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OPENSEQ.org
2A6Q
Genes: A B A+B
Length: 83 84 167
Sequences: 1236 6071 909
Seq/Len: 14.89 72.27 5.44
MirrorTree (Pazo et al. 2001) 0.74
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 5.44
2 0.00 0.02 5.50
5 0.01 0.05 5.56
10 0.01 0.07 5.64
20 0.02 0.10 5.73
100 0.05 0.21 6.02
∞ 0.25 0.69 6.65
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
67_S 6_S 2.45 1.00 1.00
66_D 8_E 2.43 1.00 1.00
70_S 8_E 2.42 1.00 1.00
68_I 55_F 2.08 1.00 0.99
71_L 76_L 2.04 1.00 0.99
75_K 7_E 1.88 1.00 0.98
70_S 7_E 1.80 1.00 0.97
63_R 79_A 1.69 1.00 0.96
70_S 6_S 1.67 0.99 0.96
76_G 6_S 1.65 0.99 0.96
72_K 69_A 1.58 0.99 0.94
79_K 5_W 1.56 0.99 0.94
57_S 82_Y 1.48 0.99 0.92
68_I 69_A 1.40 0.98 0.89
50_E 65_R 1.22 0.94 0.79
60_N 82_Y 1.13 0.90 0.72
67_S 78_A 1.13 0.90 0.72
76_G 7_E 1.12 0.90 0.71
63_R 12_D 1.10 0.89 0.69
76_G 4_I 1.10 0.88 0.69
56_R 82_Y 1.05 0.85 0.65
64_L 55_F 1.05 0.85 0.64
78_E 2_K 1.03 0.84 0.62
71_L 6_S 1.03 0.83 0.62
65_M 51_N 0.99 0.81 0.58
77_T 10_W 0.97 0.78 0.55
53_Y 66_L 0.95 0.76 0.52
67_S 55_F 0.91 0.72 0.47
29_I 12_D 0.87 0.67 0.42
31_R 57_S 0.86 0.66 0.41
83_E 32_K 0.86 0.66 0.41
41_S 54_G 0.84 0.63 0.38
32_Q 34_T 0.83 0.62 0.37
67_S 79_A 0.83 0.61 0.37
76_G 76_L 0.83 0.61 0.37
55_L 52_L 0.81 0.59 0.35
71_L 78_A 0.81 0.59 0.35
20_A 36_R 0.81 0.58 0.34
10_R 68_Y 0.80 0.57 0.34
50_E 48_L 0.80 0.57 0.33
51_T 57_S 0.80 0.57 0.33
29_I 48_L 0.80 0.57 0.33
73_S 73_D 0.79 0.56 0.32
26_P 38_P 0.79 0.55 0.32
39_L 68_Y 0.79 0.55 0.32
7_S 71_T 0.78 0.55 0.31
55_L 38_P 0.77 0.53 0.30
72_K 26_K 0.76 0.52 0.29
22_E 3_L 0.76 0.52 0.29
7_S 81_R 0.76 0.52 0.29
29_I 44_K 0.75 0.50 0.28
13_L 57_S 0.74 0.49 0.27
62_R 6_S 0.74 0.49 0.27
3_T 35_R 0.74 0.48 0.26
67_S 76_L 0.73 0.47 0.25
54_L 67_V 0.72 0.46 0.25
7_S 46_E 0.72 0.46 0.25
51_T 67_V 0.72 0.46 0.24
49_E 75_L 0.71 0.45 0.24
37_C 44_K 0.71 0.44 0.23
60_N 81_R 0.71 0.44 0.23
25_A 71_T 0.70 0.43 0.23
79_K 18_E 0.70 0.43 0.23
43_E 73_D 0.70 0.43 0.22
7_S 12_D 0.70 0.43 0.22
80_D 5_W 0.69 0.42 0.22
9_A 6_S 0.69 0.41 0.21
9_A 38_P 0.69 0.41 0.21
27_I 67_V 0.69 0.41 0.21
69_D 75_L 0.68 0.41 0.21
50_E 52_L 0.68 0.40 0.20
38_V 33_D 0.68 0.40 0.20
39_L 54_G 0.68 0.40 0.20
33_N 34_T 0.67 0.39 0.20
45_Y 7_E 0.67 0.38 0.19
67_S 9_S 0.67 0.38 0.19
50_E 46_E 0.66 0.37 0.18
53_Y 61_T 0.66 0.36 0.18
55_L 41_G 0.65 0.35 0.17
58_P 70_V 0.65 0.35 0.17
61_A 51_N 0.65 0.35 0.17
57_S 81_R 0.65 0.35 0.17
69_D 1_M 0.64 0.35 0.17
13_L 59_R 0.64 0.35 0.17
62_R 73_D 0.64 0.34 0.17
29_I 54_G 0.64 0.34 0.17
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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