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OPENSEQ.org
YEFM - YOEB
Genes: A B A+B
Length: 83 84 167
Sequences: 491 562 372
Seq/Len: 5.92 6.69 2.23
MirrorTree (Pazo et al. 2001) 0.48
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 0.00 0.00 1.55
2 0.00 0.00 1.56
5 0.00 0.00 1.56
10 0.01 0.00 1.57
20 0.01 0.01 1.59
100 0.01 0.02 1.63
∞ 0.08 0.10 2.23
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
66_D 8_E 2.34 1.00 0.99
57_S 82_Y 2.12 0.99 0.98
72_K 69_A 1.81 0.98 0.95
67_S 6_S 1.77 0.98 0.94
56_R 82_Y 1.76 0.98 0.94
70_S 6_S 1.53 0.93 0.86
79_K 5_W 1.46 0.91 0.82
70_S 7_E 1.38 0.88 0.77
63_R 79_A 1.35 0.86 0.75
60_N 82_Y 1.26 0.81 0.68
76_G 6_S 1.24 0.79 0.65
71_L 78_A 1.15 0.71 0.56
5_S 5_W 1.10 0.66 0.50
53_Y 61_T 1.08 0.64 0.48
80_D 5_W 1.08 0.64 0.47
62_R 6_S 1.06 0.62 0.46
72_K 55_F 1.02 0.58 0.41
43_E 73_D 1.02 0.57 0.40
71_L 76_L 1.01 0.56 0.39
68_I 55_F 0.97 0.52 0.35
78_E 2_K 0.96 0.51 0.34
71_L 6_S 0.96 0.51 0.34
69_D 5_W 0.96 0.51 0.34
63_R 12_D 0.94 0.49 0.32
65_M 51_N 0.94 0.48 0.32
55_L 38_P 0.93 0.47 0.30
36_A 75_L 0.91 0.45 0.28
48_L 50_H 0.90 0.45 0.28
60_N 81_R 0.89 0.43 0.27
31_R 80_C 0.87 0.41 0.24
28_L 67_V 0.85 0.39 0.23
53_Y 21_K 0.85 0.39 0.23
83_E 32_K 0.85 0.38 0.23
44_E 63_E 0.84 0.37 0.22
65_M 49_K 0.82 0.35 0.20
64_L 81_R 0.81 0.35 0.20
37_C 22_R 0.80 0.34 0.19
76_G 4_I 0.80 0.34 0.19
71_L 55_F 0.80 0.33 0.18
11_Q 26_K 0.79 0.32 0.18
27_I 11_D 0.79 0.32 0.17
36_A 66_L 0.78 0.31 0.17
66_D 49_K 0.78 0.31 0.17
83_E 64_H 0.78 0.31 0.17
55_L 52_L 0.78 0.31 0.17
17_M 82_Y 0.75 0.29 0.15
69_D 31_I 0.75 0.28 0.14
9_A 38_P 0.73 0.27 0.14
70_S 8_E 0.73 0.27 0.13
65_M 75_L 0.73 0.27 0.13
27_I 67_V 0.73 0.27 0.13
58_P 64_H 0.73 0.26 0.13
72_K 29_E 0.72 0.26 0.13
73_S 33_D 0.72 0.26 0.13
45_Y 60_I 0.72 0.26 0.12
47_S 26_K 0.71 0.25 0.12
80_D 9_S 0.71 0.24 0.12
44_E 62_E 0.71 0.24 0.12
58_P 67_V 0.70 0.24 0.12
7_S 8_E 0.70 0.24 0.11
58_P 26_K 0.70 0.24 0.11
38_V 54_G 0.69 0.23 0.11
29_I 3_L 0.69 0.23 0.11
63_R 11_D 0.69 0.23 0.11
81_I 26_K 0.68 0.22 0.10
52_A 50_H 0.68 0.22 0.10
31_R 56_W 0.68 0.22 0.10
40_M 22_R 0.68 0.22 0.10
46_N 22_R 0.67 0.21 0.10
82_I 61_T 0.67 0.21 0.10
54_L 81_R 0.67 0.21 0.10
13_L 52_L 0.66 0.21 0.09
33_N 34_T 0.66 0.21 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
4755 4.57 TA_seven Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 1.00 Done - Shared
0722 3.69 2A6Q_Jackhmmer Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 1.00 Done
0720 5.44 2A6Q Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) 1.00 Done - Shared
0068 2.23 YEFM - YOEB Δgene:(0, ∞) A:(1E-20, 8) B:(1E-20, 8) (2013_03) 0.99 Done
0010 5.05 YEFM - YOEB Δgene:(0, 20) A:(1E-04, 8) B:(1E-04, 8) (2013_03) 0.99 Done - Shared
0005 1.59 YEFM - YOEB Δgene:(0, 20) A:(1E-20, 8) B:(1E-20, 8) (2013_03) 0.99 Done - Shared
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