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OPENSEQ.org
2btf_3
Genes: A B A+B
Length: 375 140 497
Sequences: 3293 623 172
Seq/Len: 8.78 4.45 0.35
MirrorTree (Pazo et al. 2001) 0.16
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 0.04 0.06 0.01
2 0.05 0.07 0.02
5 0.05 0.07 0.09
10 0.05 0.07 0.10
20 0.06 0.07 0.12
100 0.08 0.07 0.19
∞ 0.16 0.07 0.33
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
363_D 112_L 1.79 0.66 0.00
128_N 113_L 1.17 0.25 0.00
110_L 111_V 1.16 0.24 0.00
66_T 70_K 1.15 0.24 0.00
16_M 101_I 1.11 0.22 0.00
290_R 113_L 1.11 0.22 0.00
228_A 23_V 1.10 0.22 0.00
301_G 63_G 1.04 0.19 0.00
303_T 112_L 1.04 0.19 0.00
282_I 128_C 1.02 0.18 0.00
297_T 59_F 1.02 0.18 0.00
108_A 68_G 1.01 0.18 0.00
30_V 101_I 1.00 0.17 0.00
297_T 2_A 0.99 0.17 0.00
244_D 125_N 0.99 0.17 0.00
167_E 132_A 0.99 0.17 0.00
32_P 126_K 0.99 0.17 0.00
154_D 74_I 0.99 0.17 0.00
278_T 23_V 0.98 0.16 0.00
359_K 119_V 0.97 0.16 0.00
182_G 129_Y 0.97 0.16 0.00
328_K 43_I 0.97 0.16 0.00
193_L 106_T 0.97 0.16 0.00
168_G 20_A 0.96 0.16 0.00
189_L 46_A 0.95 0.15 0.00
132_M 132_A 0.95 0.15 0.00
158_G 115_G 0.95 0.15 0.00
357_I 65_T 0.94 0.15 0.00
154_D 89_R 0.94 0.15 0.00
263_Q 111_V 0.94 0.15 0.00
248_I 37_G 0.94 0.15 0.00
293_L 71_C 0.93 0.15 0.00
31_F 56_R 0.93 0.15 0.00
146_G 113_L 0.92 0.14 0.00
314_Q 132_A 0.92 0.14 0.00
313_M 20_A 0.91 0.14 0.00
56_D 137_R 0.91 0.14 0.00
313_M 115_G 0.91 0.14 0.00
329_I 44_T 0.91 0.14 0.00
304_T 46_A 0.91 0.14 0.00
94_L 41_V 0.90 0.14 0.00
34_I 101_I 0.90 0.14 0.00
153_M 48_V 0.90 0.14 0.00
144_A 17_C 0.90 0.14 0.00
212_I 70_K 0.89 0.13 0.00
213_K 36_P 0.89 0.13 0.00
239_S 9_D 0.88 0.13 0.00
52_S 89_R 0.88 0.13 0.00
155_S 132_A 0.88 0.13 0.00
254_R 139_Q 0.88 0.13 0.00
313_M 136_R 0.88 0.13 0.00
260_A 112_L 0.87 0.13 0.00
263_Q 115_G 0.87 0.12 0.00
66_T 89_R 0.86 0.12 0.00
372_R 66_L 0.86 0.12 0.00
91_Y 104_T 0.85 0.12 0.00
157_D 75_R 0.85 0.12 0.00
347_A 20_A 0.84 0.12 0.00
360_Q 36_P 0.84 0.12 0.00
205_E 8_I 0.84 0.12 0.00
286_D 101_I 0.84 0.12 0.00
66_T 110_L 0.83 0.12 0.00
35_V 59_F 0.83 0.12 0.00
108_A 49_G 0.83 0.12 0.00
295_A 44_T 0.83 0.11 0.00
313_M 2_A 0.83 0.11 0.00
57_E 49_G 0.83 0.11 0.00
329_I 117_E 0.82 0.11 0.00
57_E 75_R 0.82 0.11 0.00
367_P 75_R 0.81 0.11 0.00
250_I 13_A 0.81 0.11 0.00
241_E 112_L 0.81 0.11 0.00
327_I 62_N 0.81 0.11 0.00
297_T 81_D 0.81 0.11 0.00
280_N 73_V 0.81 0.11 0.00
132_M 101_I 0.81 0.11 0.00
262_F 66_L 0.81 0.11 0.00
74_G 109_T 0.81 0.11 0.00
219_V 81_D 0.80 0.11 0.00
329_I 111_V 0.80 0.11 0.00
308_G 61_V 0.80 0.11 0.00
32_P 73_V 0.80 0.11 0.00
153_M 122_G 0.80 0.11 0.00
205_E 89_R 0.80 0.11 0.00
10_V 15_G 0.80 0.10 0.00
250_I 14_D 0.80 0.10 0.00
357_I 50_I 0.79 0.10 0.00
268_G 13_A 0.79 0.10 0.00
327_I 51_L 0.79 0.10 0.00
149_T 89_R 0.79 0.10 0.00
31_F 34_A 0.79 0.10 0.00
238_K 85_T 0.79 0.10 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
9006 0.41 2btf_5 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.32 Done - Shared
9005 0.42 2btf_4 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.20 Done - Shared
9004 0.35 2btf_3 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9002 0.13 2btf_2 Δgene:(0, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.07 Done - Shared
9000 0.13 2btf Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.05 Done - Shared
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