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OPENSEQ.org
I_sub_Membound_L_sub (B, 20-99)
Genes: A B A+B
Length: 330 80 387
Sequences: 888 1710 406
Seq/Len: 2.69 21.38 1.05
MirrorTree (Pazo et al. 2001) 0.86
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 0.01 0.01 0.98
2 0.01 0.01 0.98
5 0.01 0.01 0.99
10 0.01 0.01 1.03
20 0.01 0.01 1.04
100 0.02 0.02 1.07
∞ 0.04 0.06 1.25
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
303_W 73_A 1.44 0.74 0.01
292_L 29_G 1.42 0.73 0.01
61_V 20_G 1.42 0.73 0.01
145_S 20_G 1.33 0.65 0.01
228_E 63_E 1.33 0.65 0.01
227_P 63_E 1.30 0.63 0.01
304_V 62_P 1.30 0.63 0.01
302_I 46_A 1.29 0.62 0.01
174_W 28_L 1.26 0.59 0.01
9_E 26_A 1.26 0.59 0.01
46_Y 62_P 1.26 0.59 0.01
104_E 68_F 1.25 0.58 0.01
22_T 27_A 1.19 0.52 0.01
246_G 60_L 1.16 0.50 0.01
308_T 56_L 1.15 0.49 0.01
303_W 18_G 1.14 0.47 0.01
280_G 57_I 1.13 0.47 0.01
239_H 62_P 1.12 0.46 0.01
297_Q 30_T 1.12 0.46 0.01
252_L 52_F 1.11 0.45 0.01
283_H 62_P 1.11 0.45 0.01
227_P 33_A 1.10 0.44 0.01
34_P 34_Q 1.10 0.44 0.01
46_Y 64_T 1.10 0.44 0.01
249_G 64_T 1.09 0.43 0.01
252_L 38_G 1.09 0.43 0.01
247_A 74_F 1.08 0.42 0.00
285_L 52_F 1.07 0.41 0.00
92_V 16_A 1.07 0.41 0.00
246_G 62_P 1.06 0.41 0.00
278_V 40_A 1.06 0.40 0.00
142_I 67_I 1.06 0.40 0.00
251_I 71_L 1.05 0.40 0.00
297_Q 63_E 1.05 0.40 0.00
142_I 30_T 1.04 0.38 0.00
4_W 28_L 1.04 0.38 0.00
105_F 75_I 1.03 0.38 0.00
24_D 29_G 1.03 0.37 0.00
294_H 61_L 1.01 0.36 0.00
297_Q 65_L 1.01 0.36 0.00
40_I 34_Q 1.00 0.35 0.00
282_L 43_G 1.00 0.35 0.00
230_F 66_V 1.00 0.35 0.00
230_F 63_E 1.00 0.35 0.00
235_H 63_E 1.00 0.35 0.00
147_A 24_G 1.00 0.35 0.00
36_W 62_P 0.99 0.34 0.00
257_T 62_P 0.99 0.34 0.00
159_L 75_I 0.99 0.34 0.00
21_G 49_R 0.98 0.34 0.00
283_H 64_T 0.98 0.33 0.00
25_P 47_E 0.98 0.33 0.00
175_E 37_I 0.98 0.33 0.00
293_G 65_L 0.97 0.33 0.00
60_Y 49_R 0.97 0.33 0.00
246_G 71_L 0.97 0.33 0.00
50_F 15_I 0.96 0.32 0.00
304_V 46_A 0.96 0.31 0.00
297_Q 31_G 0.95 0.31 0.00
304_V 64_T 0.95 0.31 0.00
4_W 54_T 0.94 0.30 0.00
282_L 44_A 0.94 0.30 0.00
104_E 37_I 0.94 0.30 0.00
15_L 41_G 0.93 0.30 0.00
48_L 41_G 0.93 0.29 0.00
274_L 24_G 0.93 0.29 0.00
157_L 22_A 0.93 0.29 0.00
213_F 79_R 0.93 0.29 0.00
235_H 65_L 0.93 0.29 0.00
308_T 34_Q 0.92 0.29 0.00
248_A 52_F 0.92 0.29 0.00
142_I 26_A 0.92 0.28 0.00
228_E 66_V 0.91 0.28 0.00
257_T 27_A 0.91 0.28 0.00
296_L 59_L 0.91 0.28 0.00
2_P 20_G 0.91 0.28 0.00
306_F 42_V 0.91 0.28 0.00
205_L 14_L 0.91 0.28 0.00
234_G 64_T 0.90 0.27 0.00
161_A 31_G 0.90 0.27 0.00
170_M 50_S 0.89 0.27 0.00
138_A 74_F 0.88 0.26 0.00
323_F 43_G 0.88 0.25 0.00
253_A 62_P 0.88 0.25 0.00
210_F 14_L 0.87 0.25 0.00
143_L 50_S 0.87 0.25 0.00
231_T 68_F 0.87 0.25 0.00
7_P 47_E 0.87 0.25 0.00
247_A 37_I 0.87 0.25 0.00
