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OPENSEQ.org
DhaK_DhaL
Genes: A B A+B
Length: 354 209 536
Sequences: 2402 2899 1293
Seq/Len: 6.79 13.87 2.41
MirrorTree (Pazo et al. 2001) 0.70
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 0.01 0.01 2.21
2 0.07 0.06 2.26
5 0.14 0.07 2.28
10 0.14 0.07 2.30
20 0.14 0.07 2.30
100 0.14 0.07 2.31
∞ 0.16 0.09 2.31
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
118_L 88_I 1.39 0.90 0.33
117_E 89_R 1.29 0.84 0.27
121_D 88_I 1.27 0.83 0.25
121_D 92_Q 1.25 0.82 0.24
113_E 119_R 1.16 0.74 0.18
200_K 27_G 1.07 0.66 0.14
113_E 121_K 1.06 0.65 0.13
117_E 119_R 1.01 0.59 0.11
106_T 180_Y 0.97 0.55 0.10
83_D 73_S 0.95 0.52 0.09
78_T 78_A 0.93 0.50 0.08
78_T 71_L 0.92 0.49 0.08
125_K 163_S 0.92 0.48 0.08
82_P 37_H 0.87 0.43 0.07
78_T 43_R 0.84 0.40 0.06
150_A 35_A 0.84 0.39 0.06
56_E 77_G 0.83 0.38 0.06
202_S 30_R 0.80 0.35 0.05
62_Y 79_S 0.79 0.34 0.05
82_P 195_S 0.78 0.33 0.05
290_S 81_P 0.77 0.32 0.04
78_T 40_N 0.77 0.32 0.04
210_M 41_M 0.77 0.31 0.04
231_D 54_A 0.75 0.30 0.04
71_A 79_S 0.75 0.30 0.04
103_K 180_Y 0.73 0.28 0.04
322_L 179_S 0.73 0.28 0.04
75_E 43_R 0.72 0.28 0.04
59_H 180_Y 0.72 0.27 0.04
56_E 37_H 0.71 0.26 0.03
238_F 27_G 0.71 0.26 0.03
81_T 51_K 0.71 0.26 0.03
56_E 79_S 0.70 0.26 0.03
123_G 92_Q 0.70 0.25 0.03
110_L 59_D 0.70 0.25 0.03
113_E 78_A 0.70 0.25 0.03
59_H 79_S 0.70 0.25 0.03
75_E 71_L 0.69 0.25 0.03
156_E 40_N 0.69 0.24 0.03
136_A 191_P 0.69 0.24 0.03
78_T 75_V 0.68 0.23 0.03
103_K 79_S 0.68 0.23 0.03
71_A 173_A 0.67 0.23 0.03
78_T 37_H 0.67 0.23 0.03
56_E 76_G 0.67 0.23 0.03
103_K 40_N 0.66 0.22 0.03
99_L 7_I 0.66 0.22 0.03
103_K 175_K 0.64 0.21 0.03
78_T 195_S 0.64 0.20 0.03
56_E 81_P 0.64 0.20 0.02
123_G 95_Q 0.64 0.20 0.02
109_I 82_L 0.64 0.20 0.02
79_S 40_N 0.64 0.20 0.02
334_V 186_I 0.64 0.20 0.02
152_T 180_Y 0.63 0.20 0.02
145_G 179_S 0.63 0.20 0.02
202_S 133_W 0.63 0.20 0.02
152_T 77_G 0.63 0.19 0.02
43_G 27_G 0.63 0.19 0.02
78_T 32_I 0.63 0.19 0.02
70_G 90_A 0.62 0.19 0.02
290_S 37_H 0.62 0.19 0.02
212_F 23_E 0.62 0.19 0.02
49_S 76_G 0.62 0.19 0.02
174_E 141_R 0.62 0.19 0.02
75_E 63_I 0.62 0.19 0.02
305_Q 103_E 0.62 0.18 0.02
81_T 81_P 0.61 0.18 0.02
96_E 116_V 0.61 0.18 0.02
237_M 74_S 0.61 0.18 0.02
350_A 77_G 0.61 0.18 0.02
56_E 195_S 0.61 0.18 0.02
122_S 99_S 0.61 0.18 0.02
116_T 122_A 0.61 0.18 0.02
216_I 79_S 0.60 0.17 0.02
159_V 68_G 0.60 0.17 0.02
192_A 30_R 0.60 0.17 0.02
145_G 180_Y 0.60 0.17 0.02
58_M 26_T 0.60 0.17 0.02
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
5274 2.32 DhaK_DhaL Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) 0.14 Done
5273 2.09 DhaK_DhaL Δgene:(0, 0) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) 0.01 Done
5270 3.01 DhaK_DhaL Δgene:(0, 1) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.03 Done
5269 2.41 DhaK_DhaL Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) 0.33 Done - Shared
5268 1.6 DhaK_DhaL Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.06 Done - Shared
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