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OPENSEQ.org
MurA FabD
Genes: A B A+B
Length: 436 317 719
Sequences: 6298 10237 74
Seq/Len: 14.44 32.29 0.1
MirrorTree (Pazo et al. 2001) 0.21
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 0.06 0.05 0.01
2 0.06 0.07 0.01
5 0.06 0.08 0.02
10 0.06 0.09 0.05
20 0.06 0.09 0.10
100 0.10 0.11 0.62
∞ 0.22 0.17 2.85
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
113_L 280_V 1.49 0.20 0.00
251_V 13_S 1.42 0.18 0.00
148_E 275_I 1.39 0.17 0.00
282_L 105_S 1.36 0.16 0.00
379_L 228_V 1.36 0.16 0.00
251_V 72_A 1.36 0.16 0.00
72_V 50_E 1.29 0.14 0.00
113_L 13_S 1.25 0.13 0.00
253_V 134_I 1.24 0.13 0.00
376_A 272_F 1.22 0.13 0.00
143_G 104_L 1.22 0.13 0.00
376_A 101_A 1.22 0.13 0.00
376_A 117_G 1.21 0.12 0.00
240_F 36_A 1.20 0.12 0.00
346_I 9_P 1.18 0.12 0.00
251_V 245_E 1.17 0.12 0.00
135_G 97_A 1.17 0.12 0.00
275_I 27_P 1.15 0.11 0.00
390_V 100_A 1.15 0.11 0.00
381_G 266_A 1.14 0.11 0.00
399_G 159_A 1.13 0.11 0.00
217_I 145_V 1.13 0.11 0.00
147_A 275_I 1.12 0.11 0.00
276_K 21_E 1.12 0.11 0.00
128_L 135_L 1.11 0.10 0.00
400_Y 13_S 1.10 0.10 0.00
253_V 159_A 1.10 0.10 0.00
53_T 272_F 1.08 0.10 0.00
357_G 159_A 1.08 0.10 0.00
339_F 168_V 1.07 0.10 0.00
251_V 195_E 1.06 0.10 0.00
253_V 170_S 1.06 0.10 0.00
357_G 170_S 1.06 0.10 0.00
63_A 272_F 1.06 0.10 0.00
99_M 221_I 1.05 0.10 0.00
341_R 212_L 1.05 0.09 0.00
410_L 196_V 1.04 0.09 0.00
311_M 28_A 1.04 0.09 0.00
355_I 108_D 1.03 0.09 0.00
313_A 100_A 1.03 0.09 0.00
38_E 191_A 1.02 0.09 0.00
282_L 270_T 1.02 0.09 0.00
62_G 97_A 1.02 0.09 0.00
325_T 119_F 1.01 0.09 0.00
313_A 236_V 1.00 0.09 0.00
251_V 210_E 1.00 0.09 0.00
240_F 139_A 1.00 0.09 0.00
339_F 205_M 1.00 0.09 0.00
357_G 19_G 0.99 0.09 0.00
268_M 118_E 0.99 0.08 0.00
268_M 216_L 0.99 0.08 0.00
275_I 216_L 0.99 0.08 0.00
313_A 282_S 0.99 0.08 0.00
59_R 72_A 0.98 0.08 0.00
342_M 76_K 0.98 0.08 0.00
278_E 104_L 0.98 0.08 0.00
4_I 103_A 0.97 0.08 0.00
392_E 72_A 0.97 0.08 0.00
273_V 47_L 0.97 0.08 0.00
143_G 100_A 0.97 0.08 0.00
84_A 228_V 0.96 0.08 0.00
181_T 107_K 0.96 0.08 0.00
131_F 106_F 0.96 0.08 0.00
106_T 202_S 0.96 0.08 0.00
253_V 253_S 0.96 0.08 0.00
202_G 212_L 0.96 0.08 0.00
325_T 44_L 0.96 0.08 0.00
129_K 82_I 0.95 0.08 0.00
42_I 149_V 0.95 0.08 0.00
122_R 93_G 0.95 0.08 0.00
122_R 171_G 0.95 0.08 0.00
122_R 201_H 0.95 0.08 0.00
233_D 93_G 0.95 0.08 0.00
233_D 171_G 0.95 0.08 0.00
233_D 201_H 0.95 0.08 0.00
372_R 93_G 0.95 0.08 0.00
372_R 171_G 0.95 0.08 0.00
372_R 201_H 0.95 0.08 0.00
271_M 176_V 0.95 0.08 0.00
380_A 168_V 0.94 0.08 0.00
58_L 290_R 0.94 0.08 0.00
374_G 251_L 0.94 0.08 0.00
290_L 4_I 0.94 0.08 0.00
63_A 246_K 0.94 0.08 0.00
15_T 267_E 0.94 0.08 0.00
41_V 268_G 0.93 0.08 0.00
49_S 234_A 0.93 0.07 0.00
261_L 134_I 0.93 0.07 0.00
218_E 275_I 0.93 0.07 0.00
136_A 194_L 0.93 0.07 0.00
405_Q 207_P 0.93 0.07 0.00
