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OPENSEQ.org
YEFM - YOEB
Genes: A B A+B
Length: 83 84 167
Sequences: 1236 6071 844
Seq/Len: 14.89 72.27 5.05
MirrorTree (Pazo et al. 2001) 0.67
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 4.62
2 0.00 0.02 4.69
5 0.01 0.05 4.79
10 0.01 0.07 4.93
20 0.02 0.10 5.05
100 0.05 0.21 5.72
∞ 0.25 0.69 8.41
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
70_S 8_E 2.09 1.00 0.99
71_L 76_L 2.07 1.00 0.99
66_D 8_E 1.97 1.00 0.98
67_S 6_S 1.95 1.00 0.98
68_I 55_F 1.77 1.00 0.97
72_K 69_A 1.67 0.99 0.96
75_K 7_E 1.60 0.99 0.94
79_K 5_W 1.57 0.99 0.94
70_S 7_E 1.56 0.99 0.93
63_R 79_A 1.44 0.98 0.90
70_S 6_S 1.24 0.94 0.79
76_G 6_S 1.24 0.94 0.79
68_I 69_A 1.09 0.86 0.66
57_S 82_Y 1.06 0.84 0.63
56_R 82_Y 1.03 0.82 0.60
22_E 3_L 1.01 0.81 0.58
60_N 82_Y 1.00 0.79 0.56
67_S 55_F 0.96 0.75 0.51
64_L 55_F 0.95 0.74 0.50
49_E 75_L 0.94 0.73 0.49
72_K 26_K 0.93 0.72 0.48
71_L 78_A 0.93 0.72 0.48
63_R 12_D 0.93 0.71 0.47
50_E 65_R 0.90 0.69 0.44
78_E 2_K 0.89 0.67 0.43
26_P 38_P 0.89 0.67 0.42
39_L 54_G 0.87 0.64 0.40
62_R 72_D 0.85 0.62 0.38
67_S 76_L 0.84 0.61 0.37
53_Y 66_L 0.84 0.61 0.37
54_L 67_V 0.83 0.59 0.35
41_S 54_G 0.83 0.59 0.35
53_Y 61_T 0.82 0.58 0.34
77_T 10_W 0.81 0.57 0.33
76_G 76_L 0.81 0.57 0.33
71_L 6_S 0.81 0.56 0.33
65_M 51_N 0.80 0.56 0.32
55_L 52_L 0.80 0.55 0.32
16_T 70_V 0.80 0.55 0.32
67_S 78_A 0.80 0.55 0.31
76_G 4_I 0.80 0.54 0.31
13_L 59_R 0.78 0.53 0.30
46_N 4_I 0.78 0.52 0.29
32_Q 70_V 0.78 0.52 0.29
9_A 6_S 0.78 0.52 0.29
29_I 44_K 0.77 0.51 0.29
3_T 35_R 0.77 0.51 0.28
10_R 31_I 0.77 0.51 0.28
48_L 40_E 0.76 0.50 0.28
52_A 51_N 0.73 0.46 0.24
60_N 81_R 0.73 0.45 0.24
62_R 6_S 0.73 0.45 0.24
29_I 22_R 0.71 0.43 0.22
5_S 32_K 0.71 0.42 0.22
39_L 12_D 0.70 0.41 0.21
8_E 12_D 0.70 0.41 0.21
9_A 38_P 0.70 0.41 0.21
51_T 57_S 0.70 0.41 0.21
37_C 44_K 0.69 0.40 0.20
29_I 2_K 0.69 0.40 0.20
7_S 81_R 0.69 0.40 0.20
5_S 56_W 0.69 0.39 0.20
73_S 73_D 0.69 0.39 0.20
80_D 5_W 0.69 0.39 0.20
80_D 9_S 0.69 0.39 0.20
31_R 57_S 0.68 0.38 0.19
69_D 1_M 0.68 0.38 0.19
25_A 71_T 0.67 0.37 0.19
7_S 46_E 0.67 0.37 0.18
76_G 7_E 0.67 0.37 0.18
48_L 77_I 0.67 0.36 0.18
7_S 18_E 0.67 0.36 0.18
30_T 3_L 0.67 0.36 0.18
10_R 68_Y 0.67 0.36 0.18
36_A 33_D 0.67 0.36 0.18
64_L 72_D 0.66 0.36 0.18
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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