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OPENSEQ.org
2btf_4
Genes: A B A+B
Length: 375 140 500
Sequences: 6195 697 212
Seq/Len: 16.52 4.98 0.42
MirrorTree (Pazo et al. 2001) 0.21
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 0.04 0.06 0.02
5 0.04 0.06 0.09
10 0.05 0.06 0.11
20 0.05 0.06 0.14
100 0.07 0.06 0.22
∞ 0.16 0.07 0.41
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 2.06 0.84 0.20
297_T 91_K 1.22 0.31 0.02
313_M 115_G 1.18 0.29 0.02
128_N 113_L 1.16 0.28 0.01
152_V 113_L 1.14 0.27 0.01
301_G 63_G 1.12 0.25 0.01
359_K 119_V 1.09 0.24 0.01
278_T 101_I 1.09 0.24 0.01
347_A 20_A 1.06 0.22 0.01
297_T 59_F 1.04 0.21 0.01
290_R 113_L 1.02 0.20 0.01
193_L 106_T 1.02 0.20 0.01
108_A 26_K 1.01 0.20 0.01
313_M 136_R 1.01 0.20 0.01
313_M 88_L 1.00 0.20 0.01
372_R 66_L 1.00 0.19 0.01
228_A 23_V 0.99 0.19 0.01
292_D 112_L 0.99 0.19 0.01
108_A 68_G 0.97 0.18 0.01
327_I 74_I 0.97 0.18 0.01
31_F 34_A 0.97 0.18 0.01
140_L 139_Q 0.96 0.17 0.01
237_E 51_L 0.96 0.17 0.01
10_V 139_Q 0.96 0.17 0.01
329_I 111_V 0.95 0.17 0.01
260_A 112_L 0.94 0.17 0.01
313_M 64_L 0.92 0.16 0.01
110_L 111_V 0.91 0.16 0.01
32_P 126_K 0.91 0.16 0.01
309_I 22_I 0.91 0.15 0.01
303_T 112_L 0.91 0.15 0.01
71_I 132_A 0.90 0.15 0.01
122_I 74_I 0.90 0.15 0.01
16_M 101_I 0.90 0.15 0.01
221_L 133_S 0.90 0.15 0.01
66_T 70_K 0.89 0.15 0.01
357_I 65_T 0.89 0.15 0.01
76_V 31_V 0.89 0.15 0.01
154_D 74_I 0.89 0.15 0.01
329_I 44_T 0.88 0.14 0.01
37_R 92_S 0.88 0.14 0.01
30_V 101_I 0.88 0.14 0.01
335_R 44_T 0.88 0.14 0.01
361_E 59_F 0.87 0.14 0.01
154_D 20_A 0.86 0.14 0.01
293_L 71_C 0.86 0.14 0.01
304_T 46_A 0.86 0.14 0.01
314_Q 115_G 0.86 0.14 0.01
94_L 66_L 0.86 0.14 0.01
54_V 61_V 0.86 0.14 0.01
168_G 126_K 0.85 0.14 0.01
278_T 23_V 0.85 0.13 0.01
154_D 91_K 0.85 0.13 0.01
152_V 74_I 0.85 0.13 0.00
181_A 106_T 0.84 0.13 0.00
118_K 71_C 0.84 0.13 0.00
162_T 68_G 0.84 0.13 0.00
70_P 91_K 0.84 0.13 0.00
306_Y 114_M 0.84 0.13 0.00
342_G 63_G 0.83 0.13 0.00
180_L 124_I 0.83 0.13 0.00
128_N 108_K 0.83 0.13 0.00
304_T 59_F 0.83 0.13 0.00
132_M 111_V 0.82 0.12 0.00
301_G 47_E 0.82 0.12 0.00
90_F 48_V 0.82 0.12 0.00
242_L 17_C 0.82 0.12 0.00
225_Q 66_L 0.82 0.12 0.00
119_M 108_K 0.82 0.12 0.00
320_L 51_L 0.81 0.12 0.00
140_L 40_F 0.81 0.12 0.00
342_G 139_Q 0.81 0.12 0.00
106_T 68_G 0.80 0.12 0.00
171_L 2_A 0.80 0.12 0.00
328_K 43_I 0.80 0.12 0.00
313_M 50_I 0.80 0.12 0.00
52_S 91_K 0.79 0.12 0.00
336_K 113_L 0.79 0.12 0.00
359_K 105_M 0.79 0.11 0.00
212_I 77_S 0.79 0.11 0.00
213_K 36_P 0.79 0.11 0.00
25_D 112_L 0.79 0.11 0.00
183_R 92_S 0.79 0.11 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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