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OPENSEQ.org
3G5O_Jackhmmer
Genes: A B A+B
Length: 93 87 170
Sequences: 1718 3431 788
Seq/Len: 18.47 39.44 4.64
MirrorTree (Pazo et al. 2001) 0.79
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 4.38
2 0.00 0.01 4.43
5 0.01 0.02 4.57
10 0.01 0.03 4.65
20 0.02 0.03 4.76
100 0.10 0.07 5.11
∞ 0.13 0.12 5.96
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_E 10_T 2.49 1.00 1.00
67_A 8_T 2.39 1.00 1.00
70_D 8_T 2.01 1.00 0.99
68_D 52_T 1.88 1.00 0.98
72_A 65_R 1.86 1.00 0.98
79_E 7_F 1.80 1.00 0.97
56_A 80_H 1.78 1.00 0.97
63_S 77_R 1.58 0.99 0.94
78_G 4_T 1.54 0.99 0.93
76_T 8_T 1.46 0.98 0.91
70_D 10_T 1.44 0.98 0.90
65_A 48_E 1.42 0.97 0.90
68_D 65_R 1.41 0.97 0.89
70_D 9_T 1.41 0.97 0.89
76_T 6_R 1.36 0.96 0.87
75_R 9_T 1.31 0.95 0.84
71_I 8_T 1.31 0.95 0.84
57_Q 80_H 1.18 0.90 0.76
54_W 63_L 1.10 0.86 0.69
60_I 80_H 1.08 0.84 0.66
71_I 52_T 1.08 0.84 0.66
83_R 31_F 1.03 0.80 0.60
63_S 13_R 1.02 0.79 0.60
72_A 52_T 0.94 0.70 0.49
56_A 47_R 0.93 0.70 0.49
74_G 8_T 0.92 0.69 0.47
9_I 38_P 0.92 0.69 0.47
13_L 56_R 0.89 0.65 0.43
79_E 5_V 0.89 0.64 0.43
71_I 76_L 0.88 0.63 0.42
81_E 27_V 0.86 0.61 0.40
40_V 5_V 0.85 0.59 0.38
51_T 54_S 0.84 0.58 0.37
72_A 20_P 0.83 0.57 0.36
16_F 25_A 0.83 0.57 0.36
69_A 17_K 0.83 0.56 0.35
12_K 69_E 0.81 0.54 0.33
3_I 34_L 0.81 0.53 0.33
67_A 52_T 0.80 0.52 0.32
41_G 75_I 0.80 0.52 0.32
65_A 49_L 0.80 0.52 0.32
71_I 74_V 0.79 0.51 0.31
27_I 63_L 0.79 0.50 0.30
85_E 12_R 0.79 0.50 0.30
67_A 76_L 0.78 0.50 0.30
7_S 18_L 0.76 0.46 0.27
50_E 43_K 0.75 0.45 0.26
79_E 27_V 0.74 0.45 0.26
55_L 49_L 0.74 0.44 0.25
50_E 61_R 0.73 0.42 0.24
39_L 29_F 0.73 0.42 0.24
77_Y 9_T 0.72 0.42 0.23
28_T 13_R 0.71 0.40 0.23
48_L 40_R 0.70 0.39 0.21
58_P 83_D 0.70 0.39 0.21
50_E 54_S 0.70 0.39 0.21
24_Q 66_I 0.68 0.36 0.20
67_A 77_R 0.68 0.36 0.19
77_Y 12_R 0.67 0.35 0.19
52_L 47_R 0.67 0.35 0.18
61_R 48_E 0.67 0.34 0.18
71_I 7_F 0.66 0.34 0.18
8_T 5_V 0.66 0.34 0.18
38_V 49_L 0.66 0.33 0.17
38_V 15_L 0.66 0.33 0.17
36_A 62_L 0.66 0.33 0.17
73_S 17_K 0.65 0.33 0.17
79_E 12_R 0.65 0.32 0.17
65_A 76_L 0.64 0.32 0.16
48_L 47_R 0.64 0.31 0.16
50_E 38_P 0.63 0.30 0.15
75_R 8_T 0.63 0.30 0.15
5_P 76_L 0.63 0.30 0.15
7_S 67_D 0.63 0.30 0.15
82_I 31_F 0.62 0.29 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
0726 4.64 3G5O_Jackhmmer Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 1.00 Done
0152 3.64 3G5O_AB Δgene:(1, 1) A:(1E-04, 4) B:(1E-04, 4) msa: Jackhmmer (2014_03) 1.00 Done - Shared
0151 5.09 3G5O_AB Δgene:(1, ∞) A:(1E-04, 4) B:(1E-04, 4) msa: Jackhmmer (2014_03) 0.95 Done
0150 0.3 3G5O_AB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
0149 3.89 3G5O_AB Δgene:(1, 20) A:(1E-04, 4) B:(1E-04, 4) msa: Jackhmmer (2014_03) 1.00 Done - Shared
0148 0.22 3G5O_AB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed - Shared
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