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OPENSEQ.org
YE2_delta100
Genes: A B A+B
Length: 443 65 486
Sequences: 2570 1930 654
Seq/Len: 5.8 29.69 1.35
MirrorTree (Pazo et al. 2001) 0.72
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 1.29
∞ 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 2.79 1.00 0.99
376_V 17_V 2.71 1.00 0.99
31_I 49_L 2.38 0.99 0.98
192_F 42_M 1.68 0.91 0.84
368_K 12_E 1.66 0.91 0.83
168_T 19_K 1.63 0.90 0.81
114_R 18_R 1.49 0.83 0.71
240_G 22_W 1.43 0.80 0.66
371_T 40_A 1.37 0.76 0.61
228_F 36_A 1.36 0.75 0.59
371_T 9_F 1.34 0.73 0.57
243_R 21_I 1.28 0.69 0.51
341_E 41_V 1.24 0.65 0.47
345_N 9_F 1.23 0.64 0.46
242_R 16_E 1.22 0.63 0.45
414_M 31_T 1.15 0.56 0.37
358_P 22_W 1.15 0.56 0.37
197_A 43_S 1.13 0.54 0.35
125_L 10_A 1.11 0.53 0.33
201_P 18_R 1.11 0.52 0.33
319_L 40_A 1.10 0.51 0.32
239_R 27_E 1.09 0.50 0.31
30_L 45_I 1.09 0.50 0.31
197_A 46_L 1.08 0.50 0.30
127_L 61_T 1.08 0.49 0.30
229_A 40_A 1.07 0.49 0.29
44_I 24_T 1.05 0.47 0.28
320_L 26_Q 1.05 0.47 0.28
134_G 45_I 1.04 0.45 0.26
132_S 19_K 1.02 0.44 0.25
30_L 48_G 1.02 0.44 0.25
227_V 36_A 1.02 0.43 0.24
245_V 17_V 1.02 0.43 0.24
31_I 53_L 1.01 0.42 0.24
197_A 62_G 1.01 0.42 0.23
81_G 46_L 0.99 0.41 0.22
95_L 1_T 0.99 0.40 0.22
156_F 12_E 0.99 0.40 0.22
338_N 34_I 0.99 0.40 0.21
254_G 25_R 0.98 0.40 0.21
405_S 48_G 0.98 0.40 0.21
289_T 9_F 0.97 0.38 0.20
160_A 45_I 0.96 0.37 0.19
77_I 56_L 0.96 0.37 0.19
114_R 14_R 0.95 0.37 0.19
27_I 41_V 0.95 0.36 0.19
134_G 22_W 0.95 0.36 0.19
341_E 42_M 0.95 0.36 0.19
21_R 26_Q 0.94 0.36 0.18
122_Y 27_E 0.94 0.36 0.18
237_V 47_W 0.93 0.35 0.17
126_V 48_G 0.93 0.35 0.17
320_L 18_R 0.93 0.34 0.17
415_D 7_V 0.92 0.34 0.17
237_V 20_V 0.91 0.33 0.16
163_S 35_V 0.91 0.32 0.15
92_I 41_V 0.91 0.32 0.15
329_C 28_T 0.90 0.32 0.15
368_K 44_L 0.90 0.32 0.15
98_V 39_T 0.90 0.32 0.15
20_K 28_T 0.89 0.31 0.15
18_E 38_V 0.89 0.31 0.15
77_I 17_V 0.89 0.31 0.14
371_T 52_I 0.88 0.31 0.14
60_I 53_L 0.88 0.31 0.14
371_T 36_A 0.88 0.30 0.14
376_V 20_V 0.88 0.30 0.14
374_T 39_T 0.88 0.30 0.14
379_L 6_T 0.87 0.29 0.13
117_S 42_M 0.86 0.28 0.12
77_I 53_L 0.85 0.28 0.12
384_I 60_I 0.85 0.28 0.12
165_V 44_L 0.85 0.28 0.12
228_F 40_A 0.85 0.28 0.12
267_L 45_I 0.85 0.28 0.12
45_D 32_T 0.84 0.27 0.12
251_R 25_R 0.84 0.27 0.12
418_A 31_T 0.84 0.27 0.12
202_A 36_A 0.84 0.27 0.12
424_M 54_V 0.84 0.27 0.12
37_S 54_V 0.84 0.27 0.12
381_I 6_T 0.84 0.27 0.12
98_V 37_A 0.84 0.27 0.11
161_V 10_A 0.84 0.27 0.11
249_A 25_R 0.84 0.27 0.11
174_L 51_G 0.83 0.27 0.11
115_K 18_R 0.83 0.26 0.11
62_E 58_S 0.83 0.26 0.11
75_A 12_E 0.82 0.26 0.10
189_I 49_L 0.82 0.25 0.10
72_L 49_L 0.82 0.25 0.10
385_C 37_A 0.81 0.25 0.10
248_Y 9_F 0.81 0.25 0.10
325_I 45_I 0.81 0.25 0.10
344_D 23_P 0.81 0.24 0.10
35_I 52_I 0.81 0.24 0.10
369_V 60_I 0.81 0.24 0.10
190_I 38_V 0.81 0.24 0.10
347_K 19_K 0.81 0.24 0.10
48_V 11_R 0.80 0.24 0.10
107_K 40_A 0.80 0.24 0.10
168_T 45_I 0.80 0.24 0.09
75_A 62_G 0.80 0.24 0.09
220_L 48_G 0.80 0.24 0.09
338_N 32_T 0.80 0.24 0.09
13_K 34_I 0.80 0.24 0.09
310_L 57_V 0.79 0.23 0.09
224_A 10_A 0.79 0.23 0.09
39_I 33_L 0.79 0.23 0.09
194_G 43_S 0.79 0.23 0.09
240_G 23_P 0.79 0.23 0.09
340_R 5_A 0.79 0.23 0.09
347_K 28_T 0.79 0.23 0.09
306_I 17_V 0.78 0.23 0.09
424_M 31_T 0.78 0.23 0.09
168_T 9_F 0.78 0.23 0.09
217_F 48_G 0.78 0.22 0.09
80_L 62_G 0.78 0.22 0.09
39_I 48_G 0.78 0.22 0.09
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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