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OPENSEQ.org
DhaK_DhaL
Genes: A B A+B
Length: 354 209 540
Sequences: 1716 2047 1626
Seq/Len: 4.85 9.79 3.01
MirrorTree (Pazo et al. 2001) 0.77
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 0.01 0.02 2.89
2 0.07 0.05 2.91
5 0.09 0.05 2.95
10 0.10 0.05 2.95
20 0.10 0.05 2.95
100 0.11 0.06 2.96
∞ 0.14 0.09 2.96
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
106_T 180_Y 1.10 0.75 0.03
47_L 41_M 1.08 0.73 0.03
118_L 88_I 1.07 0.73 0.03
113_E 119_R 1.07 0.72 0.03
83_D 73_S 1.01 0.66 0.02
121_D 88_I 1.01 0.65 0.02
145_G 180_Y 0.97 0.61 0.02
121_D 92_Q 0.96 0.60 0.02
117_E 119_R 0.96 0.60 0.02
117_E 89_R 0.89 0.52 0.02
185_S 94_T 0.86 0.47 0.01
103_K 79_S 0.84 0.45 0.01
234_V 205_L 0.84 0.45 0.01
125_K 163_S 0.83 0.44 0.01
78_T 43_R 0.83 0.44 0.01
34_V 130_C 0.80 0.40 0.01
118_L 73_S 0.79 0.39 0.01
192_A 30_R 0.77 0.37 0.01
118_L 69_M 0.77 0.37 0.01
152_T 79_S 0.75 0.35 0.01
299_L 13_R 0.74 0.33 0.01
78_T 40_N 0.73 0.33 0.01
75_E 71_L 0.73 0.32 0.01
150_A 35_A 0.72 0.31 0.01
227_F 7_I 0.71 0.31 0.01
68_L 180_Y 0.70 0.29 0.01
145_G 179_S 0.70 0.29 0.01
78_T 71_L 0.70 0.29 0.01
25_L 156_A 0.69 0.28 0.01
56_E 77_G 0.69 0.28 0.01
113_E 121_K 0.68 0.27 0.01
48_L 155_E 0.68 0.27 0.01
113_E 78_A 0.68 0.27 0.01
340_A 20_T 0.68 0.27 0.01
33_Y 11_L 0.67 0.26 0.01
224_R 60_I 0.67 0.26 0.01
210_M 41_M 0.67 0.26 0.01
131_I 79_S 0.67 0.26 0.01
202_S 30_R 0.67 0.26 0.01
59_H 180_Y 0.67 0.26 0.01
6_D 107_Q 0.67 0.26 0.01
17_G 76_G 0.67 0.26 0.01
239_D 103_E 0.67 0.26 0.01
322_L 109_F 0.67 0.26 0.01
129_V 140_L 0.66 0.26 0.01
59_H 79_S 0.66 0.26 0.01
130_V 82_L 0.66 0.25 0.01
243_V 16_D 0.65 0.25 0.01
310_I 60_I 0.65 0.24 0.01
72_C 35_A 0.65 0.24 0.01
109_I 43_R 0.64 0.24 0.01
185_S 204_A 0.64 0.24 0.01
25_L 58_K 0.64 0.23 0.01
170_D 145_E 0.64 0.23 0.01
88_C 52_L 0.64 0.23 0.01
136_A 191_P 0.63 0.23 0.01
229_S 159_S 0.63 0.23 0.01
47_L 20_T 0.63 0.23 0.01
350_A 129_M 0.63 0.22 0.01
20_K 16_D 0.62 0.22 0.01
15_L 122_A 0.62 0.22 0.01
48_L 106_Y 0.62 0.22 0.01
180_N 189_Q 0.62 0.22 0.01
129_V 155_E 0.62 0.22 0.01
304_Q 138_E 0.62 0.22 0.01
270_P 17_I 0.62 0.21 0.01
170_D 155_E 0.62 0.21 0.01
200_K 27_G 0.61 0.21 0.01
141_L 78_A 0.61 0.21 0.01
82_P 37_H 0.61 0.21 0.01
82_P 195_S 0.61 0.21 0.01
243_V 151_P 0.61 0.21 0.01
22_H 22_S 0.61 0.21 0.01
162_A 67_T 0.60 0.20 0.01
350_A 77_G 0.60 0.20 0.01
106_T 37_H 0.60 0.20 0.01
212_F 23_E 0.60 0.20 0.01
185_S 175_K 0.60 0.20 0.01
234_V 90_A 0.59 0.20 0.01
329_I 51_K 0.59 0.20 0.01
151_N 35_A 0.59 0.19 0.01
152_T 180_Y 0.59 0.19 0.01
346_V 30_R 0.59 0.19 0.01
281_V 96_A 0.59 0.19 0.01
168_S 105_L 0.58 0.19 0.01
290_S 83_F 0.58 0.19 0.01
109_I 195_S 0.58 0.19 0.01
103_K 180_Y 0.58 0.19 0.01
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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