160_L 202_S 0.93 0.07 0.00
101_P 121_N 0.93 0.07 0.00
253_V 273_I 0.92 0.07 0.00
27_P 234_A 0.92 0.07 0.00
207_I 64_P 0.92 0.07 0.00
240_F 30_K 0.92 0.07 0.00
171_L 254_P 0.92 0.07 0.00
6_V 264_L 0.92 0.07 0.00
171_L 145_V 0.92 0.07 0.00
64_D 7_L 0.92 0.07 0.00
253_V 232_V 0.91 0.07 0.00
249_G 272_F 0.91 0.07 0.00
74_V 205_M 0.91 0.07 0.00
175_A 97_A 0.91 0.07 0.00
96_V 29_A 0.90 0.07 0.00
411_G 272_F 0.90 0.07 0.00
211_G 47_L 0.90 0.07 0.00
63_A 69_T 0.90 0.07 0.00
390_V 123_A 0.90 0.07 0.00
193_I 159_A 0.90 0.07 0.00
145_I 188_A 0.90 0.07 0.00
283_R 181_E 0.89 0.07 0.00
407_L 118_E 0.89 0.07 0.00
324_I 181_E 0.89 0.07 0.00
324_I 285_V 0.89 0.07 0.00
357_G 272_F 0.89 0.07 0.00
73_T 254_P 0.89 0.07 0.00
325_T 90_H 0.89 0.07 0.00
29_I 226_V 0.89 0.07 0.00
113_L 284_L 0.88 0.07 0.00
172_I 213_K 0.88 0.07 0.00
26_L 234_A 0.88 0.07 0.00
230_I 72_A 0.88 0.07 0.00
41_V 73_V 0.88 0.07 0.00
174_A 27_P 0.87 0.07 0.00
204_G 8_F 0.87 0.07 0.00
45_V 73_V 0.87 0.07 0.00
24_A 15_F 0.87 0.07 0.00
63_A 75_E 0.87 0.07 0.00
407_L 227_P 0.87 0.07 0.00
100_G 158_L 0.87 0.07 0.00
138_I 260_S 0.87 0.07 0.00
269_E 27_P 0.87 0.07 0.00
370_D 97_A 0.87 0.07 0.00
173_M 259_E 0.87 0.07 0.00
323_M 58_L 0.86 0.07 0.00
216_K 132_A 0.86 0.07 0.00
16_V 239_E 0.86 0.07 0.00
385_E 257_F 0.86 0.07 0.00
147_A 37_D 0.86 0.07 0.00
348_I 95_Y 0.86 0.07 0.00
184_L 285_V 0.86 0.07 0.00
102_L 69_T 0.86 0.07 0.00
292_P 119_F 0.86 0.07 0.00
309_S 212_L 0.86 0.07 0.00
390_V 109_A 0.86 0.07 0.00
204_G 133_A 0.86 0.07 0.00
410_L 249_E 0.86 0.07 0.00
222_K 44_L 0.85 0.07 0.00
4_I 128_E 0.85 0.07 0.00
366_V 284_L 0.85 0.07 0.00
290_L 27_P 0.85 0.07 0.00
370_D 18_M 0.85 0.07 0.00
345_D 218_A 0.85 0.06 0.00
177_L 30_K 0.85 0.06 0.00
180_G 113_V 0.85 0.06 0.00
87_E 288_V 0.85 0.06 0.00
34_L 243_I 0.84 0.06 0.00
122_R 281_L 0.84 0.06 0.00
233_D 281_L 0.84 0.06 0.00
372_R 281_L 0.84 0.06 0.00
122_R 91_S 0.84 0.06 0.00
233_D 91_S 0.84 0.06 0.00
372_R 91_S 0.84 0.06 0.00
253_V 156_V 0.84 0.06 0.00
214_T 165_G 0.84 0.06 0.00
193_I 170_S 0.84 0.06 0.00
228_H 35_E 0.84 0.06 0.00
355_I 75_E 0.84 0.06 0.00
13_N 226_V 0.84 0.06 0.00
193_I 280_V 0.84 0.06 0.00
98_V 234_A 0.84 0.06 0.00
131_F 163_C 0.84 0.06 0.00
244_A 164_P 0.84 0.06 0.00
237_A 59_T 0.84 0.06 0.00
284_V 203_E 0.84 0.06 0.00
17_K 3_K 0.83 0.06 0.00
267_K 48_I 0.83 0.06 0.00
116_G 117_G 0.83 0.06 0.00
370_D 255_V 0.83 0.06 0.00
366_V 226_V 0.83 0.06 0.00
244_A 273_I 0.83 0.06 0.00
16_V 261_I 0.83 0.06 0.00
296_K 119_F 0.83 0.06 0.00
338_E 13_S 0.83 0.06 0.00
266_A 273_I 0.83 0.06 0.00
172_I 107_K 0.83 0.06 0.00
387_H 104_L 0.83 0.06 0.00
135_G 93_G 0.83 0.06 0.00
135_G 171_G 0.83 0.06 0.00
135_G 201_H 0.83 0.06 0.00
309_S 230_S 0.83 0.06 0.00
381_G 18_M 0.83 0.06 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)
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