1_N 29_G 0.87 0.25 0.00
240_I 75_I 0.87 0.25 0.00
222_I 22_A 0.86 0.24 0.00
24_D 53_G 0.86 0.24 0.00
11_L 18_G 0.86 0.24 0.00
128_L 75_I 0.86 0.24 0.00
257_T 64_T 0.86 0.24 0.00
242_I 30_T 0.86 0.24 0.00
249_G 62_P 0.85 0.24 0.00
284_L 24_G 0.85 0.24 0.00
309_K 22_A 0.85 0.23 0.00
19_K 16_A 0.85 0.23 0.00
20_Y 71_L 0.85 0.23 0.00
251_I 70_L 0.85 0.23 0.00
245_V 33_A 0.85 0.23 0.00
248_A 38_G 0.85 0.23 0.00
44_I 75_I 0.85 0.23 0.00
102_Y 37_I 0.85 0.23 0.00
139_N 78_G 0.84 0.23 0.00
205_L 28_L 0.84 0.23 0.00
296_L 34_Q 0.84 0.23 0.00
235_H 33_A 0.84 0.23 0.00
33_F 41_G 0.84 0.23 0.00
155_A 7_S 0.84 0.23 0.00
150_V 20_G 0.84 0.23 0.00
296_L 31_G 0.84 0.23 0.00
26_T 31_G 0.84 0.23 0.00
326_V 43_G 0.83 0.23 0.00
145_S 37_I 0.83 0.22 0.00
244_A 60_L 0.83 0.22 0.00
293_G 62_P 0.83 0.22 0.00
189_L 61_L 0.83 0.22 0.00
185_G 64_T 0.83 0.22 0.00
85_V 29_G 0.83 0.22 0.00
216_S 46_A 0.83 0.22 0.00
231_T 59_L 0.83 0.22 0.00
253_A 38_G 0.83 0.22 0.00
290_T 64_T 0.83 0.22 0.00
296_L 61_L 0.83 0.22 0.00
275_G 32_V 0.83 0.22 0.00
260_G 32_V 0.83 0.22 0.00
245_V 65_L 0.83 0.22 0.00
42_G 53_G 0.82 0.22 0.00
218_V 70_L 0.82 0.22 0.00
85_V 24_G 0.82 0.22 0.00
247_A 39_A 0.82 0.22 0.00
185_G 52_F 0.82 0.22 0.00
227_P 65_L 0.82 0.21 0.00
172_H 74_F 0.82 0.21 0.00
151_V 35_A 0.82 0.21 0.00
104_E 63_E 0.81 0.21 0.00
276_I 32_V 0.81 0.21 0.00
176_G 68_F 0.81 0.21 0.00
157_L 70_L 0.81 0.21 0.00
95_T 77_N 0.81 0.21 0.00
242_I 54_T 0.81 0.21 0.00
15_L 27_A 0.81 0.21 0.00
233_A 60_L 0.81 0.21 0.00
237_L 70_L 0.81 0.21 0.00
219_M 79_R 0.81 0.21 0.00
35_F 53_G 0.81 0.21 0.00
41_V 64_T 0.81 0.21 0.00
236_I 64_T 0.81 0.21 0.00
283_H 16_A 0.81 0.21 0.00
302_I 34_Q 0.81 0.21 0.00
309_K 41_G 0.81 0.21 0.00
62_K 20_G 0.80 0.20 0.00
38_G 47_E 0.80 0.20 0.00
152_M 74_F 0.80 0.20 0.00
245_V 60_L 0.80 0.20 0.00
144_L 32_V 0.80 0.20 0.00
245_V 66_V 0.80 0.20 0.00
297_Q 33_A 0.80 0.20 0.00
168_R 34_Q 0.80 0.20 0.00
234_G 27_A 0.80 0.20 0.00
29_V 21_L 0.79 0.20 0.00
29_V 32_V 0.79 0.20 0.00
34_P 63_E 0.79 0.20 0.00
95_T 43_G 0.79 0.20 0.00
46_Y 30_T 0.79 0.20 0.00
317_G 41_G 0.79 0.20 0.00
93_F 22_A 0.79 0.20 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
1394 1.74 I_sub_Membound_L_sub (B, 20-99) Δgene:(1, 10) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.05 Done
1387 1.12 I_sub_Membound_L_sub (B, 20-99) Δgene:(1, 10) A:(1E-02, 8) B:(1E-04, 8) msa: HHblits (2013_03) 0.00 Done - Shared
1385 1.13 I_sub_Membound_L_sub (B, 20-99) Δgene:(1, 100) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2013_03) 0.01 Done - Shared
1384 1.05 I_sub_Membound_L_sub (B, 20-99) Δgene:(1, 5) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2013_03) 0.01 Done - Shared
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