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OPENSEQ.org
DhaK_DhaL
Genes: A B A+B
Length: 354 209 542
Sequences: 2402 2899 1132
Seq/Len: 6.79 13.87 2.09
MirrorTree (Pazo et al. 2001) 0.87
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 4.21
2 0.07 0.06 4.25
5 0.14 0.07 4.29
10 0.14 0.07 4.29
20 0.14 0.07 4.29
100 0.14 0.07 4.30
∞ 0.16 0.09 4.31
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
185_S 182_G 1.08 0.63 0.01
145_G 78_A 1.06 0.60 0.00
156_E 164_A 1.06 0.60 0.00
193_C 76_G 1.05 0.59 0.00
113_E 22_S 1.04 0.59 0.00
111_N 81_P 1.04 0.58 0.00
102_I 41_M 1.03 0.57 0.00
218_G 120_G 1.00 0.53 0.00
117_E 118_S 1.00 0.53 0.00
83_D 73_S 0.99 0.53 0.00
113_E 119_R 0.99 0.53 0.00
145_G 180_Y 0.99 0.53 0.00
117_E 119_R 0.99 0.52 0.00
158_L 11_L 0.98 0.52 0.00
110_L 119_R 0.96 0.49 0.00
103_K 79_S 0.96 0.49 0.00
110_L 81_P 0.95 0.48 0.00
73_P 43_R 0.95 0.47 0.00
170_D 53_P 0.94 0.47 0.00
207_D 98_Q 0.94 0.47 0.00
151_N 75_V 0.94 0.47 0.00
47_L 104_E 0.93 0.46 0.00
324_M 186_I 0.92 0.45 0.00
322_L 105_L 0.90 0.42 0.00
149_V 182_G 0.89 0.41 0.00
152_T 79_S 0.89 0.41 0.00
168_S 138_E 0.89 0.41 0.00
185_S 175_K 0.86 0.39 0.00
197_A 75_V 0.84 0.36 0.00
218_G 26_T 0.84 0.36 0.00
292_L 71_L 0.84 0.36 0.00
185_S 94_T 0.83 0.34 0.00
163_A 88_I 0.82 0.34 0.00
106_T 180_Y 0.82 0.34 0.00
17_G 76_G 0.82 0.34 0.00
143_T 126_D 0.82 0.34 0.00
13_E 174_R 0.81 0.33 0.00
198_A 39_L 0.81 0.33 0.00
47_L 17_I 0.81 0.33 0.00
81_T 157_A 0.81 0.33 0.00
59_H 40_N 0.81 0.33 0.00
118_L 182_G 0.81 0.33 0.00
142_Y 121_K 0.80 0.32 0.00
121_D 112_G 0.80 0.32 0.00
172_C 171_M 0.80 0.32 0.00
208_N 188_H 0.80 0.32 0.00
300_T 82_L 0.80 0.32 0.00
68_L 180_Y 0.80 0.32 0.00
283_N 37_H 0.79 0.31 0.00
156_E 132_V 0.79 0.31 0.00
82_P 81_P 0.79 0.30 0.00
330_T 114_D 0.78 0.30 0.00
73_P 171_M 0.78 0.30 0.00
131_I 79_S 0.78 0.30 0.00
293_Y 75_V 0.78 0.30 0.00
354_G 15_G 0.78 0.30 0.00
187_G 63_I 0.78 0.30 0.00
348_T 191_P 0.77 0.29 0.00
14_Q 164_A 0.77 0.29 0.00
109_I 195_S 0.77 0.29 0.00
22_H 114_D 0.77 0.29 0.00
118_L 72_L 0.77 0.29 0.00
353_W 191_P 0.77 0.29 0.00
288_P 75_V 0.76 0.28 0.00
171_A 178_A 0.76 0.28 0.00
94_G 130_C 0.76 0.28 0.00
32_V 78_A 0.76 0.28 0.00
189_A 132_V 0.76 0.28 0.00
119_L 32_I 0.75 0.28 0.00
137_V 127_K 0.75 0.28 0.00
72_C 39_L 0.75 0.27 0.00
81_T 87_F 0.74 0.27 0.00
347_H 124_P 0.74 0.27 0.00
308_L 129_M 0.74 0.27 0.00
149_V 181_L 0.74 0.27 0.00
