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OPENSEQ.org
MFD_MYCTU_1-450-UVRA_MYCTU_89-515
Genes: A B A+B
Length: 480 427 875
Sequences: 9529 7181 1580
Seq/Len: 19.85 16.82 1.81
MirrorTree (Pazo et al. 2001) 0.43
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 0.00 0.00 1.13
2 0.00 0.00 1.31
5 0.00 0.00 1.55
10 0.00 0.00 1.74
20 0.00 0.01 1.87
100 0.01 0.01 2.29
∞ 0.09 0.02 4.01
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
438_A 405_S 1.37 0.83 0.10
194_I 88_S 1.36 0.82 0.10
112_L 5_R 1.05 0.54 0.04
66_T 191_Y 1.03 0.53 0.04
161_E 123_K 0.99 0.48 0.03
196_D 385_V 0.98 0.48 0.03
194_I 147_L 0.98 0.47 0.03
211_W 89_R 0.97 0.46 0.03
116_R 249_F 0.96 0.46 0.03
193_G 119_R 0.95 0.44 0.03
113_M 162_R 0.95 0.44 0.03
341_W 266_I 0.94 0.43 0.03
246_L 193_A 0.94 0.43 0.03
142_Q 235_Y 0.93 0.42 0.03
105_V 335_E 0.93 0.42 0.03
430_L 83_N 0.92 0.41 0.02
269_V 41_A 0.91 0.40 0.02
31_Q 362_I 0.91 0.40 0.02
77_A 223_A 0.91 0.39 0.02
167_V 167_L 0.88 0.37 0.02
452_A 195_P 0.88 0.37 0.02
211_W 119_R 0.88 0.37 0.02
254_R 375_G 0.88 0.36 0.02
468_V 195_P 0.87 0.36 0.02
430_L 5_R 0.87 0.35 0.02
249_E 243_L 0.87 0.35 0.02
193_G 89_R 0.87 0.35 0.02
479_I 315_Y 0.87 0.35 0.02
287_D 5_R 0.86 0.35 0.02
108_V 405_S 0.86 0.35 0.02
173_E 78_L 0.86 0.34 0.02
247_L 14_I 0.86 0.34 0.02
430_L 87_Y 0.85 0.33 0.02
252_R 214_D 0.84 0.33 0.02
209_E 132_D 0.84 0.33 0.02
165_D 128_R 0.84 0.33 0.02
224_A 135_E 0.83 0.32 0.02
269_V 172_G 0.83 0.32 0.02
341_W 46_Q 0.83 0.32 0.02
310_D 151_D 0.83 0.32 0.02
64_V 31_P 0.82 0.31 0.02
462_K 203_R 0.81 0.30 0.02
164_F 425_T 0.81 0.30 0.02
186_G 235_Y 0.80 0.29 0.02
16_L 386_L 0.80 0.29 0.01
113_M 226_P 0.80 0.29 0.01
76_A 167_L 0.80 0.29 0.01
233_D 325_P 0.79 0.28 0.01
146_P 163_F 0.79 0.28 0.01
216_T 89_R 0.79 0.28 0.01
65_V 357_V 0.79 0.28 0.01
280_L 166_K 0.79 0.28 0.01
58_R 352_K 0.78 0.27 0.01
165_D 132_D 0.78 0.27 0.01
132_V 90_V 0.78 0.27 0.01
269_V 14_I 0.77 0.27 0.01
443_E 402_E 0.77 0.27 0.01
300_G 165_E 0.76 0.26 0.01
450_T 28_A 0.76 0.25 0.01
254_R 343_G 0.75 0.25 0.01
445_L 162_R 0.75 0.25 0.01
449_D 200_L 0.75 0.25 0.01
422_I 54_A 0.75 0.25 0.01
206_V 40_V 0.75 0.25 0.01
425_G 87_Y 0.75 0.25 0.01
47_S 36_C 0.75 0.24 0.01
390_D 312_K 0.75 0.24 0.01
462_K 195_P 0.74 0.24 0.01
164_F 132_D 0.74 0.24 0.01
341_W 273_Q 0.74 0.24 0.01
85_D 244_G 0.74 0.24 0.01
448_S 336_I 0.74 0.24 0.01
310_D 370_N 0.74 0.24 0.01
258_L 95_V 0.74 0.24 0.01
300_G 314_R 0.74 0.24 0.01
462_K 322_V 0.74 0.24 0.01
77_A 109_E 0.74 0.24 0.01
436_G 60_R 0.74 0.24 0.01
405_R 322_V 0.73 0.23 0.01
438_A 93_D 0.73 0.23 0.01
217_E 414_S 0.73 0.23 0.01
201_T 48_I 0.73 0.23 0.01
54_S 299_L 0.73 0.23 0.01
307_Q 271_D 0.73 0.23 0.01
379_G 389_I 0.73 0.23 0.01
300_G 2_S 0.72 0.23 0.01
53_A 366_A 0.72 0.23 0.01
215_I 360_L 0.72 0.23 0.01
215_I 87_Y 0.72 0.23 0.01
60_G 61_F 0.72 0.22 0.01
470_Q 119_R 0.72 0.22 0.01
264_A 54_A 0.72 0.22 0.01
460_A 115_V 0.72 0.22 0.01
