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OPENSEQ.org
2btf_5
Genes: A B A+B
Length: 375 140 499
Sequences: 5651 715 207
Seq/Len: 15.07 5.11 0.41
MirrorTree (Pazo et al. 2001) 0.19
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 0.03 0.06 0.01
2 0.04 0.06 0.03
5 0.04 0.06 0.10
10 0.04 0.06 0.12
20 0.04 0.06 0.14
100 0.06 0.06 0.22
∞ 0.14 0.07 0.40
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 2.13 0.86 0.32
278_T 23_V 1.16 0.27 0.02
347_A 20_A 1.16 0.27 0.02
193_L 106_T 1.14 0.26 0.02
209_V 51_L 1.12 0.25 0.02
128_N 113_L 1.12 0.25 0.02
260_A 112_L 1.09 0.23 0.02
327_I 74_I 1.07 0.22 0.01
71_I 132_A 1.06 0.22 0.01
108_A 68_G 1.05 0.22 0.01
140_L 139_Q 1.05 0.21 0.01
313_M 136_R 1.05 0.21 0.01
110_L 111_V 1.02 0.20 0.01
372_R 66_L 1.02 0.20 0.01
66_T 70_K 1.01 0.20 0.01
329_I 111_V 0.99 0.19 0.01
313_M 115_G 0.97 0.18 0.01
274_I 46_A 0.96 0.17 0.01
301_G 63_G 0.95 0.17 0.01
290_R 113_L 0.95 0.17 0.01
359_K 119_V 0.94 0.16 0.01
32_P 126_K 0.93 0.16 0.01
154_D 74_I 0.93 0.16 0.01
10_V 51_L 0.92 0.16 0.01
228_A 23_V 0.92 0.16 0.01
76_V 31_V 0.92 0.16 0.01
248_I 37_G 0.92 0.15 0.01
313_M 50_I 0.91 0.15 0.01
31_F 92_S 0.91 0.15 0.01
357_I 65_T 0.90 0.15 0.01
52_S 91_K 0.90 0.15 0.01
303_T 112_L 0.90 0.15 0.01
10_V 139_Q 0.90 0.15 0.01
327_I 51_L 0.90 0.15 0.01
66_T 110_L 0.90 0.15 0.01
292_D 112_L 0.89 0.15 0.01
90_F 48_V 0.88 0.14 0.01
297_T 59_F 0.88 0.14 0.01
167_E 132_A 0.88 0.14 0.01
335_R 44_T 0.88 0.14 0.01
100_E 8_I 0.88 0.14 0.01
357_I 119_V 0.88 0.14 0.01
168_G 126_K 0.88 0.14 0.01
90_F 77_S 0.88 0.14 0.01
181_A 106_T 0.88 0.14 0.01
297_T 91_K 0.88 0.14 0.01
293_L 71_C 0.87 0.14 0.01
362_Y 91_K 0.87 0.14 0.01
313_M 64_L 0.87 0.14 0.01
304_T 59_F 0.87 0.14 0.01
122_I 74_I 0.86 0.14 0.01
313_M 88_L 0.86 0.14 0.01
31_F 34_A 0.86 0.14 0.01
152_V 74_I 0.86 0.14 0.01
16_M 101_I 0.86 0.13 0.01
152_V 113_L 0.85 0.13 0.01
105_L 66_L 0.85 0.13 0.01
37_R 92_S 0.85 0.13 0.01
56_D 45_P 0.85 0.13 0.01
65_L 51_L 0.84 0.13 0.01
70_P 91_K 0.84 0.13 0.01
67_L 54_K 0.84 0.13 0.01
301_G 4_W 0.84 0.13 0.01
361_E 59_F 0.83 0.13 0.01
168_G 20_A 0.83 0.12 0.01
214_E 111_V 0.83 0.12 0.01
309_I 22_I 0.83 0.12 0.01
295_A 44_T 0.82 0.12 0.01
97_A 88_L 0.82 0.12 0.01
278_T 101_I 0.82 0.12 0.01
212_I 70_K 0.82 0.12 0.01
132_M 132_A 0.82 0.12 0.01
106_T 68_G 0.81 0.12 0.01
180_L 124_I 0.81 0.12 0.01
97_A 59_F 0.81 0.12 0.01
282_I 128_C 0.81 0.12 0.01
262_F 66_L 0.81 0.12 0.01
68_K 66_L 0.81 0.12 0.01
212_I 77_S 0.81 0.12 0.01
154_D 20_A 0.80 0.12 0.01
153_M 36_P 0.80 0.12 0.01
154_D 91_K 0.80 0.12 0.01
100_E 45_P 0.80 0.12 0.01
132_M 111_V 0.79 0.11 0.01
263_Q 115_G 0.79 0.11 0.01
67_L 65_T 0.79 0.11 0.01
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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