180_N 73_S 0.74 0.26 0.00
291_E 127_K 0.74 0.26 0.00
139_D 23_E 0.74 0.26 0.00
350_A 188_H 0.74 0.26 0.00
46_A 165_A 0.73 0.26 0.00
225_R 201_Q 0.73 0.26 0.00
106_T 37_H 0.73 0.26 0.00
119_L 164_A 0.73 0.26 0.00
331_L 116_V 0.73 0.26 0.00
103_K 28_L 0.73 0.25 0.00
87_E 50_E 0.73 0.25 0.00
149_V 40_N 0.73 0.25 0.00
111_N 87_F 0.72 0.25 0.00
132_D 105_L 0.72 0.25 0.00
14_Q 184_R 0.72 0.24 0.00
156_E 135_P 0.72 0.24 0.00
37_A 101_T 0.72 0.24 0.00
305_Q 145_E 0.72 0.24 0.00
88_C 41_M 0.72 0.24 0.00
321_S 72_L 0.71 0.24 0.00
242_L 135_P 0.71 0.24 0.00
174_E 141_R 0.71 0.24 0.00
281_V 27_G 0.71 0.24 0.00
135_V 84_G 0.71 0.24 0.00
20_K 32_I 0.71 0.24 0.00
85_I 172_Q 0.71 0.24 0.00
186_I 130_C 0.71 0.24 0.00
330_T 172_Q 0.71 0.24 0.00
81_T 135_P 0.71 0.24 0.00
193_C 15_G 0.71 0.24 0.00
70_G 73_S 0.71 0.24 0.00
334_V 59_D 0.71 0.24 0.00
120_H 197_M 0.71 0.23 0.00
292_L 82_L 0.71 0.23 0.00
141_L 78_A 0.70 0.23 0.00
145_G 37_H 0.70 0.23 0.00
149_V 11_L 0.70 0.23 0.00
330_T 117_I 0.70 0.23 0.00
62_Y 69_M 0.70 0.23 0.00
345_P 5_T 0.70 0.23 0.00
222_I 87_F 0.70 0.23 0.00
84_K 18_F 0.70 0.23 0.00
156_E 18_F 0.70 0.23 0.00
81_T 85_T 0.69 0.23 0.00
172_C 129_M 0.69 0.23 0.00
69_S 39_L 0.69 0.22 0.00
241_L 98_Q 0.69 0.22 0.00
299_L 13_R 0.69 0.22 0.00
290_S 75_V 0.69 0.22 0.00
168_S 166_Q 0.69 0.22 0.00
233_T 49_V 0.69 0.22 0.00
172_C 45_F 0.69 0.22 0.00
283_N 86_F 0.69 0.22 0.00
305_Q 155_E 0.69 0.22 0.00
144_A 70_T 0.69 0.22 0.00
232_Q 138_E 0.69 0.22 0.00
352_N 82_L 0.69 0.22 0.00
238_F 52_L 0.69 0.22 0.00
8_Q 105_L 0.69 0.22 0.00
340_A 54_A 0.69 0.22 0.00
137_V 195_S 0.69 0.22 0.00
279_A 202_M 0.69 0.22 0.00
56_E 180_Y 0.68 0.22 0.00
137_V 78_A 0.68 0.22 0.00
90_M 124_P 0.68 0.22 0.00
195_V 22_S 0.68 0.21 0.00
293_Y 173_A 0.68 0.21 0.00
22_H 81_P 0.68 0.21 0.00
114_T 108_M 0.68 0.21 0.00
284_L 132_V 0.68 0.21 0.00
278_I 62_F 0.68 0.21 0.00
19_A 144_S 0.68 0.21 0.00
150_A 85_T 0.68 0.21 0.00
193_C 94_T 0.67 0.21 0.00
109_I 121_K 0.67 0.21 0.00
47_L 41_M 0.67 0.21 0.00
56_E 77_G 0.67 0.21 0.00
60_C 73_S 0.67 0.21 0.00
53_S 123_E 0.67 0.21 0.00
137_V 44_G 0.67 0.21 0.00
88_C 20_T 0.67 0.21 0.00
120_H 126_D 0.67 0.21 0.00
114_T 88_I 0.67 0.20 0.00
110_L 45_F 0.67 0.20 0.00
229_S 62_F 0.67 0.20 0.00
352_N 179_S 0.67 0.20 0.00
100_L 195_S 0.67 0.20 0.00
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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