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OPENSEQ.org
MFD_SALTY_1_450-UVRA_SALTY_88_595
Genes: A B A+B
Length: 450 507 905
Sequences: 4321 2976 705
Seq/Len: 9.6 5.87 0.78
MirrorTree (Pazo et al. 2001) 0.41
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 0.03 0.01 0.45
2 0.03 0.01 0.51
5 0.03 0.01 0.60
10 0.03 0.01 0.69
20 0.03 0.01 0.74
100 0.05 0.02 0.97
∞ 0.20 0.06 1.92
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
170_D 306_R 1.39 0.61 0.00
165_R 212_L 1.04 0.32 0.00
182_L 314_S 1.00 0.29 0.00
22_L 273_M 0.96 0.26 0.00
415_L 393_S 0.94 0.25 0.00
25_A 446_L 0.94 0.25 0.00
168_L 87_I 0.92 0.23 0.00
351_T 483_V 0.92 0.23 0.00
141_L 163_F 0.91 0.23 0.00
387_F 335_V 0.90 0.22 0.00
395_R 175_L 0.88 0.21 0.00
283_V 291_H 0.88 0.21 0.00
423_R 423_V 0.85 0.20 0.00
82_S 184_N 0.84 0.19 0.00
297_A 168_C 0.84 0.19 0.00
184_F 172_M 0.83 0.19 0.00
109_P 186_A 0.83 0.18 0.00
309_D 438_R 0.83 0.18 0.00
415_L 40_A 0.82 0.18 0.00
330_E 303_S 0.82 0.18 0.00
22_L 446_L 0.81 0.17 0.00
128_L 497_E 0.81 0.17 0.00
160_G 222_W 0.81 0.17 0.00
408_A 158_L 0.81 0.17 0.00
243_H 203_P 0.81 0.17 0.00
257_I 78_L 0.80 0.17 0.00
264_F 74_H 0.80 0.17 0.00
202_T 290_L 0.80 0.17 0.00
415_L 461_D 0.80 0.17 0.00
25_A 273_M 0.80 0.17 0.00
196_D 168_C 0.80 0.17 0.00
308_V 199_Q 0.80 0.17 0.00
184_F 482_E 0.79 0.16 0.00
39_A 78_L 0.79 0.16 0.00
393_G 201_F 0.78 0.16 0.00
301_A 163_F 0.78 0.16 0.00
436_D 437_E 0.78 0.16 0.00
139_D 31_R 0.77 0.15 0.00
122_Y 176_E 0.77 0.15 0.00
289_E 416_G 0.76 0.15 0.00
301_A 175_L 0.76 0.15 0.00
253_L 168_C 0.76 0.15 0.00
146_D 307_E 0.75 0.15 0.00
56_H 163_F 0.75 0.15 0.00
284_N 388_N 0.75 0.15 0.00
201_R 312_F 0.74 0.14 0.00
410_K 291_H 0.74 0.14 0.00
218_P 188_A 0.74 0.14 0.00
329_S 209_N 0.74 0.14 0.00
387_F 4_H 0.74 0.14 0.00
182_L 497_E 0.74 0.14 0.00
275_Y 70_R 0.73 0.14 0.00
38_H 206_V 0.73 0.14 0.00
218_P 291_H 0.73 0.14 0.00
108_V 206_V 0.73 0.14 0.00
154_D 259_V 0.73 0.14 0.00
367_Q 345_D 0.73 0.14 0.00
305_N 212_L 0.72 0.14 0.00
263_L 384_N 0.72 0.14 0.00
28_A 485_A 0.72 0.13 0.00
89_S 329_E 0.72 0.13 0.00
386_I 17_H 0.71 0.13 0.00
408_A 199_Q 0.71 0.13 0.00
150_Y 442_T 0.71 0.13 0.00
31_V 35_H 0.71 0.13 0.00
248_V 24_F 0.71 0.13 0.00
44_L 51_V 0.71 0.13 0.00
217_F 161_A 0.71 0.13 0.00
15_D 332_H 0.71 0.13 0.00
243_H 3_S 0.71 0.13 0.00
301_A 253_A 0.71 0.13 0.00
309_D 45_S 0.70 0.13 0.00
222_A 43_T 0.70 0.13 0.00
275_Y 442_T 0.70 0.13 0.00
220_D 201_F 0.70 0.13 0.00
106_L 307_E 0.70 0.13 0.00
32_A 339_P 0.70 0.12 0.00
436_D 226_N 0.70 0.12 0.00
309_D 80_N 0.70 0.12 0.00
400_E 501_G 0.70 0.12 0.00
143_A 355_F 0.70 0.12 0.00
292_A 484_V 0.69 0.12 0.00
361_L 507_K 0.69 0.12 0.00
361_L 290_L 0.69 0.12 0.00
275_Y 416_G 0.69 0.12 0.00
374_L 328_R 0.69 0.12 0.00
350_N 209_N 0.69 0.12 0.00
367_Q 393_S 0.69 0.12 0.00
423_R 47_M 0.69 0.12 0.00
56_H 423_V 0.69 0.12 0.00
308_V 470_I 0.69 0.12 0.00
119_P 236_L 0.69 0.12 0.00
161_E 363_Q 0.69 0.12 0.00
145_L 195_L 0.69 0.12 0.00
363_I 70_R 0.68 0.12 0.00
347_K 259_V 0.68 0.12 0.00
361_L 155_E 0.68 0.12 0.00
25_A 176_E 0.68 0.12 0.00
22_L 279_T 0.68 0.12 0.00
337_L 59_R 0.68 0.12 0.00
172_F 423_V 0.68 0.12 0.00
82_S 179_L 0.68 0.12 0.00
182_L 468_H 0.67 0.12 0.00
148_A 111_T 0.67 0.12 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
7858 0.78 MFD_SALTY_1_450-UVRA_SALTY_88_595 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
7856 2 MFD_SALTY_1_450-UVRA_SALTY_88_595 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
7374 MFD_SALTY_1_450-UVRA_SALTY_88_595 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) Running - Shared
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