.00
48_V 94_T 0.95 0.12 0.00
88_V 6_I 0.95 0.12 0.00
150_G 115_C 0.95 0.12 0.00
157_G 115_C 0.95 0.12 0.00
304_L 48_S 0.95 0.12 0.00
18_L 105_A 0.94 0.12 0.00
48_V 91_Q 0.94 0.12 0.00
130_Y 111_G 0.94 0.12 0.00
164_Q 23_L 0.94 0.12 0.00
230_V 6_I 0.94 0.12 0.00
260_G 111_G 0.94 0.11 0.00
127_I 71_R 0.94 0.11 0.00
24_A 94_T 0.94 0.11 0.00
22_V 42_I 0.93 0.11 0.00
148_V 82_A 0.93 0.11 0.00
57_I 133_D 0.93 0.11 0.00
48_V 43_D 0.92 0.11 0.00
40_G 75_C 0.92 0.11 0.00
9_Q 71_R 0.92 0.11 0.00
183_A 75_C 0.92 0.11 0.00
231_V 136_L 0.91 0.11 0.00
42_Y 10_C 0.91 0.11 0.00
72_N 14_R 0.91 0.11 0.00
99_I 141_D 0.91 0.11 0.00
258_Y 136_L 0.90 0.11 0.00
240_I 93_L 0.90 0.10 0.00
218_Y 89_A 0.90 0.10 0.00
228_R 118_S 0.90 0.10 0.00
195_T 56_I 0.90 0.10 0.00
122_I 16_P 0.90 0.10 0.00
69_G 146_I 0.90 0.10 0.00
12_T 119_F 0.89 0.10 0.00
206_S 40_F 0.89 0.10 0.00
298_I 88_Q 0.89 0.10 0.00
15_Y 59_L 0.89 0.10 0.00
70_S 121_G 0.88 0.10 0.00
231_V 82_A 0.88 0.10 0.00
229_T 18_L 0.88 0.10 0.00
296_K 17_S 0.88 0.10 0.00
63_Y 48_S 0.88 0.10 0.00
311_Y 12_K 0.87 0.10 0.00
41_T 6_I 0.87 0.10 0.00
236_L 96_G 0.87 0.10 0.00
290_M 137_E 0.87 0.10 0.00
167_Q 30_A 0.87 0.10 0.00
295_A 56_I 0.87 0.10 0.00
150_G 75_C 0.86 0.10 0.00
157_G 75_C 0.86 0.10 0.00
200_C 125_I 0.86 0.10 0.00
46_V 133_D 0.86 0.10 0.00
11_G 97_D 0.85 0.09 0.00
29_S 89_A 0.85 0.09 0.00
220_G 115_C 0.85 0.09 0.00
266_G 115_C 0.85 0.09 0.00
185_G 42_I 0.85 0.09 0.00
71_L 24_E 0.85 0.09 0.00
184_Q 24_E 0.85 0.09 0.00
198_Q 119_F 0.84 0.09 0.00
51_N 47_A 0.84 0.09 0.00
298_I 121_G 0.84 0.09 0.00
199_F 124_N 0.84 0.09 0.00
304_L 77_E 0.84 0.09 0.00
55_L 12_K 0.84 0.09 0.00
304_L 14_R 0.84 0.09 0.00
230_V 42_I 0.83 0.09 0.00
240_I 139_L 0.83 0.09 0.00
230_V 147_S 0.83 0.09 0.00
233_E 27_P 0.83 0.09 0.00
269_A 59_L 0.83 0.09 0.00
51_N 68_L 0.83 0.09 0.00
257_L 46_Q 0.83 0.09 0.00
162_V 6_I 0.82 0.09 0.00
130_Y 147_S 0.82 0.09 0.00
150_G 19_C 0.82 0.09 0.00
157_G 19_C 0.82 0.09 0.00
26_P 93_L 0.82 0.09 0.00
170_A 151_P 0.82 0.09 0.00
85_L 46_Q 0.82 0.09 0.00
20_E 82_A 0.82 0.09 0.00
86_A 89_A 0.82 0.09 0.00
96_D 134_L 0.81 0.09 0.00
231_V 45_A 0.81 0.09 0.00
57_I 11_P 0.81 0.09 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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.43 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
8229 0.41 pengfei Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8081 0.24 pengfei Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (r132) 0.00 Done
8066 0.21 tt Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
8065 0.27 tt Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
8064 0.22 test Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done
8063 0.26 ss Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
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