37_P 297_A 0.71 0.22 0.01
245_L 244_G 0.71 0.22 0.01
16_L 264_K 0.71 0.22 0.01
156_L 244_G 0.71 0.22 0.01
403_S 52_V 0.71 0.22 0.01
206_V 68_V 0.71 0.21 0.01
459_Q 172_G 0.71 0.21 0.01
216_T 119_R 0.70 0.21 0.01
295_V 46_Q 0.70 0.21 0.01
33_A 189_S 0.70 0.21 0.01
27_Q 248_G 0.70 0.21 0.01
398_V 200_L 0.70 0.21 0.01
191_R 217_R 0.70 0.21 0.01
187_E 112_D 0.70 0.21 0.01
158_V 79_F 0.70 0.21 0.01
145_T 378_E 0.70 0.21 0.01
47_S 217_R 0.69 0.20 0.01
440_R 205_E 0.69 0.20 0.01
331_R 172_G 0.69 0.20 0.01
191_R 267_L 0.69 0.20 0.01
479_I 36_C 0.69 0.20 0.01
414_I 334_P 0.69 0.20 0.01
451_P 145_V 0.69 0.20 0.01
302_A 362_I 0.69 0.20 0.01
462_K 41_A 0.69 0.20 0.01
127_G 45_P 0.68 0.20 0.01
107_T 226_P 0.68 0.20 0.01
331_R 67_V 0.68 0.20 0.01
237_L 117_V 0.68 0.19 0.01
310_D 343_G 0.68 0.19 0.01
411_I 361_S 0.68 0.19 0.01
195_L 261_K 0.68 0.19 0.01
212_G 121_T 0.68 0.19 0.01
338_E 315_Y 0.67 0.19 0.01
59_Q 79_F 0.67 0.19 0.01
402_P 256_R 0.67 0.19 0.01
183_G 108_Q 0.67 0.19 0.01
80_R 340_T 0.67 0.19 0.01
37_P 338_A 0.67 0.19 0.01
151_M 68_V 0.67 0.19 0.01
405_R 369_L 0.67 0.19 0.01
339_A 217_R 0.67 0.19 0.01
429_A 18_Y 0.67 0.19 0.01
44_A 314_R 0.67 0.19 0.01
134_V 74_E 0.67 0.19 0.01
287_D 35_T 0.67 0.19 0.01
328_D 68_V 0.67 0.18 0.01
171_L 180_L 0.67 0.18 0.01
76_A 181_E 0.66 0.18 0.01
330_I 375_G 0.66 0.18 0.01
44_A 214_D 0.66 0.18 0.01
127_G 77_D 0.66 0.18 0.01
390_D 382_A 0.66 0.18 0.01
34_G 382_A 0.66 0.18 0.01
287_D 231_H 0.66 0.18 0.01
197_I 371_A 0.66 0.18 0.01
173_E 214_D 0.66 0.18 0.01
415_F 229_N 0.66 0.18 0.01
53_A 360_L 0.66 0.18 0.01
79_L 200_L 0.66 0.18 0.01
239_A 120_L 0.66 0.18 0.01
163_P 171_N 0.66 0.18 0.01
342_S 219_L 0.66 0.18 0.01
414_I 176_A 0.66 0.18 0.01
416_A 147_L 0.65 0.18 0.01
335_E 85_Q 0.65 0.18 0.01
30_M 48_I 0.65 0.18 0.01
202_A 206_V 0.65 0.18 0.01
307_Q 42_R 0.65 0.18 0.01
379_G 196_E 0.65 0.18 0.01
440_R 63_V 0.65 0.17 0.01
379_G 326_V 0.65 0.17 0.01
314_V 80_D 0.65 0.17 0.01
421_H 301_R 0.65 0.17 0.01
247_L 236_F 0.65 0.17 0.01
160_D 39_R 0.65 0.17 0.01
342_S 223_A 0.65 0.17 0.01
133_V 93_D 0.65 0.17 0.01
162_S 87_Y 0.65 0.17 0.01
47_S 299_L 0.64 0.17 0.01
133_V 77_D 0.64 0.17 0.01
390_D 386_L 0.64 0.17 0.01
452_A 132_D 0.64 0.17 0.01
460_A 244_G 0.64 0.17 0.01
296_L 99_L 0.64 0.17 0.01
447_E 318_F 0.64 0.17 0.01
174_L 67_V 0.64 0.17 0.01
430_L 42_R 0.64 0.17 0.01
424_T 370_N 0.64 0.17 0.01
222_S 293_E 0.64 0.17 0.01
404_A 266_I 0.64 0.17 0.01
203_E 300_Q 0.64 0.17 0.01
102_S 378_E 0.64 0.17 0.01
233_D 336_I 0.63 0.17 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
7440 1.81 MFD_MYCTU_1-450-UVRA_MYCTU_89-515 Δgene:(1, 10) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.10 Done - Shared
7439 1.17 MFD_MYCTU_1-450-UVRA_MYCTU_89-515 Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
7375 4.18 MFD_MYCTU_1-450-UVRA_MYCTU_89-515 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.92 Done - Shared
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