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OPENSEQ.org
YE2
Genes: A B A+B
Length: 443 65 487
Sequences: 2570 1930 980
Seq/Len: 5.8 29.69 2.01
MirrorTree (Pazo et al. 2001) 0.66
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 0.00
2 0.01 0.01 0.00
5 0.01 0.01 0.00
10 0.01 0.01 0.01
20 0.01 0.01 0.02
100 0.02 0.01 1.30
∞ 0.03 0.01 1.93
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
35_I 53_L 3.35 1.00 1.00
376_V 17_V 2.67 1.00 1.00
31_I 49_L 2.32 1.00 0.99
192_F 42_M 1.80 0.97 0.94
228_F 36_A 1.75 0.97 0.93
368_K 12_E 1.72 0.97 0.93
376_V 20_V 1.30 0.81 0.70
242_R 16_E 1.29 0.80 0.68
243_R 21_I 1.28 0.79 0.67
414_M 31_T 1.27 0.79 0.67
347_K 28_T 1.24 0.76 0.63
240_G 22_W 1.22 0.74 0.62
30_L 46_L 1.20 0.73 0.59
168_T 19_K 1.18 0.71 0.57
196_V 25_R 1.17 0.70 0.57
341_E 17_V 1.17 0.70 0.56
193_A 46_L 1.15 0.68 0.54
31_I 45_I 1.14 0.68 0.53
358_P 22_W 1.13 0.66 0.52
375_L 13_A 1.08 0.61 0.46
237_V 27_E 1.07 0.60 0.45
126_V 41_V 1.07 0.60 0.45
245_V 17_V 1.05 0.58 0.43
366_I 18_R 1.05 0.57 0.42
267_L 45_I 1.03 0.56 0.41
413_I 38_V 1.00 0.53 0.37
290_I 29_L 1.00 0.52 0.37
31_I 53_L 0.99 0.51 0.36
162_V 40_A 0.99 0.51 0.35
114_R 18_R 0.98 0.51 0.35
227_V 36_A 0.98 0.51 0.35
310_L 56_L 0.98 0.51 0.35
196_V 39_T 0.98 0.50 0.34
239_R 27_E 0.97 0.49 0.33
77_I 56_L 0.97 0.49 0.33
229_A 40_A 0.97 0.49 0.33
21_R 26_Q 0.96 0.48 0.33
39_I 32_T 0.96 0.48 0.33
32_V 32_T 0.96 0.48 0.33
232_F 32_T 0.96 0.48 0.32
45_D 44_L 0.96 0.48 0.32
27_I 41_V 0.96 0.47 0.32
405_S 48_G 0.95 0.47 0.32
81_G 46_L 0.95 0.47 0.31
169_M 41_V 0.94 0.46 0.30
366_I 11_R 0.94 0.46 0.30
18_E 37_A 0.94 0.46 0.30
32_V 30_H 0.94 0.46 0.30
75_A 12_E 0.93 0.45 0.29
237_V 47_W 0.93 0.45 0.29
95_L 34_I 0.93 0.44 0.29
269_V 18_R 0.92 0.44 0.28
371_T 9_F 0.92 0.43 0.28
379_L 6_T 0.92 0.43 0.28
125_L 10_A 0.91 0.43 0.27
246_V 41_V 0.91 0.42 0.27
73_S 54_V 0.90 0.42 0.26
183_I 42_M 0.90 0.41 0.26
171_L 27_E 0.89 0.41 0.25
160_A 45_I 0.89 0.40 0.25
141_N 56_L 0.89 0.40 0.25
269_V 17_V 0.89 0.40 0.25
160_A 24_T 0.88 0.39 0.24
127_L 61_T 0.88 0.39 0.24
240_G 23_P 0.88 0.39 0.24
194_G 46_L 0.87 0.39 0.24
27_I 32_T 0.87 0.38 0.23
251_R 25_R 0.86 0.38 0.23
383_F 45_I 0.86 0.37 0.23
237_V 25_R 0.86 0.37 0.23
161_V 10_A 0.85 0.36 0.21
430_E 21_I 0.85 0.36 0.21
322_A 8_A 0.84 0.35 0.21
381_I 2_K 0.84 0.35 0.21
371_T 36_A 0.84 0.35 0.21
371_T 40_A 0.84 0.35 0.21
329_C 28_T 0.84 0.35 0.21
232_F 28_T 0.84 0.35 0.20
117_S 42_M 0.82 0.33 0.19
333_T 47_W 0.82 0.33 0.19
225_V 61_T 0.82 0.33 0.19
283_I 43_S 0.82 0.33 0.19
295_G 48_G 0.82 0.33 0.19
133_I 20_V 0.82 0.33 0.19
320_L 26_Q 0.82 0.33 0.19
224_A 21_I 0.82 0.33 0.18
345_N 9_F 0.82 0.33 0.18
319_L 40_A 0.81 0.33 0.18
72_L 41_V 0.81 0.33 0.18
246_V 19_K 0.81 0.32 0.18
110_E 42_M 0.81 0.32 0.18
422_T 5_A 0.81 0.32 0.18
387_I 30_H 0.81 0.32 0.18
134_G 22_W 0.81 0.32 0.18
23_L 43_S 0.81 0.32 0.18
132_S 19_K 0.80 0.31 0.17
234_V 47_W 0.80 0.31 0.17
368_K 44_L 0.80 0.31 0.17
165_V 19_K 0.80 0.31 0.17
348_K 21_I 0.79 0.30 0.17
110_E 62_G 0.79 0.30 0.17
217_F 40_A 0.79 0.30 0.17
108_E 25_R 0.79 0.30 0.17
201_P 18_R 0.79 0.30 0.17
35_I 52_I 0.79 0.30 0.16
433_L 30_H 0.79 0.30 0.16
384_I 21_I 0.79 0.30 0.16
283_I 34_I 0.78 0.30 0.16
39_I 42_M 0.78 0.30 0.16
16_L 38_V 0.78 0.30 0.16
157_Y 56_L 0.78 0.29 0.16
81_G 11_R 0.78 0.29 0.15
23_L 29_L 0.78 0.29 0.15
199_L 40_A 0.78 0.29 0.15
189_I 49_L 0.78 0.29 0.15
240_G 21_I 0.77 0.28 0.15
172_M 39_T 0.77 0.28 0.15
249_A 15_T 0.77 0.28 0.15
284_I 20_V 0.77 0.28 0.15
30_L 45_I 0.76 0.28 0.14
340_R 13_A 0.76 0.28 0.14
203_I 41_V 0.76 0.27 0.14
389_E 21_I 0.76 0.27 0.14
247_N 13_A 0.76 0.27 0.14
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
9230 1.35 YE2_delta100 Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.99 Done - Shared
9228 2.01 YE2 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done - Shared
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