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OPENSEQ.org
DhaK_DhaL
Genes: A B A+B
Length: 354 209 529
Sequences: 1716 2047 849
Seq/Len: 4.85 9.79 1.6
MirrorTree (Pazo et al. 2001) 0.71
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 1.45
2 0.07 0.05 1.48
5 0.09 0.05 1.51
10 0.10 0.05 1.51
20 0.10 0.05 1.51
100 0.11 0.06 1.52
∞ 0.14 0.09 1.53
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 1.37 0.80 0.06
121_D 88_I 1.35 0.79 0.05
117_E 89_R 1.18 0.65 0.03
113_E 119_R 1.13 0.59 0.03
78_T 78_A 1.02 0.48 0.02
82_P 37_H 1.02 0.48 0.02
106_T 180_Y 0.99 0.45 0.02
210_M 41_M 0.96 0.42 0.02
150_A 35_A 0.94 0.40 0.01
200_K 27_G 0.94 0.39 0.01
202_S 30_R 0.94 0.39 0.01
78_T 32_I 0.93 0.39 0.01
78_T 71_L 0.91 0.37 0.01
117_E 119_R 0.90 0.35 0.01
75_E 71_L 0.90 0.35 0.01
113_E 121_K 0.89 0.35 0.01
125_K 163_S 0.89 0.34 0.01
9_D 138_E 0.89 0.34 0.01
82_P 195_S 0.88 0.34 0.01
96_E 116_V 0.88 0.34 0.01
121_D 92_Q 0.88 0.34 0.01
295_V 198_F 0.82 0.28 0.01
71_A 79_S 0.82 0.28 0.01
136_A 191_P 0.81 0.28 0.01
56_E 77_G 0.81 0.28 0.01
202_S 133_W 0.81 0.28 0.01
83_D 73_S 0.81 0.27 0.01
82_P 129_M 0.80 0.27 0.01
59_H 180_Y 0.79 0.26 0.01
78_T 75_V 0.78 0.25 0.01
78_T 40_N 0.78 0.25 0.01
110_L 59_D 0.78 0.25 0.01
78_T 43_R 0.77 0.25 0.01
56_E 37_H 0.76 0.24 0.01
33_Y 11_L 0.76 0.23 0.01
69_S 161_A 0.76 0.23 0.01
113_E 78_A 0.75 0.23 0.01
238_F 27_G 0.75 0.23 0.01
59_H 79_S 0.75 0.23 0.01
56_E 76_G 0.74 0.22 0.01
103_K 180_Y 0.74 0.22 0.01
103_K 79_S 0.74 0.22 0.01
234_V 205_L 0.74 0.22 0.01
123_G 92_Q 0.74 0.22 0.01
145_G 180_Y 0.74 0.22 0.01
6_D 107_Q 0.73 0.21 0.01
62_Y 79_S 0.73 0.21 0.01
70_G 90_A 0.73 0.21 0.01
350_A 77_G 0.73 0.21 0.01
118_L 73_S 0.72 0.21 0.01
75_E 43_R 0.72 0.21 0.01
72_C 35_A 0.72 0.21 0.01
87_E 123_E 0.72 0.21 0.01
290_S 37_H 0.72 0.21 0.01
103_K 40_N 0.72 0.20 0.01
305_Q 103_E 0.72 0.20 0.01
156_E 40_N 0.72 0.20 0.01
99_L 7_I 0.71 0.20 0.01
234_V 90_A 0.71 0.20 0.01
152_T 180_Y 0.71 0.20 0.01
56_E 81_P 0.71 0.20 0.01
290_S 81_P 0.71 0.20 0.01
319_C 69_M 0.70 0.19 0.01
152_T 77_G 0.70 0.19 0.01
325_T 200_M 0.70 0.19 0.01
112_F 120_G 0.69 0.19 0.01
103_K 175_K 0.69 0.19 0.01
110_L 140_L 0.69 0.19 0.01
78_T 195_S 0.69 0.19 0.01
329_I 47_K 0.69 0.18 0.01
238_F 101_T 0.69 0.18 0.01
184_H 114_D 0.69 0.18 0.01
195_V 178_A 0.69 0.18 0.01
153_V 11_L 0.68 0.18 0.01
20_K 16_D 0.68 0.18 0.01
220_P 85_T 0.68 0.18 0.01
231_D 54_A 0.68 0.18 0.01
110_L 30_R 0.68 0.18 0.01
78_T 196_V 0.68 0.18 0.01
49_S 178_A 0.68 0.18 0.01
152_T 79_S 0.68 0.18 0.01
6_D 130_C 0.67 0.17 0.01
185_S 31_E 0.67 0.17 0.01
145_G 179_S 0.66 0.17 0.01
349_P 105_L 0.66 0.17 0.01
48_L 70_T 0.66 0.17 0.01
81_T 51_K 0.66 0.17 0.01
56_E 79_S 0.66 0.17 0.01
144_A 26_T 0.65 0.16 0.01
229_S 201_Q 0.65 0.16 0.01
79_S 40_N 0.65 0.16 0.01
68_L 180_Y 0.65 0.16 0.01
151_N 35_A 0.65 0.16 0.01
216_I 79_S 0.65 0.16 0.01
216_I 180_Y 0.65 0.16 0.01
136_A 71_L 0.65 0.16 0.01
322_L 179_S 0.64 0.16 0.01
347_H 145_E 0.64 0.16 0.01
198_A 39_L 0.64 0.16 0.01
130_V 49_V 0.64 0.16 0.01
56_E 195_S 0.64 0.16 0.01
174_E 155_E 0.64 0.